# Patent

## Title
Guinea pig cytomegalovirus (CIDMTR strain)

## Abstract

The present disclosure provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR, glycoproteins from GPCMV Strain CIDMTR, and methods of use thereof.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Provisional Application No. 61/716,302 that was filed on Oct. 19, 2012. The entire content of this provisional application is hereby incorporated herein by reference.


FEDERAL GRANT SUPPORT
This invention was made with government support under HD38416 and HD044864 awarded by the National Institutes of Health. The government has certain rights in the invention.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Dec. 17, 2013, is named 09531.359US1_SL.txt and is 338,983 bytes in size.
BACKGROUND
Developing strategies to control and prevent congenital infection with cytomegalovirus (CMV) represents a major priority in perinatal medicine. CMV infection is the most common congenital infection in the developed world. The condition occurs in 0.5 to 2% of all births and is responsible for a wide range of neurodevelopmental disabilities in newborns. Of these disabilities, the most common is sensorineural hearing loss (SNHL), which occurs in up to 15% of all congenitally infected children. The outcome of SNHL is improved when antiviral therapy (ganciclovir) is administered to infants with neurological involvement who are congenitally infected with CMV. However, other forms of neurological injury associated with symptomatic congenital CMV may be irreversible.
Because pre-conceptual maternal immunity to CMV reduces the severity of injury caused by congenital CMV, the development of vaccines is considered to be of high priority. See, e.g., US Patent Publication No. 2010/0285059. A number of CMV vaccines are currently being evaluated in clinical trials, including live attenuated vaccines and subunit recombinant vaccines. Better elucidation of the determinants of the maternal immune response that result in protection of the fetus will help in prioritizing future vaccine studies for prevention of congenital infection.
Ideally, immunizations for CMV would first be evaluated in animal models prior to human clinical trials. Unfortunately, the strict species specificity of CMVs precludes any meaningful evaluation of candidate human CMV vaccines for protection in animal models. Although laboratory animals will engender immune responses to the candidate vaccines being evaluated in clinical trials, which allow study of safety and immunogenicity, laboratory animals cannot be infected with human CMV. As a result, the ability to analyze the protective effect of vaccines against experimental disease is restricted, and investigators have turned to species-specific animal CMVs to generate models of pathogenesis and immunity.
Among the small animal models of congenital CMV infection, the guinea pig cytomegalovirus (GPCMV) offers some unique advantages compared with rodent models. Chief among these advantages is the fact that GPCMV crosses the guinea pig placenta, causing infection in utero. For this reason, the guinea pig is well suited to the study of vaccines designed to interrupt vertical virus transmission. (Schleiss, ILAR Journal 47:65-72 (2006)). A limitation of the model, however, is that only one strain of the virus is available, the ATCC/22122 strain, discovered by Hartley in 1957 (Hartley J W, Rowe W P, Huebner R J. 1957. Serial propagation of the guinea pig salivary gland virus in tissue culture. Proc Soc Exp Biol Med 96:281-285). Thus, there is a current need for an alternative isolate of GPCMV.
SUMMARY
In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR, which is ATCC® deposit number PTA-120714. The guinea pig cytomegalovirus (GPCMV) Strain CIDMTR has been deposited with the American Type Culture Collection Depository (ATCC® Depository, 10801 University Boulevard, Manassas, Va. 20110-2209 USA) and assigned ATCC® Patent Deposit Designation PTA-120714. The cell line was deposited on Nov. 19, 2013. Access to this deposit will be available during the pendency of the application to the Commissioner of Patents and Trademarks and persons determined by the Commissioner to be entitled thereto upon request. The deposits will be maintained in the ATCC® Depository, which is a public depository, for a period of 30 years, or 5 years after the most recent request, or for the enforceable life of the patent, whichever is longer, and will be replaced if it becomes nonviable during that period.
In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR having at least 90% identity to SEQ ID NO:1.
In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR comprising a glycoprotein (GP), wherein the GP has having at least 75% sequence identity to GPCMV glycoprotein 129 (GP129), GPCMV glycoprotein 131 (GP131), GP74 (gO), GP75 (gH), GPCMV glycoprotein 55 (gB), GPCMV glycoprotein 73 (gN), or GPCMV glycoprotein 115 (gL).
In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR comprising a glycoprotein (GP), wherein the GP has having at least 84% sequence identity to GPCMV glycoprotein 129 (GP129, SEQ ID NO:2), at least 94% sequence identity to GPCMV glycoprotein 131 (GP131, SEQ ID NO:3), at least 78% sequence identity to gpUL74 (gO, SEQ ID NO:4), or at least 82% sequence identity to gpUL75 (gH, SEQ ID NO:5).
In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR glycoprotein (GP), wherein the GP has having at least 75% sequence identity to GPCMV glycoprotein 129 (GP129), GPCMV glycoprotein 131 (GP131), GP74 (gO), GP75 (gH), GPCMV glycoprotein 55 (gB), GPCMV glycoprotein 73 (gN), or GPCMV glycoprotein 115 (gL).
In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR glycoprotein (GP), wherein the GP has having at least 84% sequence identity to GPCMV glycoprotein 129 (GP129), at least 94% sequence identity to GPCMV glycoprotein 131 (GP131), at least 78% sequence identity to GP74 (gO), or at least 82% sequence identity to GP75 (gH).
In certain embodiments, the present invention provides a composition comprising a GP described above and a pharmaceutically-acceptable, non-toxic vehicle.
In certain embodiments, the present invention provides a purified antibody that binds specifically to GPCMV Strain CIDMTR, or the GP described above. In certain embodiments, the antibody is an antibody fragment.
In certain embodiments, the present invention provides a method of determining the effectiveness of a vaccine or therapeutic composition in preventing or ameliorating infection or re-infection with cytomegalovirus.
In certain embodiments, the present invention provides an isolated promoter sequence comprising (or consisting of) a nucleic acid of between 500 and 1801 nucleotides in length (or any integer there-between) having at least 90% identity to SEQ ID NO:10. In certain embodiments, the promoter has 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identity to SEQ ID NO:10. In certain embodiments, the promoter is between 500 and 1700 nucleotides in length, such as between 1500 and 1700 nucleotides in length. In certain embodiments, the present invention provides an isolated polynucleotide comprising (a) an element comprising at least 200 contiguous nucleotides of SEQ ID NO:10; and (b) an element comprising an expressible polynucleotide sequence, wherein said element in (a) is directly operably linked to said expressible polynucleotide sequence in (b) and is not naturally operably linked to said expressible polynucleotide sequence. In certain embodiments, the polynucleotide comprises at least 500 contiguous nucleotides of SEQ ID NO: 10. In certain embodiments, the present invention provides an expression cassette comprising the promoter described above that is functional in a transformed cell operably linked to a preselected DNA segment encoding a protein or RNA transcript. In certain embodiments, the preselected DNA segment comprises a selectable marker gene or a reporter gene. In certain embodiments, the preselected DNA segment encodes a therapeutic composition.
In certain embodiments, the present invention provides a vector comprising the expression cassette described above.
In certain embodiments, the present invention provides a transformed cell comprising the expression cassette described above, or the vector described above. In certain embodiments, the host cell is a eukaryotic cell. In certain embodiments, the eukaryotic cell is an animal cell (e.g. a mammalian cell, such as a human cell).
In certain embodiments, the present invention provides a method for producing transformed cells comprising the steps of (i) introducing into cells a recombinant DNA which comprises a promoter described above operably linked to a DNA segment so as to yield transformed cells, and (ii) identifying or selecting a transformed cell line. In certain embodiments, the recombinant DNA is expressed so as to impart a phenotypic characteristic to the transformed cells. In certain embodiments, the transformed cells exhibit significantly increased expression of a reporter gene when introduced into the cells derived from Huntington's disease patients as compared to cells derived from control individuals.
In certain embodiments, the present invention provides transformed cell made by the method described above.
In certain embodiments, the present invention provides a transformed cell comprising the isolated promoter described above.
In certain embodiments, the present invention provides transformed cell comprising the expression cassette described above.
In certain embodiments, the present invention provides method of treating a neurodegenerative disease in a mammal comprising administering (a) the vector described above, or (b) the transformed cell described above.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Genomic sequence of guinea pig cytomegalovirus Strain CIDMTR (SEQ ID NO:1). The left terminal repeat spans nucleotides 1-842, and the right terminal repeat spans nucleotides 213938-232778.
FIG. 2 summarizes the predicted ORFs identified in the CIDMTR strain.
FIGS. 3A-3B. Strain-specific Genome Structure Differences between CIDMTR and 22122 strains. (a) Two genome regions demonstrating striking sequence variability at the (shaded boxes). These polymorphisms allow sequence-specific primers to differentiate reinfection with the novel strain from reactivation of the 22122 reference strain. X-axis, CIDMTR strain sequence; Y-axis, 22122 strain sequence. (b) Linear map comparison of the two major areas of genome discontinuity. Linear maps prepared using XPlasMap. Colored boxes in blue represent predicted function. Dotted arrow arrows indicate the positions where the sequences differ. See FIG. 2 for a full list of sequenced gene annotations.
FIG. 4. Primer sequences (SEQ ID NOs: 11-18).
FIG. 5. Promoter sequence of CIDMTR (SEQ ID NO: 10).



DETAILED DESCRIPTION
GPCMV Strain CIDMTR
In certain embodiments, the present invention provides a guinea pig cytomegalovirus (GPCMV) Strain CIDMTR, deposited with the American Type Culture Collection (ATCC®, 10801 University Boulevard, Manassas, Va. 20110-2209 USA) on Nov. 19, 2013 and given Patent Deposit Designation PTA-120714.
In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR having at least 90% identity to SEQ ID NO:1 (i.e., from 90%-100% identity to SEQ ID NO:1). In certain embodiments, the GPCMV Strain CIDMTR has 95% identity, 98% identity, 99% identity, or even 100% identity with SEQ ID NO:1.
In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR comprising a glycoprotein (GP), wherein the GP has having at least 75% sequence identity to GPCMV glycoprotein 129 (GP129), GPCMV glycoprotein 131 (GP131), GP74 (gO), GP75 (gH), GPCMV glycoprotein 55 (gB), GPCMV glycoprotein 73 (gN), or GPCMV glycoprotein 115 (gL). In certain embodiments, the GPCMV Strain CIDMTR comprises a GP that has at least 84% sequence identity to GPCMV glycoprotein 129 (GP129, SEQ ID NO:2), at least 94% sequence identity to GPCMV glycoprotein 131 (GP131, SEQ ID NO:3), at least 78% sequence identity to gpUL74 (gO, SEQ ID NO:4), or at least 82% sequence identity to gpUL75 (gH, SEQ ID NO:5). In certain embodiments, the GPCMV Strain CIDMTR GP has from 78% to 100% identity with the native GP sequence, such as 80%, 85%, 90%, 95% identity, 98% identity, 99% identity, or even 100% identity with the GP sequence.
GPCMV Strain CIDMTR Glycoproteins
In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR glycoprotein (GP), wherein the GP has having at least 75% sequence identity to GPCMV glycoprotein 129 (GP129), GPCMV glycoprotein 131 (GP131), GP74 (gO), GP75 (gH), GPCMV glycoprotein 55 (gB), GPCMV glycoprotein 73 (gN), or GPCMV glycoprotein 115 (gL). In certain embodiments, the present invention provides an isolated or purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR glycoprotein (GP), wherein the GP has at least 84% sequence identity to GPCMV glycoprotein 129 (GP129, SEQ ID NO:2), at least 94% sequence identity to GPCMV glycoprotein 131 (GP131, SEQ ID NO:3), at least 78% sequence identity to gpUL74 (gO, SEQ ID NO:4), or at least 82% sequence identity to gpUL75 (gH, SEQ ID NO:5). In certain embodiments, the GPCMV Strain CIDMTR GP has from 78% to 100% identity with the native GP sequence, such as 80%, 85%, 90%, 95% identity, 98% identity, 99% identity, or even 100% identity with the GP sequence.








CIDMTR Strain gB (GP55) (SEQ ID NO: 6):



     MRPVRGIARSRILSCSWRGTWTSALTILYLGVYCESTTVTPTTVEDTTVSNGN


HSDASSNNTVIRNLTASVDFSQRKLYPYRICSMSMGTDLVRFARTIQCVPFNPRVNSE


EGIMLIYKRNILPYVFTAYTYQKELLFQRSYKYVTYDYLLGYSREFVALPMWEIFLV


NSRGQCYTSHQRVIGADRYIAYHNDNEVNETMWLMRDDMGNDDTYRYITVKEHA


RTPGSVWLYKETCSMNCIVTKTKGKSKFPYDMFVLPSGVIVNISPFYNGSNGKTFRE


QREKFHIWSNYSILKDFGSRALEARIVPKMAFYEREDVVIGWEVNDQSNVTCEMILW


ETVDRAIRTEYENAFHYVARTLTSTFVENKYSPDNNLTEDDIKCFKDDAQKKIEEVFL


RDYNETYDMDGNATYHVTTGGLVIVWQGLKQKSLKALEIAANESAVSATGSNSRR


KRSLPDESTGDISYAQLQFAYDTLRTYINQALGHIAEAWCLDQKRTAEVLHELSKINP


SNILSAIFGVPVAARVVGDVISLAKCIEVNQSTVLIKGDMRKFSDDGKLEGCYSRPVV


WFSMKNSTEVRLGQLGEDNEILLGTHRMETCQTQDYRIFVAGDIGYEFQQYVFTKKI


NLSEIDIIDTMIALKTEPLENIDFKVLELYSRDELAQANVFDLESIMREYNYQKKRLDF


VVERVINPIPPELKGLDEMMNGMGAIGKGIGEAVGAVGGAIGSFIGALVTFVTNPFG


AFVVFLFCVGCITLVITVYRRQRRAMQRPFDYFFPYASQTITSSVADSSIAVAYPGPEG


TSGDAPPPYPGEAPYGYKDLSVDADTRVSSSSAGAGADFNEEDAVRMLRAIKRLDD


KKRQEIEKSSKDSASNKNSETRRRPGIMDRLRRRGGYQKLNTEDDVHV*


 


CIDMTR Strain gH (GP75) (SEQ ID NO: 5):


     MSPAARFTVISCLVVSLITPSETSFSSWTYPDVNWTKSSLNMTCLNNHTGQRS


LTTEGLISFNFYEAPKTVRTYQVPKCIFMTTISKSIMQSVDLFESLESYKLRYYSYIIVP


VHAAFQIFIHELRTDLVPSTEELNVRADDTLPNITVWRTRSGSYVIPLLDVVTPEFEDC


NLFSNHTVVFDMKIPCSRELYLHQLGAHRFTIALTFTPNFFVLNIQTTRRSHTTEDDE


DTLLIFGDIQEIDVKAPYSKPVLTLRQSSRDDLLIVAKTSTVTTIYPFIQTQGFLKIELSN


NYLDFDRVYTEFSRLVTHNMMNGLCDAPPDNRTVSMVFSYAILIRALYHTANMTAR


LEDVTLRYVKLTLARTFLQQCFNIEPRYMRFPMIDGAVSVFLKLIRNSRDVDRAIKLS


LTFALIFGNNTNLTEERDIENALYEMKSIHRAGLVSPLSPRQRNLLYMMAYVMHHTA


AFPDIRREMLAMQTSLCSPQELYNWAPHVSSAGLTMQEMFTPCSGSGRRDYSEARIA


EIVQLNPLTTKTPADLYRILAHFDRSNLTNFPALSCISHLSGYVAVTLKDVTYVVSSN


VILKGTSYPVTNLAVDKTMIVTVSPAQQPCEQTEVAHATRSIPIVKNITIGNDCEYCKS


AIMEYDEVNGLSNIVYLADTADLVLVTNLDNRILASSPRTRYIMMTANGTLIEITSVII


DIRQTSIFMIMLYCSLGVLLLYGLYRLLHMI*


 


CIDMTR Strain gO (GP74) (SEQ ID NO: 4):


     MTWILVLFLCPLLAAVYTSPKSTNVIEQFISRFNGFMKNITVTYNSKWIQAAP


MNGSVIPIWYPKSVTNIRHHFLAYYDNATQTIQLAGPHCTTVPSPSCLDTMLAVSAD


HRGTSTCNLTTYNAQLYNIPRWTVKLRLPSGGFYHLNSDDLIYMALSVSVASRREFD


VCAGGGSYLTALSKNLFQLSPQLRSNWTLTKSFFRKLKRLQQANRTIEEEPKKSRNR


KNDTGAVKNETWIPPVSANAFLGFNFYLYGMLYKSSLCHTGRSNSYISTNATLNDM


RLSLLQNVSWADDSLNETLINTTLVHGYVQSLVLERNITNNTHPLYNTRFVRVSREL


GTDDFRHSPYPSRPTTNEHPLVTSGGLAGKRPVTTVP*


 


CIDMTR Strain gN (GP73) (SEQ ID NO: 7):


     MKSYLIGPLSAVSSPSTSSCGRRHRVTIAGLALCYLIVVSMVSGASSNSTSVTT


PSPASQASSVMSSTTVASTTKTALGFYDVGCVSHAYNVSIRSFASLWILANVFILLCSF


GIFLRHCCYRSFASETARGY*


 


CIDMTR Strain gL (GP115) (SEQ ID NO: 8):


     MFFSHRLTIGFYIPLIVLTTISSLSESLGERQKTACTVAAISCANSDTYNRTTVS


NHTFFYISDRWKYSELIRYEKPTWDLRHDKLIHVDREFLDIVSLLHNNENQLRTLLTIF


RSDSAPPWVKFMRGYSQCLDHPIIYTCVEEKCQQYNLEELPYGKDIFLENVVGFDLG


APPHNMSVLIAVSNTKPKITKVLRITSTSLTLFDALYNTVLTFFRSIGARNVDVVRRLI


LYQASLSGPHRDAPIHNYLNRDL*


 


CIDMTR Strain GP131 (SEQ ID NO: 3):


     MKRRLILLSWMMFCTSFGHAGRCYYPSTPIPKRFVKRVDTVRSLPECENDTV


AVLTLTNDAKLYVNMLNTWVDGYITTLQYVVPPTLSDIFTFIKRRIDRGSTGTAASTL


PSLTSVRTYFGDRDSSFLWHYTIRMKDGAKTLDCDVYVTSRVHFELNSYGAVQTVL


FEGGVIISRHPADSIACLLINWNWT*


 


CIDMTR Strain GP129 (SEQ ID NO: 2):


     MRVIVLLAMFCCTRPGMFDDPCCIYSSRDRLVQDFTTSNDTWRLIRCKDNLM


VAKRYTDSFCEFSLEENLFDSLALNVSRQELHTLAPECKFGPSVEVGINKQVKCIRYP


RMPKVPSKPEKPSILGVTYRVDYTVMIPTPHFPRDFNGLLCTFLEKNDTFYNTTVDVC


GSEFYSVDGNGK*


 


CISMTR Strain GP83 (pp65 phosphoprotein homolog) (SEQ ID NO: 9):


     MERYVGLGTTLHLALQVEGPFGPHETRFVHFDATFTVPRTPSVVIVAEEQVGS


HLPPSSPLRMKFRAIHSQEELDLLNLEVRNASDQPLPAKSFYDLNVVVFALPLPRVHA


APLHIFFNSALKPSRETFPTVSKTVVRRACGAIWGVRTALSNIAWTEGVGNRAHVDR


ALTVTVLLSVKPACMTHVDSLTEINVSHEDVQVFKAEVFQKGRPNVLGLTLQTTAKP


PPKKLTLFFQLLASHAQVVMRHNPYPALQSHPSNGFTIHCPGDIRLQSGQTYRLTLRN


GFDSTSHAALFFPADFPNADVSGGQWKARHNMDIVIRSHGETTVRKDEVLGTVHFF


DNDLFTFHRVAGVIDTCMMGKQFETRVRRVSESCQEQVFVKSGGRRTGNAARHRR


DRDGGDDDDDDENEDGEEGEEDGEEDVGDAKDDGSESSSESELGSGEDNDGDDDV


FECERPLAREDGASGSAERETLDESEDPSLRPRRVSEEIFPSVLFYPWALSIPTGFCAYI


HYNVVACSSEHSSGEVQDGSVWFDGVPTRPASHACSRTRRDDDGGAGTSRRSHRG


AQ*






Antibodies Specific for GPCMV Strain CIDMTR
In certain embodiments, the present invention provides a purified antibody that binds specifically to GPCMV Strain CIDMTR, or the GPs described above (i.e., gB, gH, gO, gN, GP129, GP131, GP133). As used herein the term “binds specifically” means that the antibody binds to a target agent, e.g., purified guinea pig cytomegalovirus (GPCMV) Strain CIDMTR or glycoproteins (GP) from GPCMV Strain CIDMTR, with a much higher degree of affinity than it binds to GPCMV ATCC/22122. In certain embodiments, the antibody binds to the target agent with a binding affinity of at least 2× greater than its affinity than to GPCMV ATCC/22122. As used herein the term “antibodies” includes monoclonal or polyclonal antibodies or an antibody fragments.
As used herein, the term “monoclonal antibody” refers to an antibody obtained from a group of substantially homogeneous antibodies, that is, an antibody group wherein the antibodies constituting the group are homogeneous except for naturally occurring mutants that exist in a small amount. Monoclonal antibodies are highly specific and interact with a single antigenic site. Furthermore, each monoclonal antibody targets a single antigenic determinant (epitope) on an antigen, as compared to common polyclonal antibody preparations that typically contain various antibodies against diverse antigenic determinants. In addition to their specificity, monoclonal antibodies are advantageous in that they are produced from hybridoma cultures not contaminated with other immunoglobulins.
The adjective “monoclonal” indicates a characteristic of antibodies obtained from a substantially homogeneous group of antibodies, and does not specify antibodies produced by a particular method. For example, a monoclonal antibody to be used in the present invention can be produced by, for example, hybridoma methods (Kohler and Milstein, Nature 256:495, 1975) or recombination methods (U.S. Pat. No. 4,816,567). The monoclonal antibodies used in the present invention can be also isolated from a phage antibody library (Clackson et al., Nature 352:624-628, 1991; Marks et al., J. Mol. Biol. 222:581-597, 1991). The monoclonal antibodies of the present invention particularly comprise “chimeric” antibodies (immunoglobulins), wherein a part of a heavy (H) chain and/or light (L) chain is derived from a specific species or a specific antibody class or subclass, and the remaining portion of the chain is derived from another species, or another antibody class or subclass. Furthermore, mutant antibodies and antibody fragments thereof are also comprised in the present invention (U.S. Pat. No. 4,816,567; Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851-6855, 1984).
Nucleic Acids
The present invention further provides nucleic acids that encode portions or all the GPCMV Strain CIDMTR genome. The term “nucleic acid” refers to deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) and polymers thereof in either single- or double-stranded form, composed of monomers (nucleotides) containing a sugar, phosphate and a base that is either a purine or pyrimidine. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues. A “nucleic acid fragment” is a portion of a given nucleic acid molecule.
A “nucleotide sequence” is a polymer of DNA or RNA that can be single-stranded or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases capable of incorporation into DNA or RNA polymers. The terms “nucleic acid,” “nucleic acid molecule,” “nucleic acid fragment,” “nucleic acid sequence or segment,” or “polynucleotide” are used interchangeably and may also be used interchangeably with gene, cDNA, DNA and RNA encoded by a gene.
The invention encompasses isolated or substantially purified nucleic acid compositions. In the context of the present invention, an “isolated” or “purified” DNA molecule or RNA molecule is a DNA molecule or RNA molecule that exists apart from its native environment and is therefore not a product of nature. An isolated DNA molecule or RNA molecule may exist in a purified form or may exist in a non-native environment such as, for example, a transgenic host cell. For example, an “isolated” or “purified” nucleic acid molecule or biologically active portion thereof, is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. In one embodiment, an “isolated” nucleic acid is free of sequences that naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. Fragments and variants of the disclosed nucleotide sequences are also encompassed by the present invention. By “fragment” or “portion” is meant a full length or less than full length of the nucleotide sequence.
“Naturally occurring,” “native,” or “wild-type” is used to describe an object that can be found in nature as distinct from being artificially produced. For example, a protein or nucleotide sequence present in an organism (including a virus), which can be isolated from a source in nature and that has not been intentionally modified by a person in the laboratory, is naturally occurring.
“Genome” refers to the complete genetic material of an organism.
Promoters
“Promoter” refers to a nucleotide sequence, usually upstream (5′) to its coding sequence, that controls the expression of the coding sequence by providing the recognition for RNA polymerase and other factors required for proper transcription. “Promoter” includes a minimal promoter that is a short DNA sequence comprised of a TATA-box and other sequences that serve to specify the site of transcription initiation, to which regulatory elements are added for control of expression. “Promoter” also refers to a nucleotide sequence that includes a minimal promoter plus regulatory elements that is capable of controlling the expression of a coding sequence or functional RNA. This type of promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an “enhancer” is a DNA sequence that can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue specificity of a promoter. It is capable of operating in both orientations (normal or flipped), and is capable of functioning even when moved either upstream or downstream from the promoter. Both enhancers and other upstream promoter elements bind sequence-specific DNA-binding proteins that mediate their effects. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even be comprised of synthetic DNA segments. A promoter may also contain DNA sequences that are involved in the binding of protein factors that control the effectiveness of transcription initiation in response to physiological or developmental conditions. A general discussion of promoters is provided in U.S. Pat. No. 7,501,129, which is incorporated by reference herein.
As used herein, “biologically active” means that the promoter has at least about 0.1%, 10%, 25%, 50%, 75%, 80%, 85%, even 90% or more, e.g. 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% of the activity of the CCT promoter comprising SEQ ID NO:1 or SEQ ID NO:2. The activity of a promoter can be determined by methods well known to the art. For example, see Sambrook et al., Molecular Cloning: A Laboratory Manual (1989). Promoters of the present invention that are not identical to SEQ ID NO:1 or SEQ ID NO:2, but retain comparable biological activity, are called variant promoters. The nucleotide sequences of the invention include both naturally occurring sequences as well as recombinant forms.
The invention encompasses isolated or substantially purified nucleic acid compositions. In the context of the present invention, an “isolated” or “purified” DNA molecule or RNA molecule is a DNA molecule or RNA molecule that exists apart from its native environment and is therefore not a product of nature. An isolated DNA molecule or RNA molecule may exist in a purified form or may exist in a non-native environment such as, for example, a transgenic host cell. For example, an “isolated” or “purified” nucleic acid molecule or biologically active portion thereof, is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. In one embodiment, an “isolated” nucleic acid is free of sequences that naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For example, in various embodiments, the isolated nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequences that naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived. Fragments and variants of the disclosed nucleotide sequences are also encompassed by the present invention. By “fragment” or “portion” is meant a full length or less than full length of the nucleotide sequence.
“Naturally occurring,” “native,” or “wild-type” is used to describe an object that can be found in nature as distinct from being artificially produced. For example, a protein or nucleotide sequence present in an organism (including a virus), which can be isolated from a source in nature and that has not been intentionally modified by a person in the laboratory, is naturally occurring.
In certain embodiments, the present invention provides a promoters having at least about 70% to 100% identity with the sequence of SEQ ID NO: 10. In certain embodiments, the promoter has 75%, 80%, 85%, 90%, 95% or 99% identity to the sequence of SEQ ID NO: 10.
In certain embodiments, the present invention provides vectors and expression cassettes containing the promoters described above. A “vector” is defined to include, inter alia, any viral vector, as well as any plasmid, cosmid, phage or binary vector in double or single stranded linear or circular form that may or may not be self-transmissible or mobilizable, and that can transform prokaryotic or eukaryotic host either by integration into the cellular genome or exist extrachromosomally (e.g., autonomous replicating plasmid with an origin of replication).
The selection and optimization of a particular expression vector for expressing a specific therapeutic composition (e.g., a protein) in a cell can be accomplished by obtaining the nucleic acid sequence encoding the protein, possibly with one or more appropriate control regions (e.g., promoter, insertion sequence); preparing a vector construct comprising the vector into which is inserted the nucleic acid sequence encoding the protein; transfecting or transducing cultured cells in vitro with the vector construct; and determining whether the protein is present in the cultured cells.
Nucleic acids encoding therapeutic compositions can be engineered into an AAV vector using standard ligation techniques, such as those described in Sambrook and Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press Cold Spring Harbor, N.Y. (2001). For example, ligations can be accomplished in 20 mM Tris-Cl pH 7.5, 10 mM MgCl2, 10 mM DTT, 33 μg/ml BSA, 10 mM-50 mM NaCl, and either 40 μM ATP, 0.01-0.02 (Weiss) units T4 DNA ligase at 0° C. (for “sticky end” ligation) or 1 mM ATP, 0.3-0.6 (Weiss) units T4 DNA ligase at 14° C. (for “blunt end” ligation). Intermolecular “sticky end” ligations are usually performed at 30-100 μg/ml total DNA concentrations (5-100 nM total end concentration).
In certain embodiments, the present invention provides a vector containing an expression cassette comprising a promoter operably linked to a target sequence. “Expression cassette” as used herein means a nucleic acid sequence capable of directing expression of a particular nucleotide sequence in an appropriate host cell, which includes a promoter operably linked to the nucleotide sequence of interest that may be operably linked to termination signals. The coding region usually codes for a functional RNA of interest, for example an RNAi molecule. The expression cassette including the nucleotide sequence of interest may be chimeric.
“Operably-linked” refers to the association of nucleic acid sequences on single nucleic acid fragment so that the function of one of the sequences is affected by another. For example, a regulatory DNA sequence is said to be “operably linked to” or “associated with” a DNA sequence that codes for an RNA or a polypeptide if the two sequences are situated such that the regulatory DNA sequence affects expression of the coding DNA sequence (i.e., that the coding sequence or functional RNA is under the transcriptional control of the promoter). Coding sequences can be operably-linked to regulatory sequences in sense or antisense orientation. Nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. Generally, “operably linked” means that the DNA sequences being linked are contiguous. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice. Additionally, multiple copies of the nucleic acid encoding enzymes may be linked together in the expression vector. Such multiple nucleic acids may be separated by linkers.
“Expression” refers to the transcription and/or translation of an endogenous gene or a transgene in cells. For example, in the case of antisense constructs, expression may refer to the transcription of the antisense DNA only. In addition, expression refers to the transcription and stable accumulation of sense (mRNA) or functional RNA. Expression may also refer to the production of protein.
“Expression cassette” as used herein means a DNA sequence capable of directing expression of a particular nucleotide sequence in an appropriate host cell, comprising a promoter operably linked to the nucleotide sequence of interest that is operably linked to termination signals. It also typically comprises sequences required for proper translation of the nucleotide sequence. The coding region usually codes for a protein of interest but may also code for a functional RNA of interest, for example antisense RNA or a nontranslated RNA, in the sense or antisense direction. The expression cassette comprising the nucleotide sequence of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components. The expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. Such expression cassettes will comprise the transcriptional initiation region linked to a nucleotide sequence of interest. Such an expression cassette may be provided with a plurality of restriction sites for insertion of the gene of interest to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
The present disclosure also provides a mammalian cell containing a vector described herein.
Probes and Primers
The use of the word “detect” and its grammatical variants is meant to refer to measurement of the species without quantification, whereas use of the word “determine” or “measure” with their grammatical variants are meant to refer to measurement of the species with quantification. The terms “detect” and “identify” are used interchangeably herein.
As used herein, a “detectable marker” or is an atom or a molecule that permits the specific detection of a compound comprising the marker in the presence of similar compounds without a marker. Detectable markers include, but are not limited to, radioactive isotopes, antigenic determinants, enzymes, nucleic acids available for hybridization, chromophores, fluorophores, chemiluminescent molecules, electrochemically detectable molecules, and molecules that provide for altered fluorescence-polarization or altered light-scattering.
The detectable labels used in the assays of the present invention to diagnose GPCMV, these labels are attached to the protein (e.g., antigen or antibody), can be primary labels (where the label comprises an element that is detected directly or that produces a directly detectable element) or secondary labels (where the detected label binds to a primary label, e.g., as is common in immunological labeling). An introduction to labels, labeling procedures and detection of labels is found in Polak and Van Noorden (1997) Introduction to Immunocytochemistry, 2nd ed., Springer Verlag, N.Y. and in Haugland (1996) Handbook of Fluorescent Probes and Research Chemicals, a combined handbook and catalogue Published by Molecular Probes, Inc., Eugene, Oreg. Patents that described the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241.
Primary and secondary labels can include undetected elements as well as detected elements. Useful primary and secondary labels in the present invention can include spectral labels such as green fluorescent protein, fluorescent dyes (e.g., fluorescein and derivatives such as fluorescein isothiocyanate (FITC) and Oregon GreenTM, rhodamine and derivatives (e.g., Texas red, tetrarhodimine isothiocynate (TRITC), etc.), digoxigenin, biotin, phycoerythrin, AMCA, CyDyesTM, and the like), radiolabels (e.g., 3H, 125I, 35S, 14C, 32P, 33P, etc.), enzymes (e.g., horse radish peroxidase, alkaline phosphatase etc.), spectral calorimetric labels such as colloidal gold or colored glass or plastic (e.g. polystyrene, polypropylene, latex, etc.) beads. The label can be coupled directly or indirectly to a component of the detection assay (e.g., the detection reagent) according to methods well known in the art. As indicated above, a wide variety of labels may be used, with the choice of label depending on sensitivity required, ease of conjugation with the compound, stability requirements, available instrumentation, and disposal provisions.
Exemplary labels that can be used include those that use: 1) chemiluminescence (using horseradish peroxidase and/or alkaline phosphatase with substrates that produce photons as breakdown products as described above) with kits being available, e.g., from Molecular Probes, Amersham, Boehringer-Mannheim, and Life Technologies/Gibco BRL) color production (using both horseradish peroxidase and/or alkaline phosphatase with substrates that produce a colored precipitate (kits available from Life Technologies/Gibco BRL, and Boehringer-Mannheim)); 3) fluorescence using, e.g., an enzyme such as alkaline phosphatase, together with the substrate AttoPhos (Amersham) or other substrates that produce fluorescent products, 4) fluorescence (e.g., using Cy-5 (Amersham), fluorescein, and other fluorescent tags); 5) radioactivity. Other methods for labeling and detection will be readily apparent to one skilled in the art.
Where antibodies are contemplated to be detected in a clinical setting, the labels are preferably non-radioactive and readily detected without the necessity of sophisticated instrumentation. In certain embodiments, detection of the labels will yield a visible signal that is immediately discernible upon visual inspection. One example of detectable secondary labeling strategies uses an antigen linked to an enzyme (typically by recombinant or covalent chemical bonding). The antibody/antigen complex is detected when the enzyme reacts with its substrate, producing a detectable product. In certain embodiments, enzymes that can be conjugated to detection reagents of the invention include, e.g., β-galactosidase, luciferase, horseradish peroxidase, and alkaline phosphatase. The chemiluminescent substrate for luciferase is luciferin. One embodiment of a fluorescent substrate for β-galactosidase is 4-methylumbelliferyl-β-D-galactoside. Embodiments of alkaline phosphatase substrates include p-nitrophenyl phosphate (pNPP), which is detected with a spectrophotometer; 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium (BCIP/NBT) and fast red/napthol AS-TR phosphate, which are detected visually; and 4-methoxy-4-(3-phosphonophenyl) spiro[1,2-dioxetane-3,2′-adamantane], which is detected with a luminometer. Embodiments of horseradish peroxidase substrates include 2,2′azino-bis(3-ethylbenzthiazoline-6 sulfonic acid) (ABTS), 5-aminosalicylic acid (5AS), o-dianisidine, and o-phenylenediamine (OPD), which are detected with a spectrophotometer, and 3,3,5,5′-tetramethylbenzidine (TMB), 3,3′ diaminobenzidine (DAB), 3-amino-9-ethylcarbazole (AEC), and 4-chloro-1-naphthol (4C1N), which are detected visually. Other suitable substrates are known to those skilled in the art. The enzyme-substrate reaction and product detection are performed according to standard procedures known to those skilled in the art and kits for performing enzyme immunoassays are available as described above.
The presence of a label can be detected by inspection, or a detector which monitors a particular probe or probe combination is used to detect the detection reagent label. Typical detectors include spectrophotometers, phototubes and photodiodes, microscopes, scintillation counters, cameras, film and the like, as well as combinations thereof. Examples of suitable detectors are widely available from a variety of commercial sources known to persons of skill. Commonly, an optical image of a substrate comprising bound labeling moieties is digitized for subsequent computer analysis.
By “fragment” or “portion” of a sequence is meant a full length or less than full length of the nucleotide sequence encoding, or the amino acid sequence of a polypeptide or protein. As it relates to a nucleic acid molecule, sequence or segment of the invention when linked to other sequences for expression, “portion” or “fragment” means a sequence having, for example, at least 80 nucleotides, at least 150 nucleotides, or at least 400 nucleotides. If not employed for expressing, a “portion” or “fragment” means, for example, at least 9, 12, 15, or at least 20, consecutive nucleotides, e.g., probes and primers (oligonucleotides), corresponding to the nucleotide sequence of the nucleic acid molecules of the invention. Alternatively, fragments or portions of a nucleotide sequence that are useful as hybridization probes generally do not encode fragment proteins retaining biological activity. Thus, fragments or portions of a nucleotide sequence may range from at least about 6 nucleotides, about 9, about 12 nucleotides, about 20 nucleotides, about 50 nucleotides, about 100 nucleotides or more.
In certain embodiments, the present invention provides assays for determining the presence of GPCMV Strain CIDMTR. GPCMV Strain CIDMTR can be detected by any of a variety of means, including: 1) performing a hybridization reaction between the nucleic acid sample and a probe or probes that are capable of hybridizing to the GPCMV Strain CIDMTR; 2) sequencing at least a portion of the GPCMV Strain CIDMTR; or 3) determining the electrophoretic mobility of the GPCMV Strain CIDMTR or a component thereof. In one embodiment, the GPCMV Strain CIDMTR is subject to an amplification step, prior to or in conjunction with the performance of the detection step. In certain embodiments, amplification steps are by polymerase chain reaction (PCR), ligase chain reaction (LCR), strand displacement amplification (SDA), cloning, and variations of the above (e.g., RT-PCR and GPCMV Strain CIDMTR specific amplification). In one embodiment, the sample is hybridized with a set of primers, which hybridize 5′ and 3′ to a sense or antisense sequence of GPCMV Strain CIDMTR and is subject to PCR amplification.
In one embodiment, the detecting step is by GPCMV Strain CIDMTR specific hybridization followed by primer specific extension. In one embodiment, prior to or in conjunction with detection, the nucleic acid sample is subject to an amplification step. In one embodiment, the size analysis is preceded by a restriction enzyme digestion. In one embodiment, GPCMV Strain CIDMTR or a portion thereof is amplified. In one embodiment, at least one oligonucleotide probe is immobilized on a solid surface.
“Oligonucleotide probe” can refer to a nucleic acid segment, such as a primer, that is useful to amplify a sequence in the GPCMV Strain CIDMTR genome.
A “nucleic acid fragment” is a portion of a given nucleic acid molecule. Deoxyribonucleic acid (DNA) in the majority of organisms is the genetic material while ribonucleic acid (RNA) is involved in the transfer of information contained within DNA into proteins. The term “nucleotide sequence” refers to a polymer of DNA or RNA which can be single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases capable of incorporation into DNA or RNA polymers. The terms “nucleic acid,” “nucleic acid molecule,” “nucleic acid fragment,” “nucleic acid sequence or segment,” or “polynucleotide” may also be used interchangeably with gene, cDNA, DNA and RNA encoded by a gene, e.g., genomic DNA, and even synthetic DNA sequences. The term also includes sequences that include any of the known base analogs of DNA and RNA.
In one embodiment of the present invention, the method also involves contacting the sample with at least one oligonucleotide probe to form a hybridized nucleic acid and amplifying the hybridized nucleic acid. “Amplifying” utilizes methods such as the polymerase chain reaction (PCR), ligation amplification (or ligase chain reaction, LCR), strand displacement amplification, nucleic acid sequence-based amplification, and amplification methods based on the use of Q-beta replicase. These methods are well known and widely practiced in the art. Reagents and hardware for conducting PCR are commercially available. For example, in certain embodiments of the present invention, the GPCMV Strain CIDMTR, or a portion thereof, may be amplified by PCR. In another embodiment of the present invention, at least one oligonucleotide probe is immobilized on a solid surface.
Nucleic Acid Amplification Methods
According to the methods of the present invention, the amplification of DNA present in a physiological sample may be carried out by any means known to the art. Examples of suitable amplification techniques include, but are not limited to, polymerase chain reaction (including, for RNA amplification, reverse-transcriptase polymerase chain reaction), ligase chain reaction, strand displacement amplification, transcription-based amplification, self-sustained sequence replication (or “3SR”), the Qβ replicase system, nucleic acid sequence-based amplification (or “NASBA”), the repair chain reaction (or “RCR”), and boomerang DNA amplification (or “BDA”).
The bases incorporated into the amplification product may be natural or modified bases (modified before or after amplification), and the bases may be selected to optimize subsequent electrochemical detection steps.
Polymerase chain reaction (PCR) may be carried out in accordance with known techniques. See, e.g., U.S. Pat. Nos. 4,683,195; 4,683,202; 4,800,159; and 4,965,188. In general, PCR involves, first, treating a nucleic acid sample (e.g., in the presence of a heat stable DNA polymerase) with one oligonucleotide primer for each strand of the specific sequence to be detected under hybridizing conditions so that an extension product of each primer is synthesized that is complementary to each nucleic acid strand, with the primers sufficiently complementary to each strand of the specific sequence to hybridize therewith so that the extension product synthesized from each primer, when it is separated from its complement, can serve as a template for synthesis of the extension product of the other primer, and then treating the sample under denaturing conditions to separate the primer extension products from their templates if the sequence or sequences to be detected are present. These steps are cyclically repeated until the desired degree of amplification is obtained. Detection of the amplified sequence may be carried out by adding to the reaction product an oligonucleotide probe capable of hybridizing to the reaction product (e.g., an oligonucleotide probe of the present invention), the probe carrying a detectable label, and then detecting the label in accordance with known techniques. Various labels that can be incorporated into or operably linked to nucleic acids are well known in the art, such as radioactive, enzymatic, and florescent labels. Where the nucleic acid to be amplified is RNA, amplification may be carried out by initial conversion to DNA by reverse transcriptase in accordance with known techniques.
Strand displacement amplification (SDA) may be carried out in accordance with known techniques. For example, SDA may be carried out with a single amplification primer or a pair of amplification primers, with exponential amplification being achieved with the latter. In general, SDA amplification primers comprise, in the 5′ to 3′ direction, a flanking sequence (the DNA sequence of which is noncritical), a restriction site for the restriction enzyme employed in the reaction, and an oligonucleotide sequence (e.g., an oligonucleotide probe of the present invention) that hybridizes to the target sequence to be amplified and/or detected. The flanking sequence, which serves to facilitate binding of the restriction enzyme to the recognition site and provides a DNA polymerase priming site after the restriction site has been nicked, is about 15 to 20 nucleotides in length in one embodiment. The restriction site is functional in the SDA reaction. The oligonucleotide probe portion is about 13 to 15 nucleotides in length in one embodiment of the invention.
Ligase chain reaction (LCR) is also carried out in accordance with known techniques. In general, the reaction is carried out with two pairs of oligonucleotide probes: one pair binds to one strand of the sequence to be detected; the other pair binds to the other strand of the sequence to be detected. Each pair together completely overlaps the strand to which it corresponds. The reaction is carried out by, first, denaturing (e.g., separating) the strands of the sequence to be detected, then reacting the strands with the two pairs of oligonucleotide probes in the presence of a heat stable ligase so that each pair of oligonucleotide probes is ligated together, then separating the reaction product, and then cyclically repeating the process until the sequence has been amplified to the desired degree. Detection may then be carried out in like manner as described above with respect to PCR.
Methods of Use
In certain embodiments, the present invention provides a method of determining the effectiveness of a vaccine or therapeutic composition in preventing or ameliorating re-infection with cytomegalovirus comprising:
a. administering a first GPCMV to a guinea pig,
b. administering a vaccine or therapeutic composition,
c. administering a second GPCMV to the guinea pig, and
d. determining the effectiveness of the vaccine or therapeutic composition in preventing or ameliorating re-infection. In certain embodiments, the first GPCMV is ATCC/22122 and the second GPCMV is GPCMV Strain CIDMTR. In certain embodiments, the first GPCMV is GPCMV Strain CIDMTR and the second GPCMV is ATCC/22122.
In certain embodiments, the present invention provides a method of determining the effectiveness of a vaccine or therapeutic composition in preventing or ameliorating infection with cytomegalovirus comprising:
a. administering a vaccine or therapeutic composition to a guinea pig seronegative for GPCMV,
b. administering a GPCMV that is not ATCC/22122 to the guinea pig, and
c. determining the effectiveness of the vaccine or therapeutic composition in preventing or ameliorating GPCMV infection.
In certain embodiments, the present invention provides a method of determining the effectiveness of a vaccine or therapeutic composition in preventing or ameliorating infection with cytomegalovirus comprising:

    
    
        a. administering a vaccine or therapeutic composition to a first guinea pig seronegative for GPCMV and to a second guinea pig seronegative for GPCMV,
        b. administering a GPCMV that is not ATCC/22122 to the first guinea pig and GPCMV ATCC/22122 to the second guinea pig, and
        c. comparing the effectiveness of the vaccine or therapeutic composition in preventing or ameliorating infection by the GPCMV that is not ATCC/22122 or by GPCMV ATCC/22122.
    
    


In certain embodiments, the present invention provides a method of determining the effectiveness of a vaccine or therapeutic composition in preventing or ameliorating re-infection with cytomegalovirus comprising:

    
    
        a. administering a vaccine or therapeutic composition to a guinea pig seropositive for GPCMV,
        b. administering a GPCMV that is not ATCC/22122 to the guinea pig, and
        c. comparing the effectiveness of the vaccine or therapeutic composition in preventing or ameliorating infection by the GPCMV that is not ATCC/22122.

In certain embodiments, the GPCMV that is not ATCC/22122 is GPCMV Strain CIDMTR.

    
    


In certain embodiments, an effective amount of the virus, vaccine or therapeutic composition is administered to the subject. “Effective amount” or “therapeutically effective amount” are used interchangeably herein, and refer to an amount of a compound, formulation, material, or composition, as described herein effective to achieve a particular biological result. Such results may include, but are not limited to the inhibition of virus infection as determined by any means suitable in the art.
In certain embodiments, an amount of the vaccine is administered in order to immunize to the subject. As used herein, “immunization” or “vaccination” are used interchangeably herein and are intended for prophylactic or therapeutic immunization or vaccination. “Therapeutic vaccination” is meant for vaccination of a patient with CMV infection.
“Isolated” means altered or removed from the natural state. For example, a nucleic acid or a peptide naturally present in a living animal is not “isolated.” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell. Unless it is particularly specified otherwise herein, the proteins, virion complexes, antibodies and other biological molecules forming the subject matter of the present invention are isolated, or can be isolated.
The terms “patient,” “subject,” “individual,” and the like are used interchangeably herein, and refer to any animal, or cells thereof whether in vitro or in situ, that can be infected with CMV. In certain non-limiting embodiments, the patient, subject or individual is a guinea pig. In certain embodiments, the patient, subject or individual is a human.
In certain embodiments, the vaccine, therapeutic composition or virus is administered via intramuscular, intradermal, or subcutaneous delivery. In certain embodiments, the vaccine, therapeutic composition or virus is administered via a mucosal surface, such as an oral, intranasal, or intravaginal surface. In certain embodiments, the vaccine, therapeutic composition or virus is administered via intrasternal injection, or by using infusion techniques.
In certain embodiments, “pharmaceutically acceptable” refers to those properties and/or substances which are acceptable to the patient from a pharmacological/toxicological point of view and to the manufacturing pharmaceutical chemist from a physical/chemical point of view regarding composition, formulation, stability, patient acceptance and bioavailability. “Pharmaceutically acceptable carrier” refers to a medium that does not interfere with the effectiveness of the biological activity of the active ingredient(s) and is not toxic to the host to which it is administered.
The term “therapeutic” as used herein means treatment and/or prophylaxis. A therapeutic effect is obtained by avoidance, delay, suppression, remission, or eradication of a disease state associated with CMV infection.
The term “treatment” as used within the context of the present invention is meant to include therapeutic treatment as well as prophylactic, or suppressive measures for the disease or disorder. Thus, for example, the term treatment includes the administration of an agent prior to or following the onset of a disease or disorder thereby preventing or removing all signs of the disease or disorder. As another example, administration of the agent after clinical manifestation of the disease to combat the symptoms of the disease comprises “treatment” of the disease. This includes for instance, prevention of CMV propagation to uninfected cells of an organism. The phrase “diminishing CMV infection” is sometimes used herein to refer to a treatment method that involves reducing the level of infection in a patient infected with CMV, as determined by means familiar to the clinician.
The invention will now be illustrated by the following non-limiting Example.
Example 1
The guinea-pig cytomegalovirus (GPCMV) provides a useful model system for testing “proof-of-concept” for vaccines and antivirals targeting prevention of congenital infection. One shortcoming of the model is the availability of only one strain of GPCMV, the ATCC/22122 strain. Originally isolated by Hartley in 1957, this strain underwent tissue culture-adaptation prior to deposit with ATCC, and is known to undergo deletions in cell culture that attenuate its in vivo replication. Thus, it is not clear whether this strain authentically recapitulates pathogenesis and immune response following experimental infection. Moreover, the availability of only one strain variant renders experimental evaluation of the process of re-infection problematic.
To address these deficiencies, sera from commercially purchased guinea pigs was examined by ELISA and western blot, toward the goal of identifying “naturally-infected” animals. Among a group of 24 guinea pigs, 5 (21%) were found to be GPCMV-seropositive. Western blot using purified viral particles demonstrated immunoreactivity with multiple virion-associated proteins including GP55 (GPCMV gB homolog) and GP131 (UL130 homolog). To further define the serological response of naturally seropositive guinea pigs to GP131 and another constituent of the epithelial/endothelial cell entry complex, GP129 (UL128 homolog), a series of GST fusion proteins were generated.
Sera from naturally seropositive animals, as well animals inoculated with salivary gland-adapted 22122, were highly immunoreactive with these GST fusions, providing evidence that GP129 and GP131 are targets of the humoral immune response in the context of natural infection. Next, efforts were undertaken to culture GPCMV from salivary gland homogenates from seropositive animals. A novel isolate of GPCMV, Strain CIDMTR, was propagated and successfully passaged, both in cell culture, and in vivo. In immune compromised strain 2 animals, disseminated infection was manifest as pneumonia, visceral organ disease, and viremia.
Next, DNA sequence analysis of Strain CIDMTR was performed for genes encoding GPCMV glycoproteins, and compared to reference strain 22122. There was striking sequence conservation of the gpUL55 (gB) homolog; although 13 SNPs were noted, only 2 coding changes were observed (overall identity of 99%). The gpUL100 (gM) homolog demonstrated a similar level of conservation, with 9 SNPs and one amino acid coding change (overall identity of 99%). Sequence of the gN (gpUL73), and gL (gpUL115) homologs demonstrated 93% and 99% identity, respectively. Protein coding variation for Strain CIDMTR as compared to 22122 was greater for GP129 (84% identity) than GP131 (94% identity). Sequence analysis of GP74 (gO) and GP75 (gH) demonstrated the greatest divergence from 22122 (78% and 82% identity, respectively).
In summary: 1) sera from naturally infected GPCMV-seropositive guinea pigs contain high levels of antibody to GP129 and GP131, supporting a role for testing these pentameric-complex proteins as vaccines in the GPCMV model; 2) sequence analysis of a newly isolated strain of GPCMV demonstrates the greatest divergence for the gO, gH, and UL128 homologs, suggesting that these proteins may be under substantial immunologic pressure in infected guinea pigs; 3) the availability of a new strain of GPCMV enables experimental modeling of congenital infection following maternal re-infection, a major and emerging issue in HCMV vaccine design and development.
Example 2
Development of a vaccine against human cytomegalovirus (HCMV) is a major public health priority. The suggestion that passively transferred antibody protects the fetus against infection and injury has driven efforts to develop recombinant targeting major envelope glycoproteins. Although clinical trials of recombinant gB vaccines have shown some degree of effectiveness in preventing CMV infection and disease in high risk populations, vaccine mediated protection with vaccines targeting this single envelope glycoprotein appears to be incomplete. Moreover, the effectiveness of natural immunity in preventing congenital CMV infection and its attendant sequelae is itself a matter of some controversy. A number of recent studies have described fetal CMV transmission in women with preconception immunity, due to re-infection with new strains of CMV. Such infections can produce sequelae identical to those observed in congenitally infected infants born to women with primary CMV infection in pregnancy. These observations certainly complicate CMV vaccine design, and suggest that: 1) for full protection, a CMV vaccine may need to enhance responses superior to those conferred by natural immunity; 2) there may be a strong rationale for vaccinating women of childbearing age who are already CMV seropositive, in addition to targeting and immunizing seronegative women, toward the goal of preventing re-infection with subsequent transmission of the “new” strain.
Several clinical studies have documented the phenomena of re-infection in women of childbearing age. In one prospective study performed at the University of Alabama-Birmingham, serum specimens from 46 women with preconceptional immunity against CMV obtained during a previous pregnancy and a new pregnancy were analyzed for antibodies against the strain-specific epitopes of CMV glycoprotein H (gH), and the nucleotide sequences of the gH gene from seven CMV isolates were determined. Ten of the 16 mothers with infected children (62%) acquired new antibody specificities against gH, as compared with only 4 of the 30 mothers of uninfected infants (13%), suggesting that acquisition of an infection with a virus expressing a novel strain-specific gH genotype during pregnancy was associated with congenital transmission. In another study in Brazil that followed 7,848 women prospectively, sera from 40 mothers of congenitally infected infants and 109 mothers of uninfected control newborns were analyzed for strain-specific anti-CMV antibodies, based not only on polymorphisms within gH binding sites, but also a second antibody reactivity site on gB. Seven of 40 (17.5%) study women, but only 5 of 109 (4.6%) controls acquired antibodies reactive with new CMV strains during pregnancy (p=0.002), suggesting that maternal reinfection by new strains of CMV is a major source of congenital infection in this population. In a study of re-infection (based on acquisition of new gB and/or gH antibody specificities) in 205 seropositive women performed by Ross and colleagues at UAB, approximately one-third of the study participants (59 of 205) were noted to have reinfection, using this definition, during follow-up. The molecular and immunological correlates of re-infection are unclear. There is some evidence that gB polymorphisms in clinical isolates may be less important for re-infection than polymorphisms in gH and other envelope glycoproteins. In a study in Brazil, infections in immunocompetent women with strains corresponding to more than one gB genotype were not common. Additionally, in a study of the CMV strains acquired longitudinally in women who developed infection in spite of being enrolled in the recombinant gB vaccine trial at UAB, there was no selection for or against any nonvaccine gB subtype, in spite of women being immunized only with gB protein corresponding to the Towne (gB1 subtype) strain. Other evidence suggests that the response (or lack thereof) to the envelope glycoprotein N (gN) may play a role in predisposing to re-infection with new CMV strains expressing heterologous gB and/or gH genotypes.
Irrespective of the mechanism(s) involved, the issue of re-infection is a major challenge in vaccine design. There is increasing evidence that congenital CMV infections after nonprimary maternal infections can lead to symptomatic disease and substantial long-term sequelae. Notably, recent evidence from a study at UAB indicated that the incidence of hearing loss in infants infected after nonprimary maternal infection was similar to that in infected infants born to women with primary infection, although significantly infants in the primary infection group had progressive and severe or profound hearing loss, compared to infants in the non-primary group. Since the consequences of re-infection with a new strain in a pregnant, seropositive woman can be similar to those that occur after primary infection in a CMV-seronegative woman, the study of re-infection in a small animal model of congenital transmission would be very useful for the modeling of vaccine strategies for this situation. Ideally, HCMV reinfection would be studied in an animal model prior to clinical vaccine trials. Unfortunately, the strict species-specificity of CMVs precludes preclinical testing of HCMV vaccines in animals. However, a number of rodent and primate CMVs are useful in modeling HCMV vaccines and therapies, given the conservation of many immunogenic structural proteins amongst the various viruses. Among the small animal models, the guinea pig CMV (GPCMV) is uniquely useful, since, in contrast to rodent models, transplacental infection of the fetus occurs following viral challenge during pregnancy. Hence, the GPCMV model is well-suited to the study of vaccines against congenital infection. However, to date it has not been feasible to study re-infection in the guinea pig model. In this report, we describe the isolation of a novel strain of GPCMV, the CIDMTR strain. This strain is the first GPCMV isolate reported since the originally 22122 strain isolated by Hartley in 1957. Although generally well conserved with the 22122 strain of GPCMV, this strain demonstrates some differences in genome structure, particularly in the right-hand end of the genome. There are also substantive differences in some protein coding sequences, including envelope glycoproteins, suggesting that these proteins have been the targets of immune selection during the evolution of GPCMV in the guinea pig. We describe in this paper the morphology and DNA sequence of this novel strain, and preliminary experiments regarding its pathogenesis in vivo. The availability of a second strain of GPCMV should enable the study of re-infection and, potentially, vaccination against re-infection in the guinea pig model of congenital CMV infection.
2. Results and Discussion
2.1 Isolation of the CIDMTR Strain
In the course of ongoing vaccine and pathogenesis studies, guinea pigs were screened at the time of purchase for GPCMV antibodies, using an ELISA-based assay (Schleiss, M. R.; Bourne, N.; Stroup, G.; Bravo, F. J.; Jensen, N. J.; Bernstein, D. I., Protection against congenital cytomegalovirus infection and disease in guinea pigs, conferred by a purified recombinant glycoprotein b vaccine. J Infect Dis 2004, 189, 1374-1381). Within a group of 24 guinea pigs purchased from a commercial source, 5 (21%) were found to be GPCMV-seropositive by ELISA. Western blot analysis was performed using sera from commercially purchased, ELISA-positive animals using purified virions as a target. These studies confirmed that sera from these animals were broadly cross-reactive with GPCMV virion-associated polypeptides, suggesting that these animals were infected with a CMV.
One of the seropositive animals identified in these preliminary experiments was immunosuppressed with cyclophosphamide, 100 mg/kg (Schleiss, M. R.; Bernstein, D. I.; McVoy, M. A.; Stroup, G.; Bravo, F.; Creasy, B.; McGregor, A.; Henninger, K.; Hallenberger, S., The non-nucleoside antiviral, bay 38-4766, protects against cytomegalovirus (cmv) disease and mortality in immunocompromised guinea pigs. Antiviral Res 2005, 65, 35-43), and seven days later the animal was sacrificed and salivary gland (SG) homogenates harvested. The SG homogenate was passaged in vivo by inoculation of two GPCMV seronegative inbred strain 2 guinea pigs, 1 ml by subcutaneous route in the dorsal neck. Three weeks following inoculation, these animals were also immunosuppressed with 100 mg/kg of cyclophosphamide. One week later, these animals were sacrificed and SG homogenates cultured on guinea pig fibroblast lung cells. Plaques from one of the salivary gland homogenates were noted 11 days later, and 3 days later (total of 14 days post-culture), this viral stock (P0) was then subcultured into guinea pig lung fibroblasts and expanded to large-scale (20 flasks). These flasks were then incubated for an additional week prior to harvest of viral stock (P1 stock). Some of these infected flasks were used for DNA purification for deep sequencing, as described below. The remainder of this stock was used for subsequent morphological Electron Microscopy (EM) studies) and for in vivo challenge experiments in guinea pigs, as described in section 2.4.
2.2 Morphological Analyses by EM
To confirm that the isolated virus had morphological characteristics of a CMV, EM was performed. Analysis of P1 virus stock (section 2.1) revealed 20% of the cells showed cytopathic effect. Cells were enlarged with large intranuclear and intracytoplasmic basophilic inclusions visible upon examination by light microscopy on thick section of plastic preparation stained with Toluidine blue. Ultrastructurally, both intranuclear and intracytoplasmic inclusions represented nuclear and cytoplasmactic viral factories. The nuclear inclusion was typical for the center of replication and assembly characteristic of herpesviruses. These nuclear factories showed a large amount of fibrillary electron dense material admixed with moderate to large numbers of empty capsids and nucleocapsids containing electron dense core, features that were interpreted as representative of viral DNA. First envelopment was acquired at the inner nuclear membrane. De-envelopment of nucleocapsids took place at the outer nuclear membrane during the egress. The second envelopment and tegumentation was observed in the cytoplasm factory. Rearrangement of Golgi cisterns, Golgi vesicles, multivesicular body and endoplasmic reticulum in conjunction with formation of nucleocapsids produced large aggregations that were often mixed with electron dense material. Numerous dense bodies and enveloped particles were present in the intercellular space. On negative contrast preparation, a large number of non-infectious enveloped particles (220.24±48.15 nm) and dense bodies (357.83±97.85 nm) were observed. Infectious mature virions consisted of an envelope containing a 116.5±2.68 nm in diameter icosahedral capsid with capsomeres of approximately 11.66±1.87 nm. The CIDMTR strain of GPCMV presented similar cytopathic and pathogenetic effects as those demonstrated by ATCC strain 22122 (Fong, C. K.; Bia, F.; Hsiung, G. D., Ultrastructural development and persistence of guinea pig cytomegalovirus in duet cells of guinea pig submaxillary gland. Arch Virol 1980, 64, 97-108; Fong, C. K.; Bia, F.; Hsiung, G. D.; Madore, P.; Chang, P. W., Ultrastructural development of guinea pig cytomegalovirus in cultured guinea pig embryo cells. J Gen Virol 1979, 42, 127-140; Fong, C. K.; Brigati, D., Ultrastructural localization of viral antigen in nuclear inclusions of cytomegalovirus infected guinea pig cells. Arch Virol 1982, 74, 125-133). Nevertheless, some differences were noted between these two strains. The ATCC strain in contrast to the CIDMTR strain, demonstrated more efficient infection of fibroblasts, even at the same multiplicity of infection (MOI), with over 80% of fibroblastic cells exhibiting cytopathic effect. The nuclear and cytoplasmic factories were more pronounced, with generation of larger quantities of infectious and non-infectious enveloped viral particles and dense bodies.
2.3 Sequencing and Sequence Analysis
Viral DNA (P1) was purified from the GPCMV-CIDMTR strain salivary gland homogenate isolate after passage in guinea pig lung fibroblast cells and subjected to sequence analysis using the MiSeq and PacBio platforms as described in section 3. FIG. 2 summarizes the predicted ORFs identified in the CIDMTR strain. ORFs with highly conserved ORFs with CMVs are noted in FIG. 2 in upper case/bold font (e.g., GP55). In contrast, ORFs appearing unique to GPCMV are noted in lower case (e.g., gp138). The “C” designation in FIG. 2 refers to complimentary strand. Splicing sites are predicted based on previously published reports (Kanai, K.; Yamada, S.; Yamamoto, Y.; Fukui, Y.; Kurane, I.; Inoue, N., Re-evaluation of the genome sequence of guinea pig cytomegalovirus. J Gen Virol 2011, 92, 1005-1020; Yang, D.; Tamburro, K.; Dittmer, D.; Cui, X.; McVoy, M. A.; Hernandez-Alvarado, N.; Schleiss, M. R., Complete genome sequence of pathogenic guinea pig cytomegalovirus from salivary gland homogenates of infected animals. Genome Announc 2013, 1, e0005413) and these need empiric confirmation in future studies; exons are described as coding exons. A notable observation is the codon, ATA, spanning nucleotides 191516-191518 (minus strand). This putative codon is ATG in the strain 22122 sequence, which was predicted to represent the start codon for both the IE2 homolog, GP122 (exons 3, 4 and 5) and the IE1 homolog, GP123 (exons 3, 4 and 6) of GPCMV (Yang, D.; Tamburro, K.; Dittmer, D.; Cui, X.; McVoy, M. A.; Hernandez-Alvarado, N.; Schleiss, M. R., Complet genome sequence of pathogenic guinea pig cytomegalovirus from salivary gland homogenates of infected animals. Genome Announc 2013, 1, e0005413; Yamada, S.; Nozawa, N.; Katano, H.; Fukui, Y.; Tsuda, M.; Tsutsui, Y.; Kurane, I.; Inoue, N., Characterization of the guinea pig cytomegalovirus genome locus that encodes homologs of human cytomegalovirus major immediate-early genes, ul128, and ul130. Virology 2009, 391, 99-106; Nozawa, N.; Yamamoto, Y.; Fukui, Y.; Katano, H.; Tsutsui, Y.; Sato, Y.; Yamada, S.; Inami, Y.; Nakamura, K.; Yokoi, M., et al., Identification of a 1.6 kb genome locus of guinea pig cytomegalovirus required for efficient viral growth in animals but not in cell culture. Virology 2008, 379, 45-54). Whether alternative splicing is occurring in the CIDMTR strain, or the start codon for the IE1/IE2 proteins is different between the two strains of GPCMV (in exon 4, not exon 3), requires further evaluation.
Sequence analysis demonstrated that the CR2P/CIDMTR strain was 232,778 nt in length. Comparison of the CIDMTR sequence with 22122 revealed two regions of striking discrepancy spanning nucleotides ̃198,780 to 201,300 of the CIDMTR sequence. A deletion of approximately 1.5 kb in this region in the CIDMTR strain resulted in the absence of one of the three gp138 ORFs previously annotated in 22122 (FIG. 3A). In contrast, a second region demonstrated an insertion, spanning coordinates 221,540 through 224,780. This region contained 1.45 kb of sequence that was not present in 22122, including a novel copy of a MHC class I homolog, annotated as gp147.1. Duplicate terminal repeat sequences were noted in the CIDMTR strain, as in the 22122 strain, but are slightly shorter (841 nt) than the repeats that are annotated in 22122 (953 nt). The CIDMTR strain putative coding sequences for genes encoding conserved envelope glycoproteins were compared to reference strain 22122. There was striking sequence conservation of the gB homolog; although 13 SNPs were noted, only 2 coding changes were observed (overall identity of 99%). In contrast, sequence analyses of GP74 (gO) demonstrated the greatest degree of sequence divergence, with 303/374 (81% identity) noted, followed by GP75 (gH), with 613/726 (84%) identity compared to the 22122 strain, (FIG. 3B). FIG. 3A highlights the regions of DNA sequence dissimilarity when the ATCC (22122) strain is compared to the CIDMTR strain (Yang, D.; Tamburro, K.; Dittmer, D.; Cui, X.; McVoy, M. A.; Hernandez-Alvarado, N.; Schleiss, M. R., Complete genome sequence of pathogenic guinea pig cytomegalovirus from salivary gland homogenates of infected animals. Genome Announc 2013, 1, e0005413; Kanai, K.; Yamada, S.; Yamamoto, Y.; Fukui, Y.; Kurane, I.; Inoue, N., Re-evaluation of the genome sequence of guinea pig cytomegalovirus. The Journal of general virology 2011, 92, 1005-1020). FIG. 3B illustrates in map format the regions of genomic discontinuity. To confirm that these large-scale rearrangements did not arise as a function of passage of virus in cell culture, PCR and sequence analysis was performed directly on both DNA purified from the original salivary gland homogenate (no tissue culture passage), and on DNA from the tissue culture-derived isolate, with identical results (see section 2.5). Sequence of the PCR-generated fragments was identical to that of the Illumina and PacBio sequenced virus, confirming that this genomic configuration did not arise as an artifact of tissue culture passage. Thus, these findings are compatible with a model whereby the “authentic” GPCMV sequence consists of a virus with 4 tandem copies of MHC Class I homologs, with the possible loss of one copy (with subsequent gene duplication event introducing a new gp138 homolog) having occurred in the ATCC/22122 virus. Further analysis of other primary virus isolates from “naturally infected” guinea pigs will be necessary to distinguish these two possibilities.
2.4 Sequence Characterization of DNA from Original SG Homogenate in Region of IE1/2 Start Codon
A surprising finding from the DNA sequence analysis was the finding of an ATA codon as the putative start codon of the IE1/IE2 protein product (Yamada, S.; Nozawa, N.; Katano, H.; Fukui, Y.; Tsuda, M.; Tsutsui, Y.; Kurane, I.; Inoue, N., Characterization of the guinea pig cytomegalovirus genome locus that encodes homologs of human cytomegalovirus major immediate-early genes, ul128, and ul130. Virology 2009, 391, 99-106). To further examine this issue, sequence analyses of PCR amplified DNA from the original salivary gland homogenates, as well as salivary gland homogenates from further in vivo passages, was undertaken. In these experiments DNA from original seropositive guinea pig CR2P, in vivo passages 357 (F1) and 368 (F2), and DNA from GPL cells infected with CIDMTR were examined by PCR. The PCR was done with the primer pair designated IE splice 3′ P1 (5′-TGCGAAGCGATCTCTCTCAAC-3′ (SEQ ID NO: 19)) and IE splice 5′ P1 (5′-GTGGTTGTACGTGTCGTCGTCA-3′ (SEQ ID NO: 20)) which was predicted to produce an 864 bp product in CIDMTR strain. The PCR reaction was performed in a 25 μl of total volume using Vent (NEB) or Cloned Pfu (Agilent) polymerase, 1.0 μM primers and 200 μM dNTPs. The conditions of the for the PCR were: initial denaturation at 95° C. for 5 min, followed by 95° C. for 30 s, 55° C. for 30 s, 72° C. for 2 min for a total of 30 cycles, and elongation at 72° C. for 5 min. 1 unit of Taq polymerase was added to the reaction and incubated at 72° C. for 10 minutes. The PCR product was run in a 0.7% agarose gel. A band of the expected size was cut from the gel and purified using QIAquick Gel Extraction Kit (Qiagen). The purified DNA was cloned into pCR4-TOPO (Invitrogen) using the TOPO TA Cloning Kit for Sequencing (Invitrogen). Single colonies were grown in 3 ml of LB with ampicillin. The plasmids were purified using QIAprep Spin Miniprep Kit (Qiagen). The clones were analyzed for the present of the insert by digestion with EcoR I. Three of the clones with insert from each reaction were sequenced with T7 promoter, M13 forward (−20) and the PCR primers. From this analysis we can concluded that CR2P, the original seropositive animal, 357 (F1) and 368 (F2) contain an ATG codon in the putative start codon of the IE1/IE2 protein product but the CIDMTR strain that was passage in GPL cells contain an ATA codon.
To further examine splicing of the IE region from the CIDMTR strain (tissue culture derived) virus, reverse-transcriptase PCR was performed on RNA harvested at immediate early times post-infection using RNeasy mini kit (Qiagen) according to the manufacturer's instructions. RNA was treated with RNase-free DNase Set (Qiagen) while in column according to manufacturer's instructions. cDNA was synthesized from 1 μg of total RNA using Quantitect Reverse Transcription kit (Qiagen). Conventional PCR was carried out using cDNA as template and and goTaq (Promega). The PCR was done with primer pair IE splice 3′ P1 (5′-TGCGAAGCGATCTCTCTCAAC-3′ (SEQ ID NO: 21)) and IE splice 5′ P1 (5′-GTGGTTGTACGTGTCGTCGTCA-3′ (SEQ ID NO: 20)), and primer pair IE splice 3′ P2 (5′- CTTGGACCATGGAACATGTCTG-3′ (SEQ ID NO: 22)) and IE splice 5′ P2 (5′-TCGCTATGCATATAACGTAGC-3′ (SEQ ID NO: 23)). The splice 3′ primers are in exon 5, whereas the splice 3′ primers are localized in intron 2. Therefore the primers should produce up to 3 products, depending on different splice variants and the extent of splice product accumulation in the harvested RNA. A ̃850 bp product for immature mRNA (B1) and  ̃750 bp (B2) or  ̃650 bp (B3) products were noted, representing the splicing of 1 or 2 introns, respectively. These results suggest similar IE mRNA processing for the CIDMTR strain compared to strain 22122.
To further examine splicing of the IE region from the CIDMTR strain (tissue culture derived) virus, reverse-transcriptase PCR was performed on RNA harvested at immediate early times post-infection using RNeasy mini kit (Qiagen) according to the manufacturer's instructions. RNA was treated with RNase-free DNase Set (Qiagen) while in column according to manufacturer's instructions. cDNA was synthesized from 1 μg of total RNA using Quantitect Reverse Transcription kit (Qiagen). Conventional PCR was carried out using cDNA as template and and goTaq (Promega). The PCR was done with primer pair IE splice 3′ P1 (5′-TGCGAAGCGATCTCTCTCAAC-3′) and IE splice 5′ P1 (5′-GTGGTTGTACGTGTCGTCGTCA-3′), and primer pair IE splice 3′ P2 (5′-CTTGGACCATGGAACATGTCTG-3′) and IE splice 5′ P2 (5′-TCGCTATGCATATAACGTAGC-3′). The splice 3′ primers are in exon 5, whereas the splice 3′ primers are localized in intron 2. Therefore the primers should produce up to 3 products, depending on different splice variants and the extent of splice product accumulation in the harvested RNA. A  ̃850 bp product for immature mRNA (B1) and  ̃750 bp (B2) or  ̃650 bp (B3) products were noted, representing the splicing of 1 or 2 introns, respectively. These results suggest similar IE mRNA processing for the CIDMTR strain compared to strain 22122.
Sequence analysis was performed of RT-PCR products. The conditions of the PCR were: initial denaturation at 95° C. for 2 min, followed by 95° C. for 30 s, 55° C. for 30 s, 72° C. for 1 min for a total of 30 cycles, and elongation at 72° C. for 5 min. The PCR products were run in a 1.0% agarose gel. Three bands of the expected size were cut from the gel and purified using QIAquick Gel Extraction Kit (Qiagen). The purified DNA was cloned into pCR2.1 (Invitrogen) using the TA Cloning Kit (Invitrogen). Single colonies were grown in LB with ampicillin. The plasmids were purified using QIAprep Spin Miniprep Kit (Qiagen). The clones were analyzed for the present of the insert by digestion with EcoR I. Three of the clones with insert from each reaction were sequenced with T7 promoter, M13 Reverse and the PCR primers. Analysis of the DNA sequence indicated identical splice donor/acceptor sites as those identified for the 22122 strain. All of the clones were ATA in the putative start codon of IE1/IE2 gene for the RT-PCR products. It is unclear if: 1) the ATA codons were selected for during the initial (limited) tissue culture passage and isolation of the CIDMTR strain in fibroblasts; 2) initiation of translation of the IE 1/IE2 protein products in exon 3 occurs at a non-ATG start site; 3) initiation of translation of the IE1/IE2 protein products occurs downstream at a conserved ATG in exon 4 for both the 22122 and CIDMTR strains. That the CIDMTR strain can replicate in cell culture and in vivo (section 2.6) indicates that, if there is a ATG→ATA mutation arising in tissue culture passage in fibroblasts, it does not render the virus replication incompetent. Further analysis is required to determine the precise start site of translation of the IE1 and IE2 proteins in the CIDMTR strain and to clarify the synthesis of the IE protein products in the CIDMTR strain.
2.5 PCR Confirmation of GPCMV-CIDMTR Structure and Development of a Real-Time PCR Assay
To confirm the structure of the CIDMTR strain compared to the ATCC/22122 strain, PCR was performed on viral DNA from both strains, using primers spanning the mismatched regions observed in the sequence analysis comparisons (FIG. 3a, boxed/shaded regions). The PCR was done using primers pairs mismatch [1] F1/R1 and mismatch [1] F2/R2 which amplify a 4 kb region for the 22122 strain, but a 2.5 kb region for the CIDMTR strain. The amplification region using primer pairs mismatch [2] F1/R1 or mismatch [2] F2/R2 was predicted to be 2.2 kb for the 22122 strain and 3.7 kb for the CIDMTR strain. Primer sequences are indicated in FIG. 4.
To evaluate for DNAemia and end-organ infection in the course of in vivo studies (as described in section 3), a specific real-time PCR assay was developed in order to differentiate the GPCMV-CIDMTR strain from the 22122 (ATTC) strain. DNA was extracted from either 100 μl citrated blood, or from fresh frozen tissues samples, as described in the Methods section. For quantitative PCR, both previously validated primers for the GP83 gene [sequenced shared by both the ATCC/22122 strain] and novel primers for the GPCMV 147.1 gene [sequences only found in the CIDMTR strain] were used for real-time PCR assay. These comparisons demonstrated generally good concordance for the two primer sets as used in conventional PCR (data not shown). As a control, the GPCMV 147.1 primers were used in several PCR assays of ATCC/22122 DNA, with consistently negative results (data not shown).
2.6 Characterization of GPCMV-CIDMTR Infection in vivo
Twelve young, GPCMV-seronegative outbred Hartley guinea pigs were divided into two groups of six/group. Each group was challenge with CIDMTR strain virus (p1) at a dose of 1×105 pfu, administered subcutaneously, as described in section 3. Group 1 (n=6) was treated with 200 mg/kg cyclophosphamide on day −1 and 50 mg/kg on day +6 following viral challenge (Schleiss, M. R.; Bernstein, D. I.; McVoy, M. A.; Stroup, G.; Bravo, F.; Creasy, B.; McGregor, A.; Henninger, K.; Hallenberger, S., The non-nucleoside antiviral, bay 38-4766, protects against cytomegalovirus (cmv) disease and mortality in immunocompromised guinea pigs. Antiviral Res 2005, 65, 35-43); group 2 (n=6) was sham-treated (PBS only). Whole blood and sera samples were collected on day 0, 3, 7, and 21. Animals were humanely sacrificed on day 21 and tissue, including lung, liver, spleen, and brain, were collected for PCR analysis. In group 1, 5/6 animals were DNAemic, peaking at day 7 (mean, 3.2+/−0.3 log10 genomes/ml) while in group 2, the prevalence of DNAemia was lower (3/6 animals; 2.5+/−0.35 log10 genomes/ml, p=0.06 compared to group 1). Viral DNA was most readily recovered from spleen upon dissection at day 21 post-infection. All 6 animals from each group had recoverable CIDMTR strain DNA in the spleen. Total spleen viral load in group 1 was 2.4+/−0.07 copies/mg and was 2.4+/−0.1 copies/mg in group 2 (p=NS compared to group 1).
3. Experimental Section
3.1 Cells, Virus and DNA Preparation
GPCMV (strain 22122, ATCC VR682), and CPCMV/CIDMTR were propagated on guinea pig fibroblast lung cells (GPL; ATCC CCL 158) in F-12 medium supplemented with 10% fetal calf serum (FCS; Gibco-BRI), 10,000 IU of penicillin/liter, 10 mg of streptomycin/liter (Gibco-BRL), and 7.5% NaHCO3 (Gibco-BRL). When the P1 passaged CIDMTR virus exhibited >95 CPE in GPL cell culture, cells were pelleted. An aliquot of cells was fixed in phosphotungstic acid for EM studies (see below) and the remaining cells were washed in 10 mM Tris (pH 8.0)/1 mM EDTA (TE), and lysis buffer (200 mM NaCl, 2% SDS, 200 μg/ml proteinase K, in TE), was added. Cells were gently suspended, inverted, and incubated at 68° C. overnight. Following transfer to a 37° C. water bath, three successive phenol-chloroform extractions were performed, followed by ethanol precipitation.
3.2 Transmission Electron Microscopy
Cells were fixed in 1 ml of 2.5% glutaraldehyde in 0.1 M sodium cacodylate buffer and post fixed with 1% osmium tetroxide in 0.1M sodium cacodylate buffer (all reagents from Electron Microscopy Sciences, Hatfield, Pa., USA). Followed by three washes in distilled water, samples were dehydrated using a 25-100% ethyl alcohol gradient. Samples were then infiltrated with 2:1 ethanol: Embed 812 resin (Electron Microscopy Sciences, Hatfield, Pa., USA) for 1 hour and subsequently transferred to a 1:2 ethanol: Embed 812 resin mixture for 1 hour. Cells were further infiltrated with 100% resin and were embedded and incubated at 58° C. for 24 hours to polymerize the resin. Embedded samples were trimmed and sectioned on a Leica UC6 Ultramicrotome (Leica Microsystems, Vienna, Austria). Thin sections (60-70 nm) were obtained and collected on a 200 mesh copper grid (Electron Microscopy Sciences, Hatfield, Pa., USA) using a perfect loop. Grids were contrasted with 5% uranyl acetate for 20 minutes and Satos' lead citrate for 6 minutes. For negative contrast, virions and dense bodies were collected from P1 supernatants of infected fibroblasts and transferred to airfuge tubes (Belkman-Coulter, Brea, Calif., USA) and centrifuged at 30 PSI using an airfuge (Belkman-Coulter, Brea, Calif., USA) for 20 minutes on parafilm and formvar coated copper grids (Electron Microscopy Sciences, Hatfield, Pa., USA). Excess liquid was wicked and the grids were stained with 1% phosphotungstic acid for one minute. All sections were observed under JEOL 1200 EX II transmission electron microscope (JEOL LTD, Tokyo, Japan). Images were obtained using a Veleta 2K×2K camera with iTEM software (Olympus SIS, Munster, Germany).
3.3 Deep Sequencing and Sequence Analyses
Viral DNA was purified as noted and subjected to deep sequencing. Genomic sequencing was performed using Illumina MiSeq and Pacific Biosciences PacBio RS platforms. Approximately 5.2 million 151 bp paired-end MiSeq reads were generated at the University of Minnesota's Biomedical Genomics Center with a nominal insert size of 400 bp. Removal of low quality reads and PhiX sequence resulted in a set of 4.0 million cleaned reads, approximately 11,000× coverage. Initial scaffolds were generated from the cleaned Illumina reads using the ABySS assembler (version 1.3.4) (Simpson, J. T.; Wong, K.; Jackman, S. D.; Schein, J. E.; Jones, S. J.; Birol, I., Abyss: A parallel assembler for short read sequence data. Genome Res 2009, 19, 1117-1123). Scaffold quality was assessed manually by comparison with the reference strain, 22122 (Yang, D.; Tamburro, K.; Dittmer, D.; Cui, X.; McVoy, M. A.; Hernandez-Alvarado, N.; Schleiss, M. R., Complete genome sequence of pathogenic guinea pig cytomegalovirus from salivary gland homogenates of infected animals. Genome Announc 2013, 1, e0005413; Kanai, K.; Yamada, S.; Yamamoto, Y.; Fukui, Y.; Kurane, I.; Inoue, N., Re-evaluation of the genome sequence of guinea pig cytomegalovirus. The Journal of general virology 2011, 92, 1005-1020; Schleiss, M. R.; McGregor, A.; Choi, K. Y.; Date, S. V.; Cui, X.; McVoy, M. A., Analysis of the nucleotide sequence of the guinea pig cytomegalovirus (GPCMV) genome. Virology journal 2008, 5, 139), and by remapping the reads using Bowtie 2 and scrutinizing local coverage and consensus using Tablet (Milne, I.; Bayer, M.; Cardle, L.; Shaw, P.; Stephen, G.; Wright, F.; Marshall, D., Tablet—-next generation sequence assembly visualization. Bioinformatics 2010, 26, 401-402) and SAMtools (Li, H.; Handsaker, B.; Wysoker, A.; Fennell, T.; Ruan, J.; Homer, N.; Marth, G.; Abecasis, G.; Durbin, R., The sequence alignment/map format and samtools. Bioinformatics 2009, 25, 2078-2079). Special attention was paid to correct alignment and orientation of the paired ends. Regions of weak coverage and scaffold gaps were identified and closed either by manual local assembly (Waterhouse, A. M.; Procter, J. B.; Martin, D. M.; Clamp, M.; Barton, G. J., Jalview version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25, 1189-1191) or by Sanger sequencing. Independent validation of the pseudomolecule was performed using the longer PacBio RS reads. SMRT Analysis software produced 998 high quality (“corrected”) reads ranging between 509-15,898 bp, median 6,257 bp (approximately 27× coverage), as well as another set of scaffolds. These data were used to evaluate the Illumina assembly, specifically its structural correctness, and to correct misassembled repeat regions.
3.4 GPCMV-CIDMTR Strain PCR Assay
For confirmation of viral genome structural differences noted by deep sequencing, PCR was performed for each virus using primers indicated in FIG. 4. The PCR reaction was performed in a 50 μl of total volume using GoTaq long PCR Master Mix from Promega and 1.0 μM primers. The DNA template was total genomic and viral DNA extracted from GPL cells infected with 22122 or CIDMTR tissue culture strain. The conditions for the PCR were: initial denaturation at 95° C. for 2 min, followed by 95° C. for 30 s, 53° C. for 30 s, 72° C. for 4 min for a total of 35 cycles, and elongation at 72° C. for 10 min. The PCR product (4 μl) were subjected to electrophoresis in a 0.7% agarose gel. The PCR product from mismatch 1 F2/R2 and mismatch 2 F2/R2 were purified from the gel using the Geneclean® II kit from MP Biomedicals following the manufacturer's instructions. The cleaned PCR product was then sequenced by Sanger sequencing (Functional Biosciences, Madison, Wis.). Purified PCR products were also subjected to restriction endonuclease comparisons.
The real-time PCR assay focused on the amplification of sequences corresponding to the CIDMTR strain GP147.1 ORF (FIG. 2), since this sequence is absent in the ATCC/22122 strain sequence. A GPCMV 147.1 specific real-time PCR primer pair, consisting of CIDMTR147.1_464F (5′-ATGCAACATAGCGTGCTGAC-3′ (SEQ ID NO: 24)) and CIDMTR147.1_583R (5′-GGGACAAAAGCACGATGAAC-3′ (SEQ ID NO: 25)) was designed and utilized for the real-time PCR assay. These primers amplified a 120 bp region of the 147.1 gene specific for the CIDMTR strain. The specific hydrolysis probe used for detection was CIDMTR147.1_494P (FAM-GTGTTCGTGTCCTTGATCGTACGCA-BHQ1 (SEQ ID NO: 26)). A second GPCMV 147.1 specific primer pair, CIDMTR147.1_225F (5′-AATGGTTCGCTACGGACATC-3′ (SEQ ID NO: 27)) and CIDMTR147.1_368R (5′-CGGACAACGGAACATACTTG-3′ (SEQ ID NO: 28))) was also utilized in real-time PCR assays. These primers amplified a 144 bp region of 147.1 specific for the CIDMTR strain. The specific hydrolysis probe used for detection with this primer pair was CIDMTR147.1_262P (FAM-TTCCTCGACGAAGCTCGCGGTATAAT-BHQ1 (SEQ ID NO: 29)). In each instance, the PCR reactions were performed in a 25 μl using LightCycler 480 Probes Master from Roche; as well as 0.4 μM primers, 0.1 μM probe and 0.4 u/μl of UNG. PCR was performed using the LightCycler 480 Real-Time PCR System (Roche) under the following conditions: initial denaturation at 95° C. for 10 min, followed by 95° C. for 10 s, 56° C. for 15 s, 72° C. for 10 s for a total of 45 cycles, then a final hold step at 40° C. The first primer pair (464F and 583R) was chosen for detection of viral genome for in vivo studies. Data were analyzed with the LightCycler Data Analysis Software (version 1.5; Roche) using standard curves generated using serial dilutions of plasmid pCR2.1 with 147.1 at known concentrations. Negative results were arbitrarily assigned a level of 50 for the purpose of statistical comparisons, based upon limit-of-detection analyses observed in other real-time PCR experiments (Crumpler, M. M.; Choi, K. Y.; McVoy, M. A.; Schleiss, M. R., A live guinea pig cytomegalovirus vaccine deleted of three putative immune evasion genes is highly attenuated but remains immunogenic in a vaccine/challenge model of congenital cytomegalovirus infection. Vaccine 2009, 27, 4209-4218).
3.5 Animal Challenge Studies
All animal studies were performed with the approval of the University of Minnesota Institutional Animal Care and Use Committee (IACUC). Some animals were immune suppressed at day −1 (200 mg/kg) and day +6 (50 mg/kg) with cyclophosphamide delivered by intraperitoneal route. Both cyclophosphamide-treated and untreated animals (n=6/group) were challenged with CIDMTR strain virus (P1 workpool) at a dose of 1×105 pfu by subcutaneous route. Blood samples were collected at day 0, 3, 7 and 21 post-inoculation and animals humanely sacrificed at day 21 for collection of tissue samples for PCR analyses.
4. Conclusions
In conclusion, we have isolated a new strain of GPCMV, which we designate as the CIDMTR strain. This isolate was obtained from a GPCMV seropositive guinea pig as a part of a longstanding commercial breeding colony; therefore, it is unclear if this strain represents a bona fide “wild-type” strain of GPCMV. However, this isolate was subjected to minimal passage (one passage in vivo; one passage in cell culture) prior to genomic characterization, making it more likely to represent a wild-type sequence than the highly passaged ATCC (22122) strain. Sequence comparison with the 22122 strain revealed generally good conservation of protein coding sequences, although two areas of substantial discontinuity compared to the reference (22122) strain were noted. One of these areas contains a copy of a MHC-1 homolog not found in the 22122 strain. Since these gene products appear to be of important for the in vivo pathogenesis of infection (Crumpler, M. M.; Choi, K. Y.; McVoy, M. A.; Schleiss, M. R., A live guinea pig cytomegalovirus vaccine deleted of three putative immune evasion genes is highly attenuated but remains immunogenic in a vaccine/challenge model of congenital cytomegalovirus infection. Vaccine 2009, 27, 4209-4218), further functional comparisons of the two strains are of interest. Studies in immune competent and immune compromised guinea pigs confirm the ability of the CIDMTR virus to disseminate and produce viremia (DNAemia). Variation in glycoprotein gene coding sequences were noted, particularly for the gH and gO proteins, suggesting that this virus may be a useful tool for the study of re-infection of immune guinea pigs in the guinea pig model of congenital CMV infection. Cross-neutralization studies of strain-specific immunity would enhance the usefulness of this new strain for the modeling of vaccine-mediated protection in this uniquely valuable model.
Example 3
The inventors have also determined the promoter region of CIDMTR virus (SEQ ID NO: 10), as indicated in FIG. 5.
All publications, patents and patent applications are incorporated herein by reference, While in the foregoing specification this invention has been described in relation to certain preferred embodiments thereof, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details described herein may be varied considerably without departing from the basic principles of the invention.
The use of the terms “a” and “an” and “the” and similar referents in the context of describing the invention are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.
Embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those embodiments may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

## Claims

1. A method for testing the effectiveness of a vaccine or therapeutic composition in preventing or ameliorating re-infection with cytomegalovirus comprising:
a. administering a first guinea pig cytomegalovirus (GPCMV) to a guinea pig,
b. administering a vaccine or therapeutic composition, and
c. administering a second GPCMV to the guinea pig,
wherein the first GPCMV is strain ATCC/22122 and the second GPCMV is strain CIDMTR or wherein the first GPCMV is strain CIDMTR and the second GPCMV is strain ATCC/22122; and
wherein
(a) the CIDMTR strain is ATCC® deposit number PTA-120714;
(b) the CIDMTR strain has at least 99% identity to SEQ ID NO:1;
(c) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5);
(d) the CIDMTR Strain comprises open reading frame gp147.1;
(e) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5); or
(f) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7) or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

2. The method of claim 1, wherein
(i) the first GPCMV is strain ATCC/22122, and
(ii) the second GPCMV is strain CIDMTR.

3. The method of claim 1, wherein
(i) the first GPCMV is strain CIDMTR, and
(ii) the second GPCMV is strain ATCC/22122.

4. The method of claim 1, wherein (a) the CIDMTR strain is ATCC® deposit number PTA-120714.

5. The method of claim 1, wherein (b) the CIDMTR strain has at least 99% identity to SEQ ID NO:1.

6. The method of claim 1, wherein (c) the CIDMTR Strain comprises 1)a glycoprotein (GP) having greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

7. The method of claim 1, wherein (d) the CIDMTR Strain comprises open reading frame gp147.1.

8. The method of claim 1, wherein (e) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

9. The method of claim 1, wherein (f) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7) or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

10. A method for testing the effectiveness of a vaccine or therapeutic composition in preventing or ameliorating infection with cytomegalovirus comprising:
a. administering a vaccine or therapeutic composition to a guinea pig, and
b. administering a GPCMV strain CIDMTR to the guinea pig, wherein
(a) the CIDMTR strain is ATCC® deposit number PTA-120714;
(b) the CIDMTR strain has at least 99% identity to SEQ ID NO:1;
(c) the CIDMTR Strain comprises 1)a glycoprotein (GP) having greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5);
(d) the CIDMTR Strain comprises open reading frame gp147.1;
(e) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5); or
(f) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7) or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

11. The method of claim 10, wherein the guinea pig is seronegative for GPCMV.

12. The method of claim 10, wherein the guinea pig is seropositive for GPCMV.

13. The method of claim 12, wherein the GPCMV infection is not ATCC/22122.

14. The method of claim 10, wherein the vaccine, therapeutic composition or virus is administered via intramuscular, intradermal, subcutaneous delivery, or via a mucosal surface.

15. The method of claim 14, wherein the administration is via mucosal surface, and the mucosal surface is an oral, intranasal, or intravaginal surface.

16. The method of claim 10, wherein (a) the CIDMTR strain is ATCC® deposit number PTA-120714.

17. The method of claim 10, wherein (b) the CIDMTR strain has at least 99% identity to SEQ ID NO:1.

18. The method of claim 10, wherein (c) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

19. The method of claim 10, wherein (d) the CIDMTR Strain comprises open reading frame gp147.1.

20. The method of claim 10, wherein (e) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

21. The method of claim 10, wherein (f) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7) or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

22. A method for testing the effectiveness of a vaccine or therapeutic composition in preventing or ameliorating infection with cytomegalovirus comprising:
a. administering a vaccine or therapeutic composition to a first guinea pig seronegative for GPCMV and to a second guinea pig seronegative for GPCMV, and
b. administering a GPCMV strain CIDMTR to the first guinea pig and GPCMV strain ATCC/22122 to the second guinea pig, wherein
(a) the CIDMTR strain is ATCC® deposit number PTA-120714;
(b) the CIDMTR strain has at least 99% identity to SEQ ID NO:1;
(c) the CIDMTR Strain comprises 1)a glycoprotein (GP) having greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5);
(d) the CIDMTR Strain comprises open reading frame gp147.1;
(e) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5); or
(f) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7) or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

23. The method of claim 22, wherein the vaccine, therapeutic composition or virus is administered via intramuscular, intradermal, subcutaneous delivery, or via a mucosal surface.

24. The method of claim 22, wherein (a) the CIDMTR strain is ATCC® deposit number PTA-120714.

25. The method of claim 22, wherein (b) the CIDMTR strain has at least 99% identity to SEQ ID NO:1.

26. The method of claim 22, wherein (c) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

27. The method of claim 22, wherein (d) the CIDMTR Strain comprises open reading frame gp147.1.

28. The method of claim 22, wherein (e) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8), or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).

29. The method of claim 22, wherein (f) the CIDMTR Strain comprises 1) a glycoprotein (GP) having greater than 99% sequence identity to glycoprotein 115 (gL) (SEQ ID NO:8); and 2) a GP having greater than 84% sequence identity to GPCMV glycoprotein 129 (GP129) (SEQ ID NO:2), greater than 94% sequence identity to GPCMV glycoprotein 131 (GP131) (SEQ ID NO:3), greater than 78% sequence identity to GP74 (gO) (SEQ ID NO:4), greater than 99% sequence identity to glycoprotein 55 (gB) (SEQ ID NO:6), greater than 93% sequence identity to glycoprotein 73 (gN) (SEQ ID NO: 7) or greater than 82% sequence identity to GP75 (gH) (SEQ ID NO:5).