mteb/CovidQA huggingface dataset:
during the early infectious period, of asymptomatic cases, of moderately sick cases, of (untreated) very sick cases.

To assess the effect of day care centre and school closing on the transmission of an infectious disease, we have to first make an assumption on what fraction r sch of the contacts among healthy children who are in the same age class occurs in day care centres and schools. The contact rates between very sick or hospitalized children (who do not attend day care centre or school) and other children need, therefore, be reduced to (contact rate between healthy and very sick children in the same age class, i.e. a i = a s ).

As very sick children have to be taken care of by adults at home or in hospital, their contact rate to adults increases by a factor F HC (contact rate between very sick children of age a i and adults of age a s ).
Contacts between very sick children and other children in a higher or lower age class remain unchanged: (contact rate between healthy children of age a s and very sick children of a different age a i ).

Closing day care centres and schools at time t will not necessarily prevent all the contacts that would have happened with other children. During the closing of schools and day care centres, the contact rates between susceptible children of age a s and infected children of age a i who are in their late incubation period ( ), who are asymptomatic ( ), or who are moderately sick ( ) are reduced by the factor r sch if the children are in the same age class:

where 1 sch (t) is a function which indicates when schools and day care centres are opened or closed: 

,..., While day care centres and schools are closed, children (age a i ) need adult supervision at home. Their contact with susceptible adults (age a s ) increases by the "child care factor" F CC :
Child care at home also increases the exposure of healthy children (age a s ) to contagious adults (age a i ):

Cancelling mass gathering events effects only the contacts of adults who are healthy enough to attend such events. Assuming that such an intervention at time t reduces contacts by a fraction r mass , we get for all contacts between susceptible adults of age a s and infectious adults of age a i the following contact rates:

where 1 mass (t) is a function which indicates when mass gathering events are possible or when they are closed:

As contacts with adults who are too sick to attend such mass gathering events cannot be prevented by this measure it is .
During some time in the epidemic, the general population may effectively reduce contacts which can be a result of wearing facial masks, increasing "social distance", adopting improved measures of "respiratory hygiene" or simply of a general change in behaviour. This will be implemented in the program by reducing the contacts of susceptible individuals at that time t by factor r gen (t 

while mass gathering events are forbidden while m mass gathering events are allowed. while the population reduces their contacts while the population behaves as usual.

The contact rates of cases in the late incubation period and that of asymptomatic cases remain unchanged:

for infected individuals in the late incubation period, for asymptomatic cases.

To allow for a contagiousness which changes over the course of disease, we multiply each contact rate with a weighting factor whereby k is the stage of contagiousness. This leads to the following contact rates:
for asymptomatic cases in For x = 1, contagiousness is equally high in all stages; for x = 0, only the first stage is contagious; for 0 <x < 1, the contagiousness decreases in a geometric procession. We make the simplifying assumption that contagiousness does not change during the late incubation period for cases in stage k = n -l,..,n of the incubation period.

At time t = 0 and in the absence of interventions, the next generation matrix has the following elements where is the fraction of untreated extremely severe cases who die from the disease (see below for details). The dominant eigenvalue of this matrix is called the basic reproduction number R 0 . If κ (which determines the value of the contact rates ) is given, the eigenvectors of this matrix can numerically be calculated. The user-specified value of R 0 is now used to determine numerically the scaling factor κ. Let be the eigenvector which has the largest eigenvalue R 0 . 

) ) −
Using the user-specified numbers of people N a in the age classes and the fractions F a of people under high risk within each age class (Table 2) , we obtain the initial population sizes according to age and risk class: Using these initial values, the set of differential equations is solved numerically with a Runge-Kutta method with step-size control. 

if and in treatment window otherwise 0 ⎩ ⎩
Genome Sequences of Porcine Epidemic Diarrhea Virus: In Vivo and In Vitro Phenotypes

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4056290/

SHA: f6d6d7efc1686a7d219ecfc55f9a48ce72d4fb00

Authors: Lawrence, Paulraj K.; Bumgardner, Eric; Bey, Russell F.; Stine, Douglas; Bumgarner, Roger E.
Date: 2014-06-12
DOI: 10.1128/genomea.00503-14
License: cc-by
Abstract: Since the outbreak of porcine epidemic diarrhea virus (PEDV) in May 2013, U.S. swine producers have lost almost five million baby pigs. In an attempt to understand the evolution of PEDV in the United States and possibly develop a control strategy, we compared the genome sequences of a PEDV strain isolated from an infected piglet against its in vitro adapted version. The original PEDV strain was grown in Vero cells and passed 10 times serially in a MARC145 cell line. The sequence analysis of the native PEDV strain and in vitro passaged virus shows that the cell culture adaptation specifically modifies PEDV spike protein whereas the open reading frame 1a/b (ORF1a/b)-encoded polyprotein, the nucleoprotein, NS3B (ORF3), and membrane and envelope proteins remain unchanged.
Text: highly contagious swine disease. While older pigs have a chance of survival, 80 to 100 percent of PEDV-infected piglets die within 24 h of being infected. PEDV spreads primarily through fecal-oral contact (1, 2) . Once the virus is internalized, it destroys the lining of piglets' intestines, making them incapable of digesting and deriving nutrition from milk and feed (1) . The virus causes diarrhea, vomiting, and death from dehydration and starvation (2) .

PEDV is a member of the Coronavirinae subfamily and belongs to the Alphacoronavirus genus. Its genomic size ranges from approximately 26 to 32 kb, which is relatively large for an RNA virus. Although vaccines for PEDV exist in China, Japan, and South Korea, there is no approved vaccine in the United States or Europe (3) . Furthermore, PEDV is still evolving within the U.S. swine population.
This report briefly describes the comparison of genome sequences of a PEDV strain isolated from small intestine samples of an infected piglet and its in vitro adapted version. The original PEDV strain was dubbed NPL-PEDV/2013, grown in Vero cells, and passed 10 times in a MARC145 cell line. The serial in vitro passage strain was named NPL-PEDV/2013/P10. The total viral RNA was extracted by TRIzol LS reagent and sequenced by Sanger dideoxy sequencing using a primer walking technique. The raw sequences were imported into the Geneious assembler (Biomatters, CA), assembled, annotated, and compared against each other using USA/Colorado/2013 (GenBank accession no. KF272920) as a reference sequence.
The whole-genome sequences of NPL-PEDV/2013 and NPL-PEDV/2013/P10 contain 28,038 and 28,025 nucleotides (nt), respectively, including the 5= and 3= untranslated regions (UTR). The NPL-PEDV/2013 genome shares 99% identity with all the U.S. isolates sequenced to date and many Chinese isolates as well. The top three BLAST hits were against U.S. isolates, USA/Colora-do/2013 (GenBank accession no. KF272920), IA1 (GenBank accession no. KF468753.1), and an isolate from Iowa, 13-019349 (GenBank accession no. KF267450.1). The NPL-PEDV/2013 isolate also shares 99% identity with the Chinese outbreak isolate AH2012 (GenBank accession no. KC210145).
When the NPL-PEDV/2013/P10 strain was compared against NPL-PEDV/2013 , the open reading frame 1a/b (ORF1a/b) polyprotein, the nucleoprotein, NS3B, and membrane and envelope proteins were found to be 100% identical at the amino acid level. In contrast, the spike gene contains six nonsynonymous single nucleotide polymorphisms, resulting in amino acid (aa) substitutions in the following positions: 375 (F¡L), 486 (T¡P), 856 (D¡E), 1081 (A¡V), 1099 (A¡S), and 1253 (Y¡D). The S1 domain of spike protein contains 2 aa substitutions, whereas the S2 domain contains 4 aa substitutions. PEDV has been shown to use porcine aminopeptidase N (pAPN) as the major receptor for cell entry (4, 5) . However, Vero and MARC145 cells lack pAPN, clearly indicating that other receptors or receptor-independent pathways may be used for entry (6) . The spike protein in its trimeric conformation interacts with the cell receptor and contains numerous neutralizing antibody binding epitopes (7) . Analysis of the spike
by PeptideCutter (http://web.expasy.org/ peptide_cutter/) shows that the native spike protein of NPL-PEDV/2013 has 63 trypsin and 2 chymotrypsin cleavage sites at 100% efficiency whereas NPL-PEDV/2013/P10 has lost one trypsin cleavage site but the number of chymotrypsin sites remain unchanged. This indicates that cell culture adaptation specifically modifies the PEDV spike protein; however, the immunological implications are unknown.
Nucleotide sequence accession numbers. The whole-genome sequences of the NPL-PEDV/2013 and NPL-PEDV/2013/P10 strains have been deposited at DDBJ/EMBL/GenBank under accession no. KJ778615 and KJ778616.
Serological Assays Based on Recombinant Viral Proteins for the Diagnosis of Arenavirus Hemorrhagic Fevers

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497043/

SHA: f1d308db379b3c293bcfc8fe251c043fe8842358

Authors: Fukushi, Shuetsu; Tani, Hideki; Yoshikawa, Tomoki; Saijo, Masayuki; Morikawa, Shigeru
Date: 2012-10-12
DOI: 10.3390/v4102097
License: cc-by
Abstract: The family Arenaviridae, genus Arenavirus, consists of two phylogenetically independent groups: Old World (OW) and New World (NW) complexes. The Lassa and Lujo viruses in the OW complex and the Guanarito, Junin, Machupo, Sabia, and Chapare viruses in the NW complex cause viral hemorrhagic fever (VHF) in humans, leading to serious public health concerns. These viruses are also considered potential bioterrorism agents. Therefore, it is of great importance to detect these pathogens rapidly and specifically in order to minimize the risk and scale of arenavirus outbreaks. However, these arenaviruses are classified as BSL-4 pathogens, thus making it difficult to develop diagnostic techniques for these virus infections in institutes without BSL-4 facilities. To overcome these difficulties, antibody detection systems in the form of an enzyme-linked immunosorbent assay (ELISA) and an indirect immunofluorescence assay were developed using recombinant nucleoproteins (rNPs) derived from
these viruses. Furthermore, several antigen-detection assays were developed. For example, novel monoclonal antibodies (mAbs) to the rNPs of Lassa and Junin viruses were generated. Sandwich antigen-capture (Ag-capture) ELISAs using these mAbs as capture antibodies were developed and confirmed to be sensitive and specific for detecting the respective arenavirus NPs. These rNP-based assays were proposed to be useful not only for an etiological diagnosis of VHFs, but also for seroepidemiological studies on VHFs. We recently developed arenavirus neutralization assays using vesicular stomatitis virus (VSV)-based pseudotypes bearing arenavirus recombinant glycoproteins. The goal of this article is to review the recent advances in developing laboratory diagnostic assays based on recombinant viral proteins for the diagnosis of VHFs and epidemiological studies on the VHFs caused by arenaviruses.
Text: The virus family Arenaviridae consists of only one genus, but most viruses within this genus can be divided into two different groups: the Old World arenaviruses and the New World arenaviruses (also known as the Tacaribe complex) [1, 2] . The differences between the two groups have been established through the use of serological assays. Most of the arenaviruses cause persistent infection in rodents without any symptoms, and humans acquire a variety of diseases when zoonotically infected. Lymphocytic choriomeningitis virus (LCMV) is the only arenavirus to exhibit a worldwide distribution, and causes illnesses such as meningitis [3, 4] . Congenital LCMV infections have also been reported [4, 5] . Most importantly, viral hemorrhagic fever (VHF) can be caused by several arenaviruses. Lassa fever, caused by the Lassa virus (LASV), an Old World arenavirus, is one of the most devastating VHFs in humans [6] . Hemorrhaging and organ failure occur in a subset of patients infected with
this virus, and it is associated with high mortality. Many cases of Lassa fever occur in Western Africa in countries such as Guinea, Sierra Leone, and Nigeria [7] [8] [9] [10] [11] [12] [13] . Tacaribe complex lineage B of the New World arenaviruses consists of the Junin virus (JUNV), Guanarito virus (GUNV), Sabia virus (SABV) and Machupo virus (MACV), the etiological agents of Argentine, Venezuelan, Brazilian, and Bolivian hemorrhagic fevers, respectively [14, 15] . Although genetically distinct from one another, they appear to produce similar symptoms, accompanied by hemorrhaging in humans [14, 15] . These pathogenic New World arenavirus species are closely associated with a specific rodent species [6] .
Humans are usually infected with pathogenic arenaviruses through direct contact with tissue or blood, or after inhaling aerosolized particles from urine, feces, and saliva of infected rodents. After an incubation period of 1-3 weeks, infected individuals abruptly develop fever, retrosternal pain, sore throat, back pain, cough, abdominal pain, vomiting, diarrhea, conjunctivitis, facial swelling, proteinuria, and mucosal bleeding. Neurological problems have also been described, including hearing loss, tremors, and encephalitis. Because the symptoms of pathogenic arenavirus-related illness are varied and nonspecific, the clinical diagnosis is often difficult [14, 16] . Human-to-human transmission may occur via mucosal or cutaneous contact, or through nosocomial contamination [14, 16] . These viruses are also considered to be potential bioterrorism agents [2] .
A number of arenavirus species have been recently discovered as a result of both rodent surveys and disease outbreaks [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] . A novel pathogenic New World arenavirus, Chapare virus (CHPV), has been isolated from a fatal case of VHF in Bolivia [20] . In addition, five cases of VHF have been reported in South Africa, and a novel arenavirus, named Lujo virus, was isolated from a patient [17] . The Lujo virus is most distantly related to the other Old World arenaviruses [17] . To date, there is no information concerning the vertebrate host for the Chapare and Lujo viruses.
There is some evidence of endemicity of the Lassa virus in neighboring countries [27, 28] . However, as the magnitude of international trade and travel is continuously increasing, and the perturbation of the environment (due either to human activity or natural ecological changes) may result in behavioral changes of reservoir rodents, highly pathogenic arenaviruses could be introduced to virus-free countries from endemic areas. In fact, more than twenty cases of Lassa fever have been reported outside of the endemic region in areas such as the USA, Canada, Europe, and Japan [29] [30] [31] [32] [33] . It is of great importance to detect these pathogens rapidly and specifically in order to minimize the risk and scale of outbreaks of VHFs caused by arenaviruses. However, these arenaviruses are classified as biosafety level (BSL)-4 pathogens, making it difficult to develop diagnostic techniques for these virus infections in laboratories without BSL-4 facilities. To overcome these
difficulties, we have established recombinant viral nucleoproteins (rNPs)-based serological assays, such as IgG-enzyme-linked immunosorbent assay (ELISA), indirect immunofluorescence assay (IFA), and antigen (Ag)-capture ELISA for the diagnosis of VHFs caused by highly pathogenic arenaviruses. Furthermore, virus neutralization assays using pseudotype virus-bearing arenavirus GPs have been developed. In this review, we describe the usefulness of such recombinant protein-based diagnostic assays for diagnosing VHFs caused by arenaviruses.
In outbreaks of VHFs, infections are confirmed by various laboratory diagnostic methods. Virus detection is performed by virus isolation, reverse transcription-polymerase chain reaction (RT-PCR), and antigen-capture ELISA. It has been shown that monoclonal antibody panels against pathogenic arenaviruses are useful for detecting viral antigens on the virus-infected cells as well as for investigating of antigenic relationships of arenaviruses [34] [35] [36] . Detection of the virus genome is suitable for a rapid and sensitive diagnosis of VHF patients in the early stage of illness, and extensive reviews of such RT-PCR assays have been described [37, 38] . More recently, progress in the RT-PCR method covering genetic variations of the hemorrhagic fever viruses (HFVs) [39, 40] and a multiplexed oligonucleotide microarray for the differential diagnosis of VHFs have also been reported [41] . On the other hand, antibodies against these viruses can be detected by the indirect
immunofluorescence assay (IFA), or IgG-and IgM-ELISA. An IFA detects the antibody in the serum, which is able to bind to the fixed monolayer of the virus-infected cells. Although the interpretation of immunofluorescence results requires experience, the assay has advantages over other methods, since each virus generates a characteristic fluorescence pattern that adds specificity to the assay compared to a simple ELISA readout. A serological diagnosis by the detection of specific IgM and IgG antibodies to the HFVs must be sensitive, specific and reliable, because a misdiagnosis can lead to panic in the general population. An IgM-specific ELISA is suitable for detecting recent infection, but the relevance of IgM testing for acute VHF depends on the virus and the duration of illness; specific IgM is not often present in the very early stage of illness, and patients who die of VHF often fail to seroconvert at all. An IgG-specific ELISA is efficacious, not only in the diagnosis of a large
number of VHF cases, especially during convalescence, but also for epidemiological studies in the endemic regions. The detailed methods used for the IFA and IgG-and IgM-ELISAs for the diagnosis of VHF using authentic virus-antigens have been described in detail [42] [43] [44] [45] .
Arenaviruses have a bisegmented, negative-sense, single stranded RNA genome with a unique ambisense coding strategy that produces just four known proteins: a glycoprotein, a nucleoprotein (NP), a matrix protein (Z), and a polymerase (L) [46] . Of these proteins, the NP is the most abundant in virus-infected cells. Recombinant protein technology could meet the demand for a simple and reliable VHF test system, and recombinant NP (rNP) has been shown to be useful for serological surveys of IgM-and IgG antibodies against arenaviruses [47] [48] [49] [50] .
Recombinant baculoviruses that express the full-length rNP of arenaviruses have been generated [48, 50, 51] . The method used for the purification of arenavirus rNP from insect Tn5 cells infected with recombinant baculoviruses is effective and simple compared to those for Ebola, Marburg, and Crimean-Congo hemorrhagic fever virus rNPs [51] [52] [53] [54] [55] . Most of the arenavirus rNPs expressed in insect cells using the recombinant baculoviruses are crystallized [56] and are solubilized in PBS containing 8M urea. Since the majority of Tn5 cellular proteins are solubilized in PBS containing 2M urea, the arenavirus rNPs in the insoluble fraction in PBS containing 2M urea can be solubilized by sonication in PBS containing 8M urea. After a simple centrifugation of the lysates in PBS containing 8M urea, the supernatant fractions can be used as purified rNP antigens without further purification steps [51] . The control antigen is produced from Tn5 cells infected with baculovirus lacking
the polyhedrin gene (ΔP) in the same manner as the arenavirus rNPs ( Figure 1 ).
Purified rNPs. The expression and purification efficiency of arenavirus rNP were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) after staining the gels with Coomassie blue. Purified NP antigens with approximate molecular weights of 62 kDa from Luna, LCM, Lassa, Lujo, Junin, Machupo, Guanarito, Sabia, and Chapare viruses and the purified negative control antigen (ΔP) are shown.
As described above, recombinant baculoviruses allow the delivery of rNP antigens without using infectious live arenaviruses. An ELISA plate coated with the predetermined optimal quantity of purified rNPs (approximately 100 ng/well) is used for the IgG-antibody detection assay. An advantage of using recombinant rNP for the IgG-ELISA is that it enables a direct comparison of antibody cross-reactivity among arenavirus rNPs, since antigen preparations of all arenavirus rNPs tested are performed using the same method [51] . Rabbit anti-sera raised against LCMV-rNP and LASV-rNP show cross-reactivity to LASV-rNP and LCMV-rNP, respectively, indicating that rabbit antibodies against rNPs of Old World arenaviruses cross-react with rNPs of other Old World arenaviruses (Table 1 ) [51] . Similarly, rabbit anti-sera generated against JUNV-NP show cross-reactivity to the LASV-rNP and LCMV-rNP, although the reaction is weak. However, rabbit anti-sera against LASV-NP and LCMV-NP show a negative
reaction to the JUNV-rNP (Table 1 ) [51] , indicating that rabbit antibodies against JUNV (a pathogenic New World arenavirus) NP might cross-react with the Old World arenavirus NP, whereas antibodies against Old World arenavirus NPs may not be able to react with pathogenic New World arenavirus NPs.
The rNP-based IgG-ELISA has also been used for the characterization of a mouse monoclonal antibody (MAb). Nakauchi et al. [50] have investigated the cross-reactivity of MAbs against JUNV rNP to pathogenic New World arenavirus rNPs, as well as LASV rNP. MAb C11-12 reacts at the same level with the rNPs of all of the pathogenic New World arenaviruses, including JUNV, GTOV, MACV, SABV, and CHPV, indicating that this MAb recognizes an epitope conserved among pathogenic New World arenaviruses. Another MAb, C6-9, reacts specifically with the rNP of JUNV, but does not react with those of the other pathogenic New World arenaviruses [50] . This indicates that MAb C6-9 recognizes a JUNV-specific epitope. None of these MAbs reacts with the rNP of the human pathogenic Old World arenavirus LASV. Thus, the MAb C11-12 is considered to be a broadly reactive MAb against New World arenaviruses, whereas MAb C6-9 is JUNV-specific. These findings have been confirmed by detailed epitope analyses using
peptide mapping [50] . Similarly, the cross-reactivity of MAbs against LASV rNP has been analyzed [51] . MAb 4A5 cross-reacts with the Mopeia virus (MOPV) but not with the LCMV rNP. MAb 6C11 cross-reacts with LCMV rNP, while MAb 2-11 does not cross-react with LCMV rNP [51] . Table 1 . Anti-serum reactivity for rNPs of different arenaviruses in IgG ELISAs.
Reactivity for rNP from LASV LCMV JUNV anti-LASV NP