# Patent

## Title
Nylanderia fulva virus

## Abstract

At least one novel virus capable of infecting crazy ants (Nylanderia fulva) is isolated, along with polynucleotide sequences and amino acid sequences of the virus. The virus is capable of be used as a biopesticide to control populations of crazy ants.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Patent Application 61/762,529 filed Feb. 8, 2013.


BACKGROUND OF THE INVENTION
1. Field of the Invention
This invention relates to a novel virus that infect Nylanderia fulva. The invention also relates to polynucleotide sequences of this novel virus, to biopesticides containing this novel virus, and methods of using the biopesticides.
2. Description of the Prior Art
Nylanderia fulva (Mayr), previously Paratrechina pubens (see, Gotzek, et al., PLoS ONE 7(9):e45314 (2012); LaPolla, et al., Syst. Entomol. 35:118-131 (2010)), is an invasive ant species that in recent years has developed into a serious pest problem in the Caribbean and United States (see, e.g., Wetterer and Keularts, Entomol. 91:423-427 (2008); and MacGown and Layton, Midsouth Entomol. 3:44-47 (2010)). A rapidly expanding range, explosive localized population growth, and control difficulties have elevated this ant to pest status. Professional entomologists and the pest control industry in the United States are urgently trying to understand its biology and develop effective control methods (see, e.g., Drees, et al., College Station: Texas A&M. 129-134 p. (2009) (insects.tamu.edu/fireant/research/projects/pdf/rasberrycrazyant.pdf); Warner and Scheffrahn, Gainesville: University of Florida, (2010) (edis.ifas.ufl.edu/pdffiles/IN/IN56000.pdf); Calibeo and Oi, ENY-2006 (IN889) ed. Gainesville: University of Florida (2011) (edis.ifas.ufl.edu/pdffiles/IN/IN88900.pdf)). Efforts have primarily focused on pursuing development of insecticide-based control strategies (Meyers, College Station: Texas A&M. 163 p. (2008) (urbanentomology.tamu.edu/pdf/meyer_dissertation.pdf)), as well as the effort to identify self-sustaining, biological control agents specific to N. fulva. While viruses can be important biological control agents against pest insect populations (Lacey, et al., Biol. Cont. 21:230-248 (2001)), none are known to infect N. fulva. 
There remains a need for biocontrol agents and/or biopesticides that eliminate or at least reduce the spread of N. fulva and their colonies. The present invention is directed to a novel N. fulva virus, polynucleotides of the novel virus, biopesticides containing the novel N. fulva virus, and methods of using the biopesticides to control the N. fulva population in an area.
BRIEF DESCRIPTION OF THE INVENTION
It is an object of this invention to have at least one novel virus that infects Nylanderia fulva and other types of crazy ants.
It is an object of this invention to have a biopesticide containing at least one novel virus that infects Nylanderia fulva and other types of crazy ants.
It is another object of this invention to have a biopesticide containing at least one novel virus that infects Nylanderia fulva and other types of crazy ants. It is a further object of this invention that the biopesticide contains a carrier. The carrier can be a liquid or solid. It is another object of this invention that the carrier be a food source for the crazy ants.
It is an object of this invention to have a novel cDNA sequence having the sequence set forth in SEQ ID NO: 93; or that has at least 95% identity to SEQ ID NO: 93; or that has at least 90% identity to SEQ ID NO: 93; or that has at least 85% identity to SEQ ID NO: 93.
It is an object of this invention to have a novel cDNA sequence having the sequence set forth in SEQ ID NO: 93; or that has at least 95% identity to SEQ ID NO: 93; or that has at least 90% identity to SEQ ID NO: 93; or that has at least 85% identity to SEQ ID NO: 93. It is a further object of this invention to have the RNA equivalent of these sequences, or the RNA equivalent of the reverse complement of these sequences and which are viral genomic sequences. It is another object of this invention that the virus having these sequences infects crazy ants.
It is another object of this invention to have a novel virus that infects crazy ants and contains genomic RNA, the genomic RNA being the RNA equivalent of SEQ ID NO: 93; the RNA equivalent of the reverse complement of SEQ ID NO: 93; or a sequence that has at least 95%, 90% or 85% identity to these sequences. It is a further object of this invention to have a biopesticide containing this novel virus and, optionally, a carrier. It is another object of this invention that the carrier is optionally a food source for crazy ants, or optional a substance that eases distribution of the biopesticide. The carrier can be optionally a liquid, gel or a solid. It is another object of this invention to have a method of reducing the population of crazy ants in a colony or eradicating a colony of crazy ants by spreading this biopesticide in areas around a crazy ant colony or in areas where the crazy ants feed.
It is an object of this invention to have a novel polyprotein that is encoded by the novel cDNA sequence contained in SEQ ID NO: 93; the complement of SEQ ID NO: 93; or the reverse complement of SEQ ID NO: 93; or a sequence that has at least 95%, 90% or 85% identity to these sequences.
It is an object of this invention to have a novel virus that contains RNA which encodes a novel polyprotein that is encoded by the novel cDNA sequence contained in SEQ ID NO: 93; the complement of SEQ ID NO: 93; or the reverse complement of SEQ ID NO: 93; or a sequence that has at least 95%, 90% or 85% identity to these sequences. It is a further object of the invention that the novel virus which encodes this novel polyprotein infects crazy ants. It is another object of this invention to have a biopesticide containing this novel virus. The biopesticide can optionally contain a carrier. The carrier can be a solid, gel or a liquid. Optionally the carrier is a food source for crazy ants, or optional a substance that eases distribution of the biopesticide. It is another object of this invention to have a method of reducing the population of crazy ants in a colony or eradicating a colony of crazy ants by spreading this biopesticide in areas around a crazy ant colony or in areas where the crazy ants feed.
It is an object of this invention to have a polyprotein encoded by the amino acid sequence of SEQ ID NO: 94; or a sequence that has at least 95%, 90% or 85% identity to SEQ ID NO: 94. It is another object of this invention to have a novel virus that contains RNA which encodes the novel polyprotein having the amino acid sequence of SEQ ID NO: 94, or a sequence that has at least 95%, 90% or 85% identity to SEQ ID NO: 94. It is a further object of this invention that the novel virus infects crazy ants. It is another object of this invention to have a biopesticide containing this novel virus. The biopesticide can optionally contain a carrier. The carrier can be optionally a solid, gel or a liquid. Optionally the carrier is a food source for crazy ants, or optional a substance that eases distribution of the biopesticide. It is another object of this invention to have a method of reducing the population of crazy ants in a colony or eradicating a colony of crazy ants by spreading this biopesticide in areas around a crazy ant colony or in areas where the crazy ants feed.
It is an object of this invention to have a polyprotein containing at least one amino acid sequence selected from SEQ ID NOs: 95, 96, and 97; or a sequence that has at least 95%, 90% or 85% identity to SEQ ID NOs: 95, 96, and 97. It is another object of this invention to have a novel virus that contains RNA which encodes the novel polyprotein having at least one amino acid sequence selected from SEQ ID NOs: 95, 96, and 97; or a sequence that has at least 95%, 90% or 85% identity to SEQ ID NOs: 95, 96, and 97. It is a further object of this invention that the novel virus infects crazy ants. It is another object of this invention to have a biopesticide containing this novel virus. The biopesticide can optionally contain a carrier. The carrier can be optionally a solid, gel or a liquid. Optionally the carrier is a food source for crazy ants, or optional a substance that eases distribution of the biopesticide. It is another object of this invention to have a method of reducing the population of crazy ants in a colony or eradicating a colony of crazy ants by spreading this biopesticide in areas around a crazy ant colony or in areas where the crazy ants feed.
It is an object of this invention to have a novel virus that can be identified by containing genomic RNA, the cDNA of which can hybridize to a primer having a sequence set forth in SEQ ID NOs: 11-88 and mixtures thereof. It is further object of this invention that this novel virus infects crazy ants. It is another object of this invention to have a biopesticide containing this novel virus that infects crazy ants which contains genomic RNA, the cDNA of which can hybridize to a primer having a sequence set forth in SEQ ID NOs: 11-88 and mixtures thereof. It is also an object of this invention that the biopesticide sickens and/or kills crazy ants. It is a further object of this invention that the biopesticide contains a carrier where the carrier can be a food of crazy ants or a substance that eases distribution or application of the biopesticide. It is another object of this invention that the carrier be either a solid, gel or a liquid. It is another object of this invention to have a method of reducing the population of crazy ants in a colony or eradicating a colony of crazy ants by spreading this biopesticide in areas around a crazy ant colony or in areas where the crazy ants feed.


DETAILED DESCRIPTION OF THE INVENTION
N. fulva is a species of ants formerly called Paratrechina pubens and is commonly called “crazy ants”. Crazy ants can include tawny crazy ants, brown crazy ants, hairy crazy ants, Caribbean crazy ants, and Rasberry crazy ants. Any hybrid ants that are infected by the virus of this invention are included in the term “crazy ants”. Crazy ants are an invasive species that are a serious pest in the Caribbean and United States. Chemical pesticides may kill crazy ants but can also kill other beneficial or desired insects and animals. To date, no virus or bacteria has been identified which infects crazy ants and which can be used as a biopesticide against crazy ants. This invention identifies at least one virus that infects N. fulva, NfV, and can be used as a biopesticide against crazy ants.
A “biocontrol agent” or “biopesticide” are interchangeable terms and are broadly defined as a composition containing a protein, glycoprotein, polysaccharide, lipid, or other substance produced by animals, plants, bacteria, viruses, phages, fungi, protozoa, etc., that, when a pest ingests, touches, or otherwise comes in contact with the composition, exerts a deleterious effect on the pest. Such deleterious effect can include, but is not limited to, inhibiting reproduction and/or killing the pest. Viruses, bacteria, phages, protozoa, fungi, etc., can be biocontrol agents or biopesticides in that these organisms can infect the pest, injure, and/or kill the pest. Further, some animals are biocontrol agents or biopesticides, such as endoparasitic wasps. In this invention, the at least one virus described herein, NfV, can be a biocontrol agent or biopesticide for the crazy ants.
A biopesticide can optionally include a carrier component which can be a liquid or a solid material. The carrier usually is an inert agent that does not repel the pest. The carrier may assist in the delivery of the biocontrol agent that targets the pest. The carrier may be a food source for crazy ants. A carrier can be a liquid or gel, such as, but not limited to, water, sugar water, saline solution, oil, or any other liquid or gel that does not adversely affect the viability and/or activity of the biocontrol organism or compound. A solid carrier can be, for example, the pest's food or a substance that assists with the application or distribution of the biocontrol agent. For crazy ants, non-limiting examples of solid carriers include corn cob grits, extruded corn pellets, boiled egg yolks, and frozen insects such as crickets.
Optionally, a chemical pesticide, insecticide, or synergists can be included in the biopesticide. Non-limiting examples of pesticides, insecticides, or synergists for this invention include, abamectin, dinotefuran, avermectins, chlorfenapyr, indoxacarb, metaflumizone, imidacloprid, fipronil, hydramethylon, sulfluramid, hexaflumuron, pyriproxyfen, methoprene, lufenuron, dimilin, chlorpyrifos, neem, azadiractin, boric acid, their active derivatives, and the like. These pesticides/insecticides act as stressor which may be required to initiate replication of the biocontrol organism which, in turn, results in death of the pests.
An “effective amount” or “amount effective for” is the minimum amount of a biocontrol agent to affect the desired effect on the organism targeted by the biocontrol agent. For this invention, an “effective amount” or “amount effective for” is the minimum amount of the virus(es) or composition containing the virus(es) needed to cause the death of crazy ants. An effective amount of the virus(es) of this invention will infect and kill a sufficient number of crazy ants such that the colony is reduced in size as compared to a similar colony that is not treated, or such that the colony collapses completely thereby eradicating the crazy ants. The precise amount needed may vary in accordance with the particular virus used, the other components of the biopesticide, the colony being treated, the environment in which the colony is located, and the environment before, during, and after application of the biocontrol agent. The exact amount of virus needed per dose of biopesticide and/or the amount of biopesticide needed can be easily determined by one of ordinary skill in the art using the teachings presented herein.
The present invention includes the method of using the virus(es) of the present invention to reduce or eradicate a population of crazy ants. These methods involve spreading, distributing, or administrating the virus(es) of the present invention or the biopesticide of the present invention to crazy ants, their colonies, areas around their colonies, and/or areas where the crazy ants forage and obtain food. The amount of biopesticide used is an effective amount for killing crazy ants, reducing the size of the colony compared to an untreated colony, or eradicating the crazy ants and their colony.
The terms “isolated”, “purified”, or “biologically pure” as used herein, refer to material that is substantially or essentially free from components that normally accompany the material in its native state. In an exemplary embodiment, purity and homogeneity are determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A nucleic acid that is the predominant species present in a preparation is substantially purified. In an exemplary embodiment, the term “purified” denotes that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. An isolated or purified virus is a virus that is separated from other viruses with which it is found in nature or from the virus' host. Typically, isolated nucleic acids or proteins or viruses have a level of purity expressed as a range. The lower end of the range of purity for the component is about 60%, about 70% or about 80% and the upper end of the range of purity is about 70%, about 80%, about 90% or more than about 90%.
The term “nucleic acid” as used herein, refers to a polymer of ribonucleotides or deoxyribonucleotides. Typically, “nucleic acid” polymers occur in either single- or double-stranded form, but are also known to form structures comprising three or more strands. The term “nucleic acid” includes naturally occurring nucleic acid polymers as well as nucleic acids comprising known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Exemplary analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs). “DNA”, “RNA”, “polynucleotides”, “polynucleotide sequence”, “oligonucleotide”, “nucleotide”, “nucleic acid”, “nucleic acid molecule”, “nucleic acid sequence”, “nucleic acid fragment”, and “isolated nucleic acid fragment” are used interchangeably herein.
Unless otherwise indicated, a particular nucleic acid sequence also implicitly 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 deoxyino sine residues (see e.g., Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); and Rossolini et al., Mol. Cell. Probes 8:91-98(1994)).
In addition to the degenerate nature of the nucleotide codons which encode amino acids, alterations in a polynucleotide that result in the production of a chemically equivalent amino acid at a given site, but do not affect the functional properties of the encoded polypeptide, are well known in the art. Thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue, such as glycine, or a more hydrophobic residue, such as valine, leucine, or isoleucine. Similarly, changes which result in substitution of one negatively charged residue for another, such as aspartic acid for glutamic acid, or one positively charged residue for another, such as lysine for arginine or histidine, can also be expected to produce a functionally equivalent protein or polypeptide.
As used herein a nucleic acid “probe”, oligonucleotide “probe”, or simply a “probe” refers to a nucleic acid capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation. As used herein, a probe may include natural (i.e., A, G, C, or T) or modified bases (e.g., 7-deazaguanosine, inosine, etc.). In addition, the bases in a probe may be joined by a linkage other than a phosphodiester bond, so long as it does not interfere with hybridization. Thus, for example, probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages. It will be understood by one of skill in the art that probes may bind target sequences lacking complete complementarity with the probe sequence depending upon the stringency of the hybridization conditions. Probes may contain a label so that one can determine if the probe is bound to the target sequence. By assaying for the presence or absence of the probe, one can detect the presence or absence of the select sequence or subsequence. A probe can be bound, either covalently, through a linker or a chemical bond, or noncovalently, through ionic, van der Waals, electrostatic, or hydrogen bonds, to a label such that the presence of the probe may be detected by detecting the presence of the label bound to the probe. In other exemplary embodiments, probes are indirectly labeled e.g., with biotin to which a streptavidin complex may later bind.
The term “label” as used herein, refers to a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. Exemplary labels include 32P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins for which antisera or monoclonal antibodies are available. In one exemplary embodiment, labels can be isotopes, chromophores, lumiphores, chromogens, etc. Labels can also involve two or more compounds, only one of which need be attached to the probe. An example of a pair of compounds that are labels is biotin and streptavidin, where biotin is attached to the probe and later reacts with streptavidin which is added after the probe binds the target sequence.
The term “primer” as used herein, refers to short nucleic acids, typically a DNA oligonucleotide of at least about 15 nucleotides in length. In an exemplary embodiment, primers are annealed to a complementary target DNA or RNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA or RNA strand. Annealed primers are then extended along the target strand by a DNA polymerase enzyme or reverse transcriptase. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR) or other nucleic-acid amplification methods known in the art.
PCR primer pairs are typically derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5 ©1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.). One of ordinary skill in the art will appreciate that the specificity of a particular probe or primer increases with its length. Thus, for example, a primer comprising 20 consecutive nucleotides of a promoter complex sequence will anneal to a related target sequence with a higher specificity than a corresponding primer of only 15 nucleotides. Thus, in an exemplary embodiment, greater specificity of a nucleic acid primer or probe is attained with probes and primers selected to comprise 20, 25, 30, 35, 40, 50 or more consecutive nucleotides of a selected sequence.
Nucleic acid probes and primers are readily prepared based on the nucleic acid sequences disclosed herein. Methods for preparing and using probes and primers and for labeling and guidance in the choice of labels appropriate for various purposes are discussed, e.g., in Green and Sambrook, Molecular Cloning, A Laboratory Manual 4th ed. 2012, Cold Spring Harbor Laboratory; and Ausubel et al., eds., Current Protocols in Molecular Biology, 1994—current, John Wiley & Sons). The term “recombinant” when used with reference, e.g., to a cell, or nucleic acid, protein, or vector, indicates that the cell, organism, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found within the native (non-recombinant or wild-type) form of the cell or express native genes that are otherwise abnormally expressed, over expressed, under expressed or not expressed at all.
The following terms are used to describe the sequence relationships between two or more nucleic acids or polynucleotides: “reference sequence”, “comparison window”, “sequence identity”, “percentage of sequence identity”, and “substantial identity”. A reference sequence is a defined sequence used as a basis for a sequence comparison; a reference sequence may be a subset of a larger sequence, or gene sequence given in a sequence listing.
The terms “identical” or percent “identity”, in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (e.g., 85% identity, 90% identity, 99%, or 100% identity), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using a sequence comparison algorithm or by manual alignment and visual inspection.
The phrase “substantially identical”, in the context of two nucleic acids or polypeptides, refers to two or more sequences or subsequences that have at least about 85%, identity, at least about 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using a sequence comparison algorithm or by visual inspection. In an exemplary embodiment, the substantial identity exists over a region of the sequences that is at least about 50 residues in length. In another exemplary embodiment, the substantial identity exists over a region of the sequences that is at least about 100 residues in length. In still another exemplary embodiment, the substantial identity exists over a region of the sequences that is at least about 150 residues or more, in length. In one exemplary embodiment, the sequences are substantially identical over the entire length of nucleic acid or protein sequence.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from about 20 to about 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Ausubel et al., eds., Current Protocols in Molecular Biology, 1995 supplement).
An exemplary algorithm for sequence comparison is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments to show relationship and percent sequence identity. It also plots a tree or dendogram showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng & Doolittle, J. Mol. Evol. 35:351-360 (1987). The method used is similar to the method described by Higgins & Sharp, CABIOS 5:151-153 (1989). The program can align up to 300 sequences, each of a maximum length of 5,000 nucleotides or amino acids. The multiple alignment procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster is then aligned to the next most related sequence or cluster of aligned sequences. Two clusters of sequences are aligned by a simple extension of the pairwise alignment of two individual sequences. The final alignment is achieved by a series of progressive, pairwise alignments. The program is run by designating specific sequences and their amino acid or nucleotide coordinates for regions of sequence comparison and by designating the program parameters. Using PILEUP, a reference sequence is compared to other test sequences to determine the percent sequence identity relationship using the following parameters: default gap weight (3.00), default gap length weight (0.10), and weighted end gaps. PILEUP can be obtained from the GCG sequence analysis software package, e.g., version 7.0 (Devereaux et al., Nuc. Acids Res. 12:387-395 (1984)).
Another example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., 1990). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues; always<0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) or 10, M=5, N4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=4, and a comparison of both strands.
The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul, Proc. Natl. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.
An indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid, as described below. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions, as described below. Yet another indication that two nucleic acid sequences are substantially identical is that the same primers can be used to amplify the sequence.
The phrase “selectively hybridizes to” or “specifically hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA). In general, two nucleic acid sequences are said to be “substantially identical” when the two molecules or their complements selectively or specifically hybridize to each other under stringent conditions.
The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acid, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Hybridization with Nucleic Probes Parts I and II, Elsevier (1993). Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (Tin) for the specific sequence at a defined ionic strength pH. The Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For high stringency hybridization, a positive signal is at least two times background, preferably 10 times background hybridization. Exemplary high stringency or stringent hybridization conditions include: 50% formamide, SxSSC and 1% SDS incubated at 42° C. or SxSSC and 1% SDS incubated at 65 ° C., with a wash in 0.2×SSC and 0.1% SDS at 65° C. However, other high stringency hybridization conditions known in the art can be used.
Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides that they encode are substantially identical. This situation can occur, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary “moderately stringent hybridization conditions” include hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 1×SSC at 45° C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.
For nucleic acids, sizes are given in either kilobases (kb) or base pairs (bp). Estimates are typically derived from agarose or acrylamide gel electrophoresis, from sequenced nucleic acids, or from published DNA sequences. For proteins, sizes are given in kilodaltons (kDa) or amino acid residue numbers. Proteins sizes are estimated from gel electrophoresis, from sequenced proteins, from derived amino acid sequences, or from published protein sequences.
Oligonucleotides and polynucleotides that are not commercially available can be chemically synthesized e.g., according to the solid phase phosphoramidite triester method first described by Beaucage and Caruthers, Tetrahedron Letts. 22:1859-1862 (1981), or using an automated synthesizer, as described in Van Devanter et al., Nucleic Acids Res. 12:6159-6168 (1984). Other methods for synthesizing oligonucleotides and polynucleotides are known in the art. Purification of oligonucleotides is by either native acrylamide gel electrophoresis or by anion-exchange HPLC as described in Pearson & Reanier, J. Chrom. 255:137-149 (1983).
The sequence of the cloned genes and synthetic oligonucleotides can be verified after cloning using, e.g., the chain termination method for sequencing double-stranded templates of Wallace et al., Gene 16:21-26 (1981). Using of machines for sequencing DNA or RNA is known in the art field.
This invention utilizes routine techniques in the field of molecular biology. Basic texts disclosing the general methods of use in this invention include Green and Sambrook, 4th ed. 2012, Cold Spring Harbor Laboratory; Kriegler, Gene Transfer and Expression: A Laboratory Manual (1993); and Ausubel et al., eds., Current Protocols in Molecular Biology, 1994—current, John Wiley & Sons. Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology maybe found in e.g., Benjamin Lewin, Genes IX, published by Oxford University Press, 2007 (ISBN 0763740632); Krebs, et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).
For all examples described herein, unless otherwise stated, the crazy ants colonies are obtained from field sites located in Desoto (April, 2011), Hillsborough (April, 2011), Alachua (March through May, 2011), and Duval (March, 2011) counties in Florida and subsequently are maintained in the laboratory. Colonies are reared separately in nesting tubes as described by Oi and Williams, Environ. Entomol. 32:1171-1176 (2003). The colonies are fed frozen crickets, 10% sucrose solution, and water. Identifications of crazy ants are made based on characters listed in Trager (Sociobiol. 9:51-162 (1984)), LaPolla, et al. (Syst Entomol 35: 118-131 (2010)), and Gotzek, et al. (PloS ONE 7(9): e45314 10 p. (2012)). While there may possible be some uncertainty regarding species assignment of the crazy ants from Florida, Texas, Louisiana and Mississippi based on morphometric and DNA sequence data, all of these types of arts are considered crazy ants for the purpose of this invention. In addition, NfV has been confirmed present in N. fulva collected in Nassau County, Fla., and a different site in Alachua County, Fla., in 2013.
Having now generally described this invention, the same will be better understood by reference to certain specific examples and the accompanying drawings, which are included herein only to further illustrate the invention and are not intended to limit the scope of the invention as defined by the claims. The examples and drawings describe at least one, but not all embodiments, of the inventions claimed. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements.
EXAMPLE 1
cDNA Library Generation and Analysis
Total RNA is extracted from samples of the colonies of N. fulva using TRIzol® RNA isolation reagents (Life Technologies, Carlsbad, Calif.) according to the manufacturer's instructions. Samples are taken from nine colonies. A total of 609 ants of different life stages (workers, alates, queens, larvae, pupae, and eggs) are used to prepare the total RNA. RNA quality of each preparation is assessed by microfluidic analysis on an Agilent 2100 Bioanalyzer (Agilent, Cary, N.C.) using the RNA 6000 Nano kit (Agilent, Cary, N.C.) according to the manufacturer's directions. Microfluidic assays are completed immediately after RNA extraction using a 1 μl volume of purified sample. RNA samples of acceptable quality are pooled and are used as source material for mRNA purification. mRNA is isolated from the total RNA sample using the Oligotex mRNA Mini Kit (Qiagen, Valencia, Calif.) following the manufacturer's instructions. The isolated mRNA is then utilized to prepare a non-normalized fragment library suitable for 454 platform sequencing using the NEBNext mRNA Sample Pre Reagent Set 2 (New England BioLabs, Ipswich, Mass.) following the manufacturer's protocol. The library is used as a template for emulsion PCR using the GS Titanium LV emulsion PCR Kit (Lib-L; Roche, Basel, Switzerland) following the manufacturer's instructions. DNA beads generated from the emulsion PCR reactions are used for Titanium plate 454 sequencing, using the GS Titanium Sequencing Kit XLR70 (Roche, Basel, Switzerland). De novo assembly is performed for the generated sequencing data using the Newbler software (Roche).
The initial assembly of the sequences is performed with Newbler Assembler Version 2.3 (454 Life Science, Branford, Conn.), employing masking and trimming sequencing repeats, primers and/or adaptors used in cDNA library preparation. The hybridized sequences (contigs and leftover singletons) are further assembled with Paracel Transcript Assembler version 3.0.0 (PTA; Paracel Inc., Pasadena, Calif.).
In PTA, all sequences are masked for universal and species-specific vector sequences, adaptors, and PCR primers used in cDNA library creation. Escherichia coli contamination and mitochondrial and ribosomal RNA genes are identified and are removed from input sequences using default settings to ascertain the novelty of the sequences. The poly (A/T) tails and intrinsic repeats, such as simple sequence repeats and short interspersed elements (SINE), are annotated prior to clustering and assembly. Low base-call quality data are trimmed from the ends of individual sequences and sequences<75 by are excluded from consideration during initial pair-wise comparisons. After cleanup, sequences are passed to the PTA clustering module for pair-wise comparison and then to the CAP3-based PTA assembly module for assembly. The PTA assembly is performed based on the sequences of the contigs and the leftover singletons generated from the Newbler assembly.
The single production GS-FLX Titanium 454 platform sequencing run (two half plates) of the non-normalized N. fulva expression library generates 1,306,177 raw sequence reads comprising 450 Mbp. De novo assembly of the raw data with Newbler yields 22,044 contigs and 232,338 singletons. Subsequent assembly by PTA results in the generation of 59,017 non-redundant sequences, including 27,348 contigs (average size 794 bp) and 31,669 singlets (average size 295 bp). Among these sequences, 27.9% (16,458) are greater than 500 by and 72.1% (42,533) are greater than 300 bp. BLASTX analysis of these non-redundant nucleotide sequences identifies 25,898 (43.9%) nucleotide sequences with significant (e-value<1e4) similarity, and 33,119 (56.1%) nucleotide sequences have no significant similarity. A significant percentage (47%) of the gene sequences (12,174) identified is found to be unique to N. fulva. 
Large-scale homology database searches of the PTA sequence data set are conducted against the National Center for Biotechnology Information (NCBI) NR and NT databases using BLAST (blastx and blastn) with an in-house computational pipeline. To obtain a more accurate and complete description of potential gene function for each queried sequence, the top 100 BLAST hits are retrieved. Sequences with the best scoring BLAST hit (≦1e−5) and the corresponding gene ontology (GO) classification are annotated to the queried sequence (Koski and Golding, J. Molec. Evol. 52:540-542 (2001)). GO term assignments are binned according to the categories, biological processes, cellular components, and molecular functions. BLAST results and GO term assignments are completed in BlastQuest, an SQL database developed by the Interdisciplinary Center for Biotechnology Research, University of Florida, that facilitates similarity-based sequence annotation with gene ontology information (Farmerie, et al., Data Know Eng. 53:75-97 (2005)). In addition, the sequences are characterized with respect to functionally annotated genes by BLAST searching against NCBI specific reference sequences (RefSeq) for Homo sapiens (38,556 sequences), Drosophila (21,099 sequences) and Formicidae (74,540 sequences). Queries are considered to have a clear homolog of the searched organism when e-values are<1e−4, the length of the aligned segment is≧50 bp, and identity>85%, which essentially eliminates spurious hits while preventing elimination of medium-sized proteins.
Raw 454 reads and assembled contigs are deposited in the NCBI database. The N. fulva sequence data are publicly available and accessible through the NCBI website accession numbers Ant—454Assem_NCBI.sqn: JP773711 - JP820231.
EXAMPLE 2
Identification of Viral Sequences
Sequences identified as exhibiting significant viral homology/identity are selected and are further evaluated in an attempt to establish their origin, viral, host, or otherwise. Evaluations are also conducted to ascertain whether identified viral sequences are simply being ingested by the ants or are replicating (i.e., N. fulva is serving as host). BLAST analysis of the 59,017 non-redundant sequences yielded from the N. fulva library results in the identification of 51 sequences of putative viral origin. Among them, 31 sequences do not meet the threshold for significance (an expectation score>1e−4)and are not examined further to establish their source; viral, host, or otherwise. However, despite expectation scores greater than 1e−4, some of these sequences could represent a virus that infect N. fulva. 
Twenty sequences from the N. fulva expression library yield significant BLAST expectation scores of putative viral origin; nine sequences are similar to DNA virus sequences and eleven to RNA virus sequences. Of the eleven sequences related to genes of RNA viruses, six negative-sense and five positive-sense, single-stranded RNA virus genes are identified. Three sequences of ostensibly positive-sense, single-stranded RNA virus(es) are examined in more detail.
EXAMPLE 3
Confirmation of Viral Sequences
To confirm that the suspected RNA virus sequences are actually from RNA viruses, the forward and reverse oligonucleotide primers listed in Table 1 are designed based on EST Assem.3776.C1 (GenBank Accession No. JP780688.1; SEQ ID NO: 1), EST Assem.13287.C1 (GenBank Accession No. JP790645.1; SEQ ID NO: 2), and EST Assem.8702.C1 (GenBank Accession No. JP786492.1; SEQ ID NO: 3).









TABLE 1






Forward oligo-
Reverse oligo-



nucleotide primer 
nucleotide primer 



name, sequence
name, sequence


EST
(5′→3′), and
(5′→3′), and 


Designation
SEQ ID NO.
SEQ ID NO.







Assem.3776.C
p1167
p1168


1
CCCTACTGACTGACGAAC
TGTTGTTGAGCGTAATGA


SEQ ID NO: 1
AGATTGCTTC
GTCCGTCCT



SEQ ID NO: 4
SEQ ID NO: 5


 


Assem.13287.
p1169
p1170


C1
ACTTCACTTGTATATGGA
TTGCTTCGTGATATGTCA


SEQ ID NO: 2
GATCCCTCCATACAA
TTCCTGGATACAAT



SEQ ID NO: 6
SEQ ID NO: 7


 


Assem.8702.C
p1172
p1171


1
TGGTACTGGTATGTCGGA
TGAGGTCTTGACACTGGT


SEQ ID NO: 3
TGTGATGAGCT
AGTGTTGAAATGA



SEQ ID NO: 8
SEQ ID NO: 9









PCR is conducted with RNase-treated DNA extracted from the same N. fulva colonies used in expression library creation in Example 1. No amplicon is generated indicating that the sequences are not N. fulva genomic sequences. Next, mRNA is isolated from N. fulva colonies as per the protocol in Example 1 and the primers in Table 1 are used to generate amplicons using RT-PCR. Two-step RT-PCR is employed to amplify a portion of the genome strand. First, 1 μl (50 ng) of total RNA is mixed with 10 mM dNTPs and 1 μm of the appropriate tagged oligonucleotide primer, is heated to 65° C. for 5 minutes, and then is placed on ice for at least 1 minute. First strand buffer and Superscript reverse transcriptase (RT, Invitrogen, Carlsbad, Calif.) are then added, and the reaction mixture is incubated at 55° C. for 1 hour before inactivating the RT at 70° C. for 15 minutes. Unincorporated oligonucleotides are digested with 10 units of Exonuclease I (New England Biolabs, Ipswich, Mass.) at 37° C. for 1 hour. The reaction is terminated by heating to 80° C. for 20 minutes. Amplification is observed in approximately 50% to approximately 66% of the samples, thus it is assumed that the sequences are not host (or other) origin, because viral infections rarely exhibit an incidence of 100% among field-collected arthropods (Fuxa and Tanada, Epizootiology of insect diseases. New York: John Wiley and Sons. (1987)).
Next, tagged-RT-PCR is conducted with the above indicated primers to detect the replicating genomic strand (see Craggs, et al., J. Virol. Methods 94:111-120 (2001)). This method permits discrimination of each genome strand without carryover effects causing false positive detection of either strand. Tagged-RT-PCR employs the use of the appropriate oligonucleotide primer in Table 1 appended at the 5′ end with a TAG sequence (5′-GGCCGTCATGGTGGCGAATAA-3′; SEQ ID NO: 10) that is used in a cDNA-synthesis reaction (forward primer for positive-strand viruses and reverse primer for negative-strand viruses).
PCR is subsequently conducted in a 25 μl volume containing 2 mM MgCl2, 200 μM dNTP mix, 0.5 units of Platinum Taq DNA polymerase (Invitrogen, Carlsbad, Calif.), 0.2 μM of each oligonucleotide primer, and 5 μl of the cDNA preparation. PCR is conducted with the following temperature regime, 94° C. for 2 minutes followed by 35 cycles of 94° C. for 15 seconds, 56-60° C. for 15 seconds; 68° C. for 30 seconds and a final 68° C. step for 5 minutes in a thermal cycler. PCR products are separated on a 1% agarose gel and are visualized by SYBR-safe (Invitrogen, Carlsbad, Calif.) staining. The replicating strand for each of these ESTs are detected by tagged-PCR which indicates that N. fulva is a host for the virus. Next, the amplicon is cloned by ligating into the pCR4 expression vector and transforming the pCR4 expression vector into TOP10 competent cells (Invitrogen, Carlsbad, Calif.). Its sequence is verified by Sanger sequencing which is performed by the University of Florida, Interdisciplinary Center for Biotechnology Research (Gainesville, Fla.). Thus, EST Assem.3776.C1, EST Assem.13287.C1, and EST Assem.8702.C1 are considered to be from at least one virus infecting N. fulva. 
The sequences of Assem.13287.C1, Assem.8702.C1, and Assem.3776.C1 exhibit some homology to unclassified positive-strand RNA viruses. Specifically, Assem.13287.C1 exhibits some homology with the helicase region (ATPase chaperone functionality) of Kelp fly virus (Hartley, et al., J. Virol. 79:13385-13398 (2005)), and Assem.8702.C1 exhibits some homology with the 3C-like protease region of polyprotein 1 (5′-proximal ORF) of Solenopsis invicta virus 3 (SINV-3) (Valles and Hashimoto, Virology 388:354-361 (2009)). Assem3776.C1 also exhibits some homology with SINV-3 at the interface of the 3C-protease and RNA-dependent RNA polymerase. The replicative form of the genome (minus or negative strand) is detected in a small percentage of field-collected N. fulva providing strong evidence that these sequences correspond to positive-strand RNA viruses that infect N. fulva. All of these sequences exhibit identity to viruses that infect arthropods (Diptera and Hymenoptera). Thus, detection of Assem.13287.C1, Assem.8702.C1, and Assem.3776.C1 by tagged-RT-PCR among a small percentage of field-collected N. fulva colonies suggests that these sequences are of viral origin and appear to replicate in N. fulva. Sanger sequencing of these amplicons verifies their identity.
The primers listed in Table 1 (SEQ ID NOs: 4, 5, 6, 7, 8, and 9) can be used to identify NfV. The reverse primers (SEQ ID NOs: 5, 7, and 9) can hybridize to the RNA genome of NfV and to a cDNA of the viral genome. The forward primers (SEQ ID NOs: 4, 6, and 8) hybridize to a negative RNA strand of the viral genome and to a cDNA of the viral genome. NfV, as a positive-strand RNA virus, contains only the positive strand, single-strand RNA in its capsid. But during active replication in infected cells, the infected cells contain copies of both the positive-strand RNA and the negative-strand RNA which serves as template to make additional copies of the positive-strand RNA.
EXAMPLE 4
Characteristics of Virus
The virus of this invention, referred to as Nylanderia fulva virus or NfV represents the first virus to be discovered from an ant in the Formicine. The virus of this invention possesses features consistent with placement within the order Picornavirales: 1. non-enveloped particles with a diameter around 30 nm, 2. a positive-sense, single-stranded RNA genome, 3. no production of subgenomic RNA, and 4. a polyprotein containing helicase, protease, and RNA-dependent RNA polymerase (RdRp) domains (Le Gall, et al., Archives of Virology 153, 715-27 (2008)).
A series of 5′ RACE reactions are conducted to obtain the upstream sequences of the genome of the virus(es) of this invention using the 5′ RACE system (Invitrogen, Carlsbad, Calif.) and primer walking. For each reaction, cDNA is synthesized for 50 minutes at 48° C. with 2.5 μg of total RNA extracted with TRIzol® RNA isolation reagents (Life Technologies, Carlsbad, Calif.) according to manufacturer's instructions from Nylanderia fulva virus or Nylanderia fulva virus-infected ants with gene-specific oligonucleotide primer, the RNA template is degraded with RNase H, and the cDNA purified. The 3′ end of the cDNA is polycytidylated with terminal deoxynucleotidyl transferase and dCTP. The tailed cDNA is then amplified with a nested GSP (3′ end) and an abridged anchor primer (AAP). Gel-purified amplicons are ligated into the pCR4-TOPO vector, transformed into TOP10 competent cells (Invitrogen, Carlsbad, Calif.) and are sequenced by the Interdisciplinary Center for Biotechnology Research (University of Florida).
To obtain sequences downstream of the amplicon, 3′ RACE reactions are conducted with the GeneRacer kit (Invitrogen, Carlsbad, Calif.) according to manufacturer's instructions. cDNA is synthesized from total RNA (1 μg) using the GeneRacer appended Oligo dT primer. The cDNA is amplified by PCR with a GSP and GeneRacer 3′ primer. Amplicons are cloned and sequenced as described for 5′ RACE. Table 2 contains the sequences of the GSP primers, as well as the sequences of other primers where were purchased from Invitrogen (AUAP, AAP, 3′ primer, and oligo dT primer) (Carlsbad, Calif.).
The GSP primers listed in Table 2 (SEQ ID NOs: 11-88) can be used to identify NfV. The reverse primers (SEQ ID NOs: 11-16, 18-20, 22, 24, 25, 27-31, 33, 35, 40, 42-44, 46, 49-54, 56-59, 62, 64-68, 72, and 75-85) can hybridize to the RNA genome of NfV and to a cDNA of the viral genome. The forward primers (SEQ ID NOs: 17, 21, 23, 26, 32, 34, 36-39, 41, 45, 47, 48, 55, 60, 61, 63, 69-71, 73, 74, 86, 87, and 88) hybridize to a negative RNA strand of the viral genome and to a cDNA of the viral genome. NfV, as a positive strand, single-strand RNA virus, contains only the positive strand RNA in its capsid. But during active replication in infected cells, the infected cells contain copies of both the positive-strand RNA and the negative-strand RNA which serves as template to make additional copies of the positive-strand RNA.








TABLE 2





Primer name/



Orientation
Sequence







p1230/R
GAAGCAATCTGTTCGTCAGTCAGTAGGGT



(SEQ ID NO: 11)


 


p1231/R
TGTCATTTTCCATAGGTAGTTTCGTAGGCAGT



(SEQ ID NO: 12)


 


p1232/R
TCCGTCACTATCCTTCAACAAATCAAACCA



(SEQ ID NO: 13)


 


p1236/R
AATTCTTGTGTAGCCTTGAGTTGTTGAAATTGA



(SEQ ID NO: 14)


 


p1237/R
TTCTCAAACAAATTACCTGAGACGTTCTGAGT



(SEQ ID NO: 15)


 


p1238/R
ACCTTTTCCTTGACAGCTACCGCACGT



(SEQ ID NO: 16)


 


P1267/F
AGCATGGTATTGAATTTATAGCTCATGAAGAAT



(SEQ ID NO: 17)


 


P1268/R
ATTCTTCATGAGCTATAAATTCAATACCATGCT



(SEQ ID NO: 18)


 


P1269/R
AATCAGGAAATTGGATTACTTGATCTTTTGGAATGT



(SEQ ID NO: 19)


 


p1270/R
GTATTCAAATTCATTAAGTTTCCAAAGGTAATTTCAT



GT (SEQ ID NO: 20)


 


p1271/F
CAATTCTATCTTATTTCCACTTCACTAAGAGC



(SEQ ID NO: 21)


 


p1272/R
GCTCTTAGTGAAGTGGAAATAAGATAGAATTG



(SEQ ID NO: 22)


 


p1273/F
TCCTCAATGGGAGAAGTGTTGTGCTT



(SEQ ID NO: 23)


 


p1278/R
TCGCACCATTCATCTTTATATATGATAACGC



(SEQ ID NO: 24)


 


p1279/R
ATGCCTTCTGGCTCATTTATAACTGCGCCA



(SEQ ID NO: 25)


 


p1280/F
AGCATTGAGATTCCCGATTCAGCCGACTT



(SEQ ID NO: 26)


 


p1281/R
AAGTCGGCTGAATCGGGAATCTCAATGCT



(SEQ ID NO: 27)


 


p1282/R
AATCGAGATTTATAAGTTCCTCTTTCCTCCTAACA



(SEQ ID NO: 28)


 


p1283/R
AAGAGCCAATATAGCAAATTTGCCAAGATGAGGA



(SEQ ID NO: 29)


 


p1290/R
TCTTAGTGAAGTGGAAATAAGATAGAATTGTTTCCT



(SEQ ID NO: 30)


 


p1291/R
ACGTTTATAATCTATGGCAAATACGTGATCGAAT



(SEQ ID NO: 31)


 


p1292/F
ACTGCCTACGAAACTACCTATGGAAAATGACA



(SEQ ID NO: 32)


 


p1303/R
GTCTTGTCAAACGTTTATAATCTATGGCAAATACGTGA



(SEQ ID NO: 33)


 


p1304/F
TCACGTATTTGCCATAGATTATAAACGTTTGACAAGAC



(SEQ ID NO: 34)


 


p1305/R
TCAGCTCCACAAACATGTCATGAAAATTCGCATAGG



(SEQ ID NO: 35)


 


p1306/F
CCTATGCGAATTTTCATGACATGTTTGTGGAGCTGA



(SEQ ID NO: 36)


 


p1307/F
TATGCGTGTTGAGACTTGCCTGCTCTGGCA



(SEQ ID NO: 37)


 


p1308/F
ATGAATTTGAATACAACTAATCAAACCTTTTTCGACA



(SEQ ID NO: 38)


 


p1309/F
ACAGGCTATCATGGGCCCTGGTACA



(SEQ ID NO: 39)


 


p1318/R
AGCCACTTCATGTATTGTTTATAGATCATGTCCTT



(SEQ ID NO: 40)


 


p1319/F
AAGGACATGATCTATAAACAATACATGAAGTGGCT



(SEQ ID NO: 41)


 


p1320/R
GGTTCATATACTACCAAATAGTCCTTCCGACTATC



(SEQ ID NO: 42)


 


p1321/R
GTTATAAACAGTTTCCATGGTGCATCACACTTATC



(SEQ ID NO: 43)


 


p1322/R
ACGGGACTTGACAAATATTCCATAATTAACTGCCT



(SEQ ID NO: 44)


 


p1323/F
AGGCAGTTAATTATGGAATATTTGTCAAGTCCCGT



(SEQ ID NO: 45)


 


p1324/R
TCCTGAGAAACTTCATCAAAGAAGTTCAGGTCTGGT



(SEQ ID NO: 46)


 


p1325/F
ACCAGACCTGAACTTCTTTGATGAAGTTTCTCAGGA



(SEQ ID NO: 47)


 


p1330/F
TGTTAGGTCGCTCTCTTCTTTGATAGATGCATCTT



(SEQ ID NO: 48)


 


p1331/R
AAGATGCATCTATCAAAGAAGAGAGCGACCTAACA



(SEQ ID NO: 49)


 


p1332/R
AGATTTATGCTGCATGCAGGCAATTTGGGT



(SEQ ID NO: 50)


 


p1333/R
TCCAGTTCCAGTGAACAGAACTGCTACAGGTTCCT



(SEQ ID NO: 51)


 


p1334/R
TTGTAAGCCAAGTTCATCAACGCCTGAGTCT



(SEQ ID NO: 52)


 


p1335/R
AAGAAGGTTTGGTTGGTTGTATTCAGGTTCAT



(SEQ ID NO: 53)


 


p1336/R
TACCCTGCTGCTAGTTGTGTACCAGGGCCCAT



(SEQ ID NO: 54)


 


p1337/F
AAGGGTAACGTTCCCAACAAGGGTGAGCAAT



(SEQ ID NO: 55)


 


p1338/R
ATTGCTCACCCTTGTTGGGAACGTTACCCTT



(SEQ ID NO: 56)


 


p1339/R
CAATCTGTCGTAGTGGGATCAATGTTCGTACCGT



(SEQ ID NO: 57)


 


p1340/R
ATTGAATCACTCTGGTTGACTCCTTCAACTGGCT



(SEQ ID NO: 58)


 


p1341/R
AAGAGCACCAAGCACAACACTTCTCCCATTGAGGA



(SEQ ID NO: 59)


 


p1342/F
TCCTCAATGGGAGAAGTGTTGTGCTTGGTGCTCTT



(SEQ ID NO: 60)


 


p1343/F
AACTTAAACCTTTCGACACTTGGGAAGAAGTA



(SEQ ID NO: 61)


 


p1344/R
AGCGAAGGAGTTGGTGAACAATGGCGA



(SEQ ID NO: 62)


 


p1353/F
AGAATGTTCTCGACCCAGTTTACGGTTG



(SEQ ID NO: 63)


 


p1354/R
CAACCGTAAACTGGGTCGAGAACATTCT



(SEQ ID NO: 64)


 


p1355/R
ACTCGGACACTCCCTGATCTGAATTTCTGGA



(SEQ ID NO: 65)


 


p1356/R
ACTTTCTCGACCATCTCTACATTAGTACGCA



(SEQ ID NO: 66)


 


p1364/R
AGTGTAGGCCATCTATTCTCTTTTGTCAGT



(SEQ ID NO: 67)


 


p1365/R
TAGGGACATAGTCAATTTCCATCGCAAGG



(SEQ ID NO: 68)


 


p1366/F
ACTAAGAGCCTTGAGCCACAGCACCTATCTTCATT



(SEQ ID NO: 69)


 


p1367/F
TCTTAAGAAGGAAACAATTCTATCTTACTTCCACT



(SEQ ID NO: 70)


 


p1368/F
ACTACGACAGATTGGGCCGAAGCAGCAAAT



(SEQ ID NO: 71)


 


p1369/R
TGCTGCTCCTTTACACATATCAAAGAAGGTT



(SEQ ID NO: 72)


 


p1370/F
TCAACAGAACCTTTTCTCATGTACCAAAATCA



(SEQ ID NO: 73)


 


p1383/F
ATGTTCTCGACCCAGTTTACGGTTGGCGGT



(SEQ ID NO: 74)


 


p1384/R
TTGTGGTTCAACCACTTTCTCGACCATCTCTACA



(SEQ ID NO: 75)


 


p1385/R
TGGAATAGCATTGACACAAATGATATAATCGCAGA



(SEQ ID NO: 76)


 


p1386/R
TCATCAACCTTTTCATCAGTCAACAATTCGGA



(SEQ ID NO: 77)


 


p1387/R
ATCTACTACAAGCTGTGCCTCATTTACTGAAGGA



(SEQ ID NO: 78)


 


p1388/R
AAGAAGGGACGGAGGGTCGCCGTTGAA



(SEQ ID NO: 79)


 


p1389/R
TGTAGGCCATCTATTCTCTTTTGTCAGTTTAGTA



(SEQ ID NO: 80)


 


p1390/R
ACTCAAGCTTCAAATTCTGGCACCAGGTCTGGA



(SEQ ID NO: 81)


 


p1391/R
ATTACACGTGTATGTGTATGTGTGTGTGTAT



(SEQ ID NO: 82)


 


p1392/R
ACATTGCAAAATAATGTTTATTTATCAAGGATAATAT



(SEQ ID NO: 83)


 


p1393/R
ACGACGTTATTACGTTCTTATCGGCATATTTACT



(SEQ ID NO: 84)


 


p1394/R
TATAGACATCGTATTTCGTTTGCTTACTATCA



(SEQ ID NO: 85)


 


p1395/F
TACTAAACTGACAAAAGAGAATAGATGGCCTACA



(SEQ ID NO: 86)


 


p1396/F
TGAAATTAAAGACTTTCCTCGCCTTGCGATGGA



(SEQ ID NO: 87)


 


p1397/F
TGGGAGGACTTGACTATTCCTATACGTGACGGA



(SEQ ID NO: 88)


 


AUAP
GGCCACGCGTCGACTAGTAC (SEQ ID NO: 89)


 


AAP
GGCCASGCGTCGACTAGTACGGGIIGGGIIGGGIIG



(SEQ ID NO: 90)


 


3′ Primer
GCTGTCAACGATACGCTACGTAACG



(SEQ ID NO: 91)


 


Oligo dT
GCTGTCAACGATACGCTACGTAACGGCATGACAGT


primer
G(T)24 (SEQ ID NO: 92)





R = reverse


F = forward






The cloning and sequencing described above, using the primers in Table 2, resulted in a DNA sequence of approximately 80% of the NfV's genome (SEQ ID NO: 93). Of course, the viral sequence, being RNA, will contain uracil bases instead of the indicated thymidine bases. Analysis of this genomic sequence reveals an amino acid sequence of a putative polypeptide of 2634 amino acids with a molecular weight of 300863 daltons (SEQ ID NO: 94). Within the polypeptide exist the following domains: RNA helicase domain from amino acid 501-751 (SEQ ID NO: 95); NTP binding protein from amino acid 2000-2200 (SEQ ID NO: 96); and RNA-dependent RNA polymerase (RdRp) from amino acid 2251-2550 (SEQ ID NO: 97).
EXAMPLE 5
Viral Transmission
To evaluate the transmission of the virus of this invention, uninfected crazy ant nests are identified by RT-PCR as per Example 1, excavated from the field, and parsed into equivalent colonies. Colonies are infected by a modification of the method described by Ackey and Beck (J. Insect Physiol. 18:1901-1914 (1972)). Briefly, approximately 1 to approximately 5 grams of crazy ants from a colony infected with the virus of this invention are homogenized in a Waring blender with either 30 ml of 10% sucrose prepared with deionized water or 30 ml of refined soybean oil for 1 minute at high speed. The homogenates are filtered through three layers of cheesecloth and then filtered by vacuum in a Buchner funnel through a number 1 Whatman paper. The 10% sucrose-virus bait is used in this form. The oil-virus bait preparation is mixed with pregel defatted corn grit (Illinois Cereal Mills, Paris, Ill.) at 30% oil-virus by weight to adsorb the oil onto the corn grit. In addition, approximately 1 to approximately 5 grams of infected crazy ants are mixed with 21 g of freeze-killed adult house crickets. The mixture is pulverized with a mortar and pestle to create a crude paste. These three types of infected food sources are placed in a position that the uninfected crazy ant colony will find it and partake thereof. The control colony is provided the same three food sources, but without the infected crazy ants added to it. Crazy ants from the treated and untreated colonies are sampled at about 3, 11 and 18 days after introduction of the food source (infected or non-infected) and analyzed for the presence of the virus of this invention by RT-PCR using the primers in Table 1 or Table 2 and the protocol described above.
EXAMPLE 6
Biopesticide Efficacy
To evaluate the efficacy of using the virus of this invention as a biopesticide, non-infected colonies are obtained and placed in the laboratory. Homogenates of crazy ant colonies infected with the virus of this invention are used as sources of virus for preparation of the bait formulations. Aliquots are blended in a Waring blender with either 30 ml of 10% sucrose prepared with deionized water or 30 ml of refined soybean oil for 1 minute at high speed. The homogenates are filtered through three layers of cheesecloth and then filtered by vacuum in a Buchner funnel through a number 1 Whatman paper. The 10% sucrose-virus bait is used in this form. The oil-virus bait preparation is mixed with pregel defatted corn grit (Illinois Cereal Mills, Paris, Ill.) at 30% oil-virus by weight to adsorb the oil onto the corn grit. The third aliquot of infected crazy ants is mixed with 21 g of freeze-killed adult house crickets. The mixture is pulverized with a mortar and pestle to create a crude paste. Virus content of each bait formulation is determined by quantitative PCR using the primers in Table 1 or Table 2.
Test colonies (n=10/treatment) are transferred into clean trays without food two days before test treatments and then pulse exposed to virus bait formulations for 24 hours. Control colonies receive access to crickets, sugar water, and oil on corn grits, all without the virus homogenate. The baits are subsequently placed on the floor of the ant rearing tray. Treatment and control colonies are randomly distributed in the holding trays until virus replication was confirmed in the treatments, after which, colonies positive for virus replication are removed into separate holding trays in an adjacent rack to limit chances for contamination of uninfected colonies.
Bait-treated and control colonies are periodically evaluated to ascertain their relative health by monitoring the ratio of brood to workers. Colonies are assigned a score of 4 if they are rapidly growing with brood mass greater than worker mass. A score of 3 indicates a healthy growing colony with brood mass approximately 70% of worker mass. A score of 2 indicates a colony in poor health with brood mass of approximately 50% of worker mass. A score of 1 indicates a sick colony with brood mass approximately 25% of worker mass. A score of 0 is reserved for colonies without any brood. During evaluations each nest tube is manually checked and intermediate scores are assigned as appropriate. Control colonies are always checked first and gloves were changed between each colony to avoid mechanically transmitting the virus. Each colony is evaluated to determine the quantity of workers (g) and brood (g), worker and larval mortality (number of dead workers counted in the housing tray), the queen weight, queen ovary rating, the number of eggs laid by the queen in a 24 hour period.
Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation. All documents cited herein are incorporated by reference.

## Claims

1. A method of reducing the population of crazy ants in a colony or eradicating a colony of crazy ants comprising applying, in an amount effective to kill crazy ants, a biopesticide to areas around a crazy ant colony or to areas where the crazy ants feed, wherein said biopesticide comprises a virus that infects and kills crazy ants and a carrier, wherein said virus comprises a polynucleotide having a sequence which encodes an RNA-dependent RNA polymerase having the amino acid sequence of SEQ ID NO: 97.

2. The method of claim 1 wherein said carrier comprises a food source for crazy ants.

3. The method of claim 2 wherein said food source is selected from the group consisting of corn grits, extruded corn pellets, boiled egg yolks, dead insects, and a combination thereof.

4. The method of claim 1 wherein said carrier is selected from the group consisting of water, sugar water, saline solution, and oil.

5. A method of reducing the population of crazy ants in a colony or eradicating a colony of crazy ants comprising applying, in an amount effective to kill crazy ants, a biopesticide to areas around a crazy ant colony or to areas where the crazy ants feed, wherein said biopesticide comprises a virus that infects and kills crazy ants and a carrier, wherein said virus comprises a polynucleotide having a sequence which encodes an RNA-dependent RNA polymerase having an amino acid sequence selected from the group consisting of an amino acid sequence that is at least 95% identical to amino acids 1-300 of SEQ ID NO: 97, an amino acid sequence that is at least 90% identical to amino acids 1-300 of SEQ ID NO: 97, and an amino acid sequence that is at least 85% identical to amino acids 1-300 of SEQ ID NO: 97, and wherein said encoded RNA-dependent RNA polymerase has RNA-dependent RNA polymerase activity.

6. The method of claim 5 wherein said carrier comprises a food source for crazy ants.

7. The method of claim 6 wherein said food source is selected from the group consisting of corn grits, extruded corn pellets, boiled egg yolks, dead insects, and a combination thereof.

8. The method of claim 5 wherein said carrier is selected from the group consisting of water, sugar water, saline solution, and oil.