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Rotavirus infection is a dilemma for developing countries, including Malaysia. Although commercial rotavirus vaccines are available, these are not included in Malaysia's national immunization program. A scarcity of data about rotavirus genotype distribution could be partially to blame for this policy decision, because there are no data for rotavirus genotype distribution in Malaysia over the past 20 years. From January 2018 to March 2019, we conducted a study to elucidate the rotavirus burden and genotype distribution in the Kota Kinabalu and Kunak districts of the state of Sabah. Stool specimens were collected from children under 5 years of age, and rotavirus antigen in these samples was detected using commercially available kit. Electropherotypes were determined by polyacrylamide gel electrophoresis of genomic RNA. G and P genotypes were determined by RT-PCR using type specific primers. The nucleotide sequence of the amplicons was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method. Rotavirus was identified in 43 (15.1%) children with watery diarrhea. The male:female ratio (1.9:1) of the rotavirus-infected children clearly showed that it affected predominantly boys, and children 12-23 months of age. The genotypes identified were G3P[8] (74% n = 31), followed by G1P[8] (14% n = 6), G12P[6](7% n = 3), G8P[8](3% n = 1), and GxP[8] (3% n = 1). The predominant rotavirus circulating among the children was the equine-like G3P[8] (59.5% n = 25) with a short electropherotype. Eleven electropherotypes were identified among 34 strains, indicating substantial diversity among the circulating strains. The circulating genotypes were also phylogenetically diverse and related to strains from several different countries. The antigenic epitopes present on VP7 and VP4 of Sabahan G3 and equine-like G3 differed considerably from that of the RotaTeq vaccine strain. Our results also indicate that considerable genetic exchange is occurring in Sabahan strains. Sabah is home to a number of different ethnic groups, some of which culturally are in close contact with animals, which might contribute to the evolution of diverse rotavirus strains. Sabah is also a popular tourist destination, and a large number of tourists from different countries possibly contributes to the diversity of circulating rotavirus genotypes. Considering all these factors which are contributing rotavirus genotype diversity, continuous surveillance of rotavirus strains is of utmost importance to monitor the pre- and post-vaccination efficacy of rotavirus vaccines in Sabah., Competing Interests: The authors have declared that no competing interests exist.

Cross-reactive T cell immunity to seasonal coronaviruses (HCoVs) may lead to immunopathology or protection during SARS-CoV2 infection. To understand the influence of cross-reactive T cell responses, we used IEDB (Immune epitope database) and NetMHCpan (ver. 4.1) to identify candidate CD8 + T cell epitopes, restricted through HLA-A and B alleles. Conservation analysis was carried out for these epitopes with HCoVs, OC43, HKU1, and NL63. 12/18 the candidate CD8 + T cell epitopes (binding score of ≥0.90), which had a high degree of homology (>75%) with the other three HCoVs were within the NSP12 and NSP13 proteins. They were predicted to be restricted through HLA-A*2402, HLA-A*201, HLA-A*206, and HLA-B alleles B*3501. Thirty-one candidate CD8 + T cell epitopes that were specific to SARS-CoV2 virus (<25% homology with other HCoVs) were predominantly identified within the structural proteins (spike, envelop, membrane, and nucleocapsid) and the NSP1, NSP2, and NSP3. They were predominantly restricted through HLA-B*3501 (6/31), HLA-B*4001 (6/31), HLA-B*4403 (7/31), and HLA-A*2402 (8/31). It would be crucial to understand T cell responses that associate with protection, and the differences in the functionality and phenotype of epitope specific T cell responses, presented through different HLA alleles common in different geographical groups, to understand disease pathogenesis.

Flaviviruses circulate worldwide and cause a number of medically relevant human diseases, such as dengue, Zika, yellow fever, and tick-borne encephalitis (TBE). Serology plays an important role in the diagnosis of flavivirus infections, but can be impeded by antigenic cross-reactivities among flaviviruses. Therefore, serological diagnosis of a recent infection can be insufficiently specific, especially in areas where flaviviruses co-circulate and/or vaccination coverage against certain flaviviruses is high. In this study, we developed a new IgM assay format, which is well suited for the specific diagnosis of TBE, Zika and dengue virus infections. In the case of TBE and Zika, the IgM response proved to be highly specific for the infecting virus. In contrast, primary dengue virus infections induced substantial amounts of cross-reactive IgM antibodies, which is most likely explained by structural peculiarities of dengue virus particles. Despite the presence of cross-reactive IgM, the standardized nature and the quantitative read-out of the assay even allowed the serotype-specific diagnosis of recent dengue virus infections in most instances.

Rotavirus infection is the most common cause of viral diarrhea in infants and young children but uncommon and usually asymptomatic in adults. In the winter of 2017-2018, a large-scale outbreak of rotavirus in both children and adults was reported in Thailand. The current study focused on the prevalence, genotyping, and molecular characterization of rotavirus infections in Thai adults from July 2016 to December 2019. In 2,598 stool samples collected from adult residents of Bangkok (aged #x2265; 15 years) with acute gastroenteritis, rotavirus was detected via real-time RT-PCR analysis of the VP6 gene. G, P and I genotypes were determined by direct sequencing of VP7, VP4, and VP6 genes, respectively. Our results showed 8.7% (226/2,598) of stool samples were positive for rotavirus. The incidence of rotavirus was high during the winter season of 2017-2018 (17.7%) compared to another studied periods (4.5% between July 2016- October 2017 and 2.8% between March 2018- December 2019). Nucleotide sequencing of VP7 and VP4 revealed G3P[8] as the predominant strain (33.2%,75/226), followed by G9P[8] (17.3%,39/226), and G2P[4] (15.0%,34/226). Uncommon G and P combinations were additionally detected at low frequencies. VP6 sequencing was conducted to discriminate I genotype between the Wa and DS-1 genogroup. The unusual DS-1-like G3P[8] strain was most prevalent amomg rotavirus strains detected in this study (29.6%, 67/226), and the corresponding VP7 sequences showed high nucleotide identity with unusual DS-1-like globally circulating strains. Our study demonstrates that rotavirus outbreaks in adults are attributable not only to high prevalence of RV infection but also the unusual DS-like genogroup. The collective findings reinforce the importance of investigating rotavirus diagnosis in adults suffering from acute gastroenteritis and taking appropriate preventive measures., Competing Interests: The authors have declared that no competing interests exist.

The term "neoantigen," as applied to molecules newly expressed on tumor cells, has a long history. The groundbreaking discovery of a cancer causing virus in chickens by Rous over 100 years ago, followed by discoveries of other tumor-causing viruses in animals, suggested a viral etiology of human cancers. The search for other oncogenic viruses in the 1960s and 1970s resulted in the discoveries of Epstein-Barr virus (EBV), hepatitis B virus (HBV), and human papilloma virus (HPV), and continues until the present time. Contemporaneously, the budding field of immunology was posing the question can the immune system of animals or humans recognize a tumor that develops from one's own tissues and what types of antigens would distinguish the tumor from normal cells. Molecules encoded by oncogenic viruses provided the most logical candidates and evidence was quickly gathered for both humoral and cellular recognition of viral antigens, referred to as neoantigens. Often, however, serologic responses to virus-bearing tumors revealed neoantigens unrelated to viral proteins and expressed on multiple tumor types, foreshadowing later findings of multiple changes in other genes in tumor cells creating nonviral neoantigens., (Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.)

The antigenic relationships between the natural reassortment field strains of infectious bursal disease virus (IBDV), and between the field strains and the vaccine strains are poorly understood. In the present study, the antigenicity of four representative natural reassortment IBDV isolates designated JS7, GD10111, NN1005 and NN1172 from southern China during the years 2005-2011 and their antigenic relationship with the most commonly used vaccine strain B87 were investigated in vivo. For this purpose, cross-challenge studies were performed on 28-day-old birds, which were 2 weeks post-vaccination by oil-emulsion vaccines (OEVs) prepared from the four field viruses and B87, respectively. The protection related values (PRV) were evaluated based on the protection rate measured by clinical signs and mortality, bursa/body weight (B/BW) ratio and the viral load in the bursal samples at 3 and 7 days post challenge. As a result, the PRV showed that the isolates NN1172 and GD10111 belonged to the same antigenic subtype, while the isolates NN1005 and JS7 belong to another subtype. The vaccine strain B87 was grouped with the isolates NN1005 and JS7 but actually belongs to another small subgroup and provided only 60-80% protection against the challenge of the four field strains. The results demonstrated that different antigenic subtypes co-existed among the field natural reassortment IBDV strains and the commonly used vaccine strain B87 was antigenically different from the prevalent IBDVs in southern China., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Canine distemper virus (CDV) is an RNA virus of the genus Morbillivirus within the family Paramyxoviridae. CDV produces multi-systemic disease in dogs and other terrestrial carnivores. With the development of modified live vaccines in the 1950s and 1960s, the disease, with a few exceptions, has been successfully controlled. However, recently the cases of CDV in vaccinated dogs have been increasing throughout the world, including the United States. There are many reasons that can lead to vaccine failure, including antigenic differences between the vaccine strains and the currently circulating wild-type strains. Currently, there are at least three genetically different CDV lineages circulating in the US. Therefore, in this study, we evaluated various wild-type CDV and vaccine isolates to determine if the genetic differences observed among various strains result in significant antigenic differences based on changes to the neutralizing epitopes. The results of a cross-neutralization assay revealed that there are antigenic differences among the tested CDV wild-type isolates as well as between the tested isolates and the vaccine strains currently used in the US. Therefore, these results suggest the need to develop an updated CDV vaccine., (Copyright © 2018 Elsevier B.V. All rights reserved.)

The strategies for developing rotavirus (RV) vaccines have always been controversial. At present, both the monovalent RV vaccine and the multivalent RV vaccine have displayed excellent safety and efficacy against RV infection and shown cross-reactive immunity, which laid the question whether the multivalent RV vaccine could be replaced by the monovalent RV vaccine. In this study, we focused on comparing the immunogenicity (serum neutralization activity and protection against homotypic and heterotypic RVs' challenge) of individual standard RV strains (monovalent RV immunogens) and different combinations of them (multivalent RV immunogens). In result, RV immunogens showed general immunogenicity and heterotypic reaction but the multivalent RV immunogens exhibited greater serum neutralization activity and stronger heterotypic reaction than the monovalent RV immunogens (P<0.05). As to the protection, the multivalent RV immunogens also revealed more rapid and stronger protection against homotypic and heterotypic RVs' challenge than the monovalent RV immunogens. The results demonstrated that both the monovalent and multivalent RV immunogens exhibited high immunogenicity, but the monovalent RV immunogens could not provide enough neutralization antibodies to protect MA104 cells against the infection with heterotypic RV strains and timely protection against homotypic and heterotypic RVs, so the multivalent RV vaccine could not be replaced by the monovalent RV vaccine.

The results of selection of composition of antigens to cytomegalovirus in the structure of multiplex test on the basis of FOSFAN™ technique are presented. In the process of detection of immunoglobulin G (IgG) to this virus the best indicators of sensitivity were registered with mosaic antigen containing immunodominant sequences of proteins pp150, gB, pp28 and pp52; reliably lower indicators of sensitivity was registered with phosphoprotein pp150; the lowest indicators of sensitivity were registered with proteins gB and pp65. The specificity made up from 93.5% to 96.8% independently of type of antigen. The mosaic antigen ensured the best ratio between sensitivity and specificity of immunoassay and is considered as the main component of immunochip for detecting IgG to cytomegalovirus.

Bovine respiratory syncytial virus (BRSV) plays a significant role in the etiopathogenesis of the respiratory syndrome in young cattle during their first year of life. Development of rapid and accurate BRSV diagnostic tools would aid in the appropriate control of this important pathogen. The objective of this study was to characterize infections induced by BRSV by means of rapid patient-side immunomigration assays used for diagnosis of human respiratory syncytial virus (hRSV) in humans. Nasal and tracheal swabs were obtained from healthy calves of various beef and dairy breeds - Holstein-Friesian, Simmental, Charolais, Belgian Blue and Limousin, between the ages of 5 and 12 months, from 26 farms. BRSV was identified using two rapid immunomigration assays, TruRSV® and Clearview® RSV, and compared with RT-PCR as a reference technique. BRSV was found in 73.1% of all the herds tested. High agreement with RT-PCR was obtained for TruRSV® (κ = 0.824), while in the case of the Clearview® RSV test, agreement with PCR was moderate (κ = 0.420). The results demonstrate that rapid patient-side immunomigration assays designed to detect hRSV can be used to accurately detect BRSV in field samples collected from cattle., (© 2013 Blackwell Verlag GmbH.)

Intragenotypic heterogeneity of co-circulating rotaviruses is remarkable. Sequence and phylogenetic analyses of the rotavirus VP7 and VP4 genes were performed on selected human G4P[8] strains identified in Parma, Northern Italy, during 2004-2005 and 2008-2012. All the strains clustered into lineages Ic (VP7) and P[8]-III (VP4) in different subclusters with a nucleotide sequence variation up to 4 %. VP7 and VP4 amino acid sequences of the Italian rotaviruses showed multiple changes with the corresponding reference strains as well as with vaccine viruses in the neutralizing epitopes. There is concern that the progressive intra-lineage diversification in the VP7 and VP4 through the accumulation of point mutations and amino acid differences between vaccine strains and currently circulating rotaviruses could generate, over the years, vaccine-resistant variants.

The demonstrated link between the emergence of H3N2 variant (H3N2v) influenza A viruses (IAVs) and swine exposure at agricultural fairs has raised concerns about the human health risk posed by IAV-infected swine. Understanding the antigenic profiles of IAVs circulating in pigs at agricultural fairs is critical to developing effective prevention and control strategies. Here, 68 H3N2 IAV isolates recovered from pigs at Ohio fairs (2009 to 2011) were antigenically characterized. These isolates were compared with other H3 IAVs recovered from commercial swine, wild birds, and canines, along with human seasonal and variant H3N2 IAVs. Antigenic cartography demonstrated that H3N2 IAV isolates from Ohio fairs could be divided into two antigenic groups: (i) the 2009 fair isolates and (ii) the 2010 and 2011 fair isolates. These same two antigenic clusters have also been observed in commercial swine populations in recent years. Human H3N2v isolates from 2010 and 2011 are antigenically clustered with swine-origin IAVs from the same time period. The isolates recovered from pigs at fairs did not cross-react with ferret antisera produced against the human seasonal H3N2 IAVs circulating during the past decade, raising the question of the degree of immunity that the human population has to swine-origin H3N2 IAVs. Our results demonstrate that H3N2 IAVs infecting pigs at fairs and H3N2v isolates were antigenically similar to the IAVs circulating in commercial swine, demonstrating that exhibition swine can function as a bridge between commercial swine and the human population.

Rotavirus (RV) is an important cause of gastrointestinal disease in animals and humans. In this study, we developed an RT-PCR to detect RV group B (RVB) and characterized the VP7 (G) gene segment detected in porcine samples. One hundred seventy three samples were tested for RV group A (RVA), RVB, and C (RVC) by RT-PCR and examined for RV-like lesion using histopathology. A majority (86.4%) of the samples had mixed RV infections and co-infections of RVA/RVB/RVC were detected at a higher rate (24.3%) than previously reported. RVB was identified in 46.8% of the 173 samples. An adapted VP7 classification was developed using previously published (n=57) and newly sequenced (n=68) RVB strains, resulting in 20 G genotypes based on an 80% nucleotide identity cutoff value. Our results revealed a broad genetic diversity of porcine RVB strains, suggesting RVB has been the cause of common/pre-existing, yet undiagnosed, disease in pigs., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Three different rapid strip tests: TRU RSV, BinaxNOW RSV and RSV Respi-strip were compared with RT-PCR and ELISA BRSV Ag for the ability to detect bovine respiratory syncytial virus (BRSV) in nasal swabs collected from calves experimentally vaccinated with live vaccine Rispoval RS-PI3. The reference strains of BRSV (375 and A51908) were detected by ELISA BRSV Ag whereas the strains of human respiratory syncytial virus (HRSV) and bovine parainfluenza virus type 3 (BPIV-3) were not. All rapid strip tests as well as RT-PCR reacted positively both to HRSV and BRSV reference strains and negatively to BPIV-3. The detection limit for RT-PCR was 39.1 TCID50 (strain 375 of BRSV), whereas for each of the rapid tests it was approximately 156 TCID50 and 312 TCID50 for antigen ELISA. Diagnostic sensitivity in detecting BRSV in nasal swabs for TRU RSV and RSV Respi-strip tests was 33% and 50% for BinaxNOW RSV. Diagnostic specificity of TRU RSV was 100%, whereas for both BinaxNOW and Respi-strip it was 87%. We concluded that TRU RSV could be used as a supportive rapid test for BRSV screening in nasal swabs taken directly on a farm. However, due to the small group of animals used in the experiment, the results should be regarded as preliminary and the study should be repeated on a larger number of animals.

Equine influenza virus is a major respiratory pathogen in horses, and outbreaks of disease often lead to substantial disruption to and economic losses for equestrian industries. The hemagglutinin (HA) protein is of key importance in the control of equine influenza because HA is the primary target of the protective immune response and the main component of currently licensed influenza vaccines. However, the influenza virus HA protein changes over time, a process called antigenic drift, and vaccine strains must be updated to remain effective. Antigenic drift is assessed primarily by the hemagglutination inhibition (HI) assay. We have generated HI assay data for equine influenza A (H3N8) viruses isolated between 1968 and 2007 and have used antigenic cartography to quantify antigenic differences among the isolates. The antigenic evolution of equine influenza viruses during this period was clustered: from 1968 to 1988, all isolates formed a single antigenic cluster, which then split into two cocirculating clusters in 1989, and then a third cocirculating cluster appeared in 2003. Viruses from all three clusters were isolated in 2007. In one of the three clusters, we show evidence of antigenic drift away from the vaccine strain over time. We determined that a single amino acid substitution was likely responsible for the antigenic differences among clusters.

During May 22-September 3, 2011, the United States experienced low levels of influenza activity; 2009 influenza A (H1N1), influenza A (H3N2), and influenza B viruses were detected worldwide and identified sporadically in the United States. Typical seasonal patterns of influenza activity occurred in the Southern Hemisphere. This report summarizes influenza activity in the United States and worldwide since the last update.

Vaccination against avian influenza (AI) is now included amongst the prevention and control measures recommended by international animal health organizations to combat the disease in poultry. For optimal control of human influenza infections, the antigenic variability within subtypes requires the annual update of seed strains for inclusion in vaccines. The decisions taken are based on serological cross-reactivity of viral strains measured by haemagglutination inhibition (HI) tests. The reason for this is to ensure that the vaccine contains strains that are related antigenically to the current circulating field strain as field viruses evolve or are substituted by variants of distinct antigenicity. Such an annual approach is not viable economically for the poultry industry. In the current study, we have applied a similar HI-based approach to demonstrate, as proof of principle, that cross-reactive strains can be identified. Applying the same approach used by the World Health Organization to investigate antigenic differences among human influenza viruses, we assessed the serological cross-reactivity of a selection of natural H5 and H7 subtype viruses. Analysing HI data, we have identified strains that are cross-reactive and may have the potential to act as seed viruses for future vaccine development. This study should be considered a starting point for a more informed approach to the selection of seed strains for the development of avian influenza vaccines against field infections caused by viruses of H5 and H7 subtypes.

Multiple reassortment events between different subtypes of endemic avian influenza viruses have increased the genomic diversity of influenza viruses circulating in poultry in southern China. Gene exchange from the natural gene pool to poultry has contributed to this increase in genetic diversity. However, the role of domestic ducks as an interface between the natural gene pool and terrestrial poultry in the influenza virus ecosystem has not been fully characterized. Here we phylogenetically and antigenically analyzed 170 H6 viruses isolated from domestic ducks from 2000 to 2005 in southern China, which contains the largest population of domestic ducks in the world. Three distinct hemagglutinin lineages were identified. Group I contained the majority of isolates with a single internal gene complex and was endemic in domestic ducks in Guangdong from the late 1990s onward. Group II was derived from reassortment events in which the surface genes of group I viruses were replaced with novel H6 and N2 genes. Group III represented H6 viruses that undergo frequent reassortment with multiple virus subtypes from the natural gene pool. Surprisingly, H6 viruses endemic in domestic ducks and terrestrial poultry seldom reassort, but gene exchanges between viruses from domestic ducks and migratory ducks occurred throughout the surveillance period. These findings suggest that domestic ducks in southern China mediate the interaction of viruses between different gene pools and facilitate the generation of novel influenza virus variants circulating in poultry.

Signature peptides of the neuraminidase antigen across all common circulating human subtypes of type A and B influenza are identified through the bioinformatic alignment of translated gene sequences. The detection of these peptides within the high-resolution mass spectra of whole antigen, virus, and vaccine digests enables the strains to be rapidly and directly typed and subtyped. Importantly, unique signature peptides for pandemic (H1N1) 2009 influenza are identified and detected that enable pandemic strains to be rapidly and directly differentiated from seasonal type A (H1N1) influenza strains. The detection of these peptides can enable the origins of the neuraminidase gene to be monitored in the case of reassorted strains.

The emergence and spread of 2009 pandemic influenza A (H1N1) virus resulted in substantial influenza activity in the United States throughout the summer and fall months of 2009, with activity peaking in late October. Activity declined beginning in November 2009 but continued at lower levels through March 2010. The 2009 H1N1 virus remained the dominant circulating influenza virus throughout the season; <1% of characterized viruses were seasonal influenza A (H1), A (H3), and influenza B viruses. This report summarizes U.S. influenza activity from August 30, 2009, the start of the 2009-10 influenza season, through March 27, 2010, and also reports on the 2010-11 Northern Hemisphere influenza vaccine strain selection.

Available empirical data on the natural occurrence of ruminant pestiviruses has shown that in cattle, bovine viral diarrhoea virus (BVDV) is nearly exclusively found, whereas both border disease virus (BDV) and BVDV can be isolated from sheep. During routine genetic typing of pestivirus RNA from UK cattle diagnosed as BVDV positive between 2006 and 2008, five samples that were classified as BDV positive yielded positive virus isolates in cell cultures. The samples originated from animals that had shown signs typical for BVD. Phylogenetic analysis of the bovine BDVs showed that two belonged to the BDV-1a group and three to the BDV-1b group, thereby matching the genetic diversity seen for previously described UK ovine BDVs. Antigenic typing with a set of monoclonal antibodies (MABs) showed that all bovine BDVs lacked one or more epitopes conserved among ovine BDV-1 isolates, and that they had gained reactivity with at least one BVDV-1 specific MAB. Serial passaging of two of the virus isolates in ovine cell cultures did not change the epitope expression pattern. These findings suggest that the presumed natural resistance of cattle against infection with BDV no longer holds. A consequence of this is that BVD diagnostic assays should be checked for their ability to also detect BDV, and also highlights the need for monitoring of the BDV status in sheep that may be in contact with cattle in areas with organised BVD control programmes., (Crown Copyright 2009. Published by Elsevier B.V. All rights reserved.)

Human influenza A viruses are classic examples of antigenically variable pathogens that have a seemingly endless capacity to evade the host's immune response. The viral hemagglutinin (HA) and neuraminidase (NA) proteins are the main targets of our antibody response to combat infections. HA and NA continuously change to escape from humoral immunity, a process known as antigenic drift. As a result of antigenic drift, the human influenza vaccine is updated frequently. The World Health Organization (WHO) coordinates a global influenza surveillance network that, by the hemagglutination inhibition (HI) assay, routinely characterizes the antigenic properties of circulating strains in order to select new seed viruses for such vaccine updates. To facilitate a quantitative interpretation and easy visualization of HI data, a new computational technique called "antigenic cartography" was developed. Since its development, antigenic cartography has been applied routinely to assist the WHO with influenza surveillance activities. Until recently, antigenic variation was not considered a serious issue with influenza vaccines for poultry. However, because of the diversification of the Asian H5N1 lineage since 1996 into multiple genetic clades and subclades, and because of the long-term use of poultry vaccines against H5 in some parts of the world, this issue needs to be re-addressed. The antigenic properties of panels of avian H5N1 viruses were characterized by HI assay, using mammalian or avian antisera, and analyzed using antigenic cartography methods. These analyses revealed antigenic differences between circulating H5N1 viruses and the H5 viruses used in poultry vaccines. Considerable antigenic variation was also observed within and between H5N1 clades. These observations have important implications for the efficacy and long-term use of poultry vaccines.

Background: In a study performed in 1983, 18 adult volunteers received oral challenge with the virulent human rotavirus strain D (G1P1A[8],NSP4[B]). To identify correlates of resistance to rotavirus infection, we analyzed levels of serum immunoglobulin (Ig) A and IgG antibodies to various rotaviral antigens in 16 of the 18 volunteers., Methods: We used immunocytochemical assays that involved a total of 16 different recombinant baculoviruses, with each baculovirus expressing one of the following major serotype/genotype rotavirus proteins for the serologic assays: (1) viral protein (VP) 4 with P1A[8], P1B[4], P2A[6], P3[9], or P4[10] specificity; (2) VP7 with G1-G4 or G9 specificity; and (3) nonstructural viral protein (NSP) 4 with genotype A, B, C, or D specificity., Results: The prechallenge titers of IgG antibody to VP7 types G1, G3, G4, and G9; VP4 types P1A[8], P1B[4], P2A[6], and P4[10]; and NSP4 type [A] in the group of noninfected volunteers (n = 11) were significantly higher than those in the group of infected volunteers (n = 5; of these 5 volunteers, 4 were symptomatically infected). Moreover, logistic regression analysis showed that resistance to rotavirus infection most closely correlated with higher prechallenge titers of IgG antibody to homotypic VP7 (G1) and VP4 (P1A[8])., Conclusions: These results suggest that protection against rotavirus infection and disease is primarily VP7/VP4 homotypic and, to a lesser degree, heterotypic.

Monoclonal antibodies (MAbs) developed against different foot-and-mouth disease virus (FMDV) vaccine strains were extensively used to study any possible antigenic variations during vaccine production in Argentine facilities. Additionally, a typing ELISA using strain specific MAbs was developed to detect potential cross contaminations among FMDV strains in master and working seeds with high specificity and sensitivity and to confirm strains identity in formulated vaccines. This assay was carried out for the South American strains currently in use in production facilities in Argentina (A24/Cruzeiro, A/Argentina/01, O1/Campos and C3/Indaial) and for the strain O/Taiwan, produced only for export to Asia. These non-cross reactive MAbs were also used to analyze the integrity of viral particles belonging to each one of the individual strains, following isolation of 140S virions by means of sucrose density gradients from the aqueous phase of commercial polyvalent vaccines. Antigenic profiles were defined for FMDV reference strains using panels of MAbs, and a coefficient of correlation of reactivity with these panels was calculated to establish consistent identity upon serial passages of master and production seeds. A comparison of vaccine and field strain antigenic profiles performed using coefficients of correlation allowed the rapid identification of two main groups of serotype A viruses collected during the last FMD epidemic in Argentina, whose reactivity matched closely to A/Argentina/2000 and A/Argentina/2001 strains.

Triple-reassortant swine influenza A (H1) viruses, containing genes from avian, human, and swine influenza viruses, emerged and became an outbreak among humans worldwide. Over a 1,000 cases were identified within the first month, chiefly in Mexico and the United States. Here, the phylogenetic analysis of haemagglutin (HA), neuraminidase (NA), and matrix protein (MP) was carried out. The analysis showed that the H1 of this reassortant originated from American pigs, while NA and MP were more likely from European pigs. All of the 2009 isolates appear homogeneous and cluster together, although they are distinct from classical human A (H1N1) viruses.

Background: We administered a single dose of influenza A/Vietnam/1203/2004 (H5N1, clade 1) vaccine to subjects who had received 2 doses of influenza A/Hong Kong/156/1997 (H5N1, clade 0) vaccine in 1998., Methods: Thirty-seven subjects previously vaccinated with a baculovirus-expressed recombinant hemagglutinin A/Hong Kong/156/1997 vaccine in 1998 received a single intramuscular dose of 90 microg of inactivated subvirion A/Vietnam/1203/2004 vaccine in 2006. Serum antibody was measured before vaccination and 28 and 56 days after vaccination. Antibody responses were compared with those measured after one or two 90-microg doses in H5-naive subjects., Results: On day 28 after a single dose, the geometric mean titer (GMT) of hemagglutination-inhibition antibody in primed subjects was 64.0 (95% confidence interval [CI], 37.8-108.5), with 68% responding (4-fold increase in antibody level to a titer of >or=1:40). In contrast, H5-naive subjects who received two 90-microg doses had a day 56 (28 days after the second dose) GMT of 27.7 (95% CI, 20.3-38.0), with only 43% responding., Conclusions: This study suggests that priming can result in immune responses to a single dose of an antigenically variant strain of H5N1 influenza virus and could be a useful strategy for pandemic control., Trial Registration: ClinicalTrials.gov identifier: NCT00240903.

Antigenic profiles of post-2002 H5N1 viruses representing major genetic clades and various geographic sources were investigated using a panel of 17 monoclonal antibodies raised from five H5N1 strains. Four antigenic groups from seven clades of H5N1 virus were distinguished and characterized based on their cross-reactivity to the monoclonal antibodies in hemagglutination inhibition and cell-based neutralization assays. Genetic polymorphisms associated with the variation of antigenicity of H5N1 strains were identified and further verified in antigenic analysis with recombinant H5N1 viruses carrying specific mutations in the hemagglutinin protein. Modification of some of these genetic variations produced marked improvement to the immunogenicity and cross-reactivity of H5N1 strains in assays utilizing monoclonal antibodies and ferret antisera raised against clade 1 and 2 H5N1 viruses, suggesting that these sites represent antigenically significant amino acids. These results provide a comprehensive antigenic profile for H5N1 virus strains circulating in recent years and will facilitate the recognition of emerging antigenic variants of H5N1 virus and aid in the selection of vaccine strains.

Feline Calicivirus (FCV) has been recognised as major oral and respiratory pathogen of cats. The high correlation among the field viruses and FCV-F9 serotype has represented the immunological bases for the employ of FCV-F9 serotype as a vaccine for calicivirosis in cats. The aim of this paper was to evaluate, by in vitro neutralization assays, the antigenic correlation among the vaccine F9 and FCV field strains isolated in Sicily (Italy) from cats showing clinical forms referable to calicivirus infection. The results confirm the low correlation between FCV-F9 strain and calicivirus strains spread in the feline population.

Of 322 stool specimens collected from children with diarrhea from October 2005 through September 2006 in Wuhan, China, group A rotavirus was identified in 101 (31.4%). The most prevalent group A rotavirus genotype was G3P[8] (62.6%), followed by G1P[8](17.6%), G1+G3P[8](8.8%), G3P[4](6.6%), G1P[4](2.2%), and G9P[8](2.2%). The G9 strains were first detected in Wuhan.

The extensive diversity of human immunodeficiency virus type 1 (HIV-1) and its capacity to mutate and escape host immune responses are major challenges for AIDS vaccine development. Ancestral sequences, which minimize the genetic distance to circulating strains, provide an opportunity to design immunogens with the potential to elicit broad recognition of HIV epitopes. We developed a phylogenetics-informed algorithm to reconstruct ancestral HIV sequences, called Center of Tree (COT). COT sequences have potentially significant benefits over isolate-based strategies, as they minimize the evolutionary distances to circulating strains. COT sequences are designed to surmount the potential pitfalls stemming from sampling bias with the consensus method and outlier bias with the most-recent-common-ancestor approach. We computationally derived COT sequences from circulating HIV-1 subtype B sequences for the genes encoding the major viral structural protein (Gag) and two regulatory proteins, Tat and Nef. COT genes were synthesized de novo and expressed in mammalian cells, and the proteins were characterized. COT Gag was shown to generate virus-like particles, while COT Tat transactivated gene expression from the HIV-1 long terminal repeat and COT Nef mediated downregulation of cell surface major histocompatibility complex class I. Thus, retrodicted ancestral COT proteins can retain the biological functions of extant HIV-1 proteins. Additionally, COT proteins were immunogenic, as they elicited antigen-specific cytotoxic T-lymphocyte responses in mice. These data support the utility of the COT approach to create novel and biologically active ancestral proteins as a starting point for studies of the structure, function, and biological fitness of highly variable genes, as well as for the rational design of globally relevant vaccine candidates.

Phylogenetic analyses conducted on isolates of rabbit hemorrhagic disease virus (RHDV) from throughout the world have shown well-defined genogroups comprising representative strains of the virus and antigenic variants. In this work, we have isolated and characterized RHDV from the major epizootic that occurred in Cuba in 2004-2005. Sequence analysis of the capsid protein gene and antigenic characterization of this strain has allowed its inclusion as a member of the distinct RHDVa subtype. We also found that specific antibodies directed against RHDV reference strains bound to the Cuban isolate in a competition ELISA and inhibited virus hemagglutination in vitro. This is the second report on the molecular characterization of RHDVa circulating in the American region.

Rotaviruses are the most common agents of diarrhoeal illness in infants and young children. Gastroenteritis caused by rotaviruses is also more likely to be associated with severe dehydration compared to other viral gastroenteritis. We determined the G-genotype of rotaviruses circulating in the Salento. During 2004, 144 stool samples were collected from subjects with a positive screening test and stored at -20 degrees C until confirmation could take place using molecular biology techniques. A reverse transcription-polymerase chain reaction (RT-PCR) assay for the amplification of gene VP7 of rotavirus was developed and used; G-genotype was determined by sequencing and phylogenetic analysis. A total of 101 stool samples were detected positive by RT-PCR and 35 were sequence analyzed and classified into G1, G2, G4, G9 and G12 type. The overall relative incidence of G-types in Salento is different to that of other developed countries. The most prevalent genotype was G2 while genotype G1 was present at low levels. It is also interesting to note the presence of G9 rotavirus, which is now recognized as the fifth globally important rotavirus genotype. In this study, therefore, we demonstrate the usefulness of a simple method for correctly determining the G genotypes circulating in a geographic region.

A novel double-antigen sandwich enzyme-linked immunosorbent assay (ELISA) was developed to measure rabies antibodies in dogs. In contrast to the 4 days required for detecting rabies antibody with conventional rabies antibody virus neutralization assays, this ELISA can be completed in hours, without using live virus, in routine laboratories.

The paper presents the results of isolation of influenza A virus from 97 cloacal swabs of 11 species of aquatic and semiaquatic wild birds collected on the Chany Lake (the south of Western Siberia, Ob-Irtysh interarea). Six strains with subtypes H2 (2 strains), H3 (3 strains), and H5 (1 strain) were isolated from mallard ducks (Anas platyrhynchos). The total infection rate in the examined birds was 6.2% and that in the ducks was 9.7%. The paper deals with the phylogenetic analysis of hemagglutinin of genes of isolates and with the comparison of the obtained results with the 2002 data in the same region. Analysis of H5 strain hemagglutinin proteolytic site permits one to regard this strain as non-pathogenic.

Objective: To investigate molecular epidemiologic features of rotavirus (RV) infection in infantile diarrhea in Hangzhou area., Methods: Stool specimens of 683 infants with suspected acute viral enteritis in the autumn and winter of 2001 - 2003 were collected. RV (group A) was detected by using latex agglutination test (LAT). VP7 serotype (G) positive specimens were detected by using enzyme linked immunosorbent assay (ELISA) and then the RNA of the virus was determined with reverse transcription polymerase chain reaction (RT-PCR). cDNA of VP7 gene fragment was sequenced by automatic gene analyzor (ABI3730) and compared with the RV VP7 gene sequences stored in Genebank., Results: RV was detected in 297 of 683 (43.5%) specimens by LAT. The highest frequency of RV (group A) detected was 52.9% (228/431) in patients aged 7 - 18 months. The prevalent serotypes were G1 (36.7%, 109/297) and G3 (30.9%, 92/297), followed by mixed type (11.8%, 35/297), untyped (9.4%, 28/297), G4 (7.1%, 21/297) and G2 (4.0%, 12/297). The prevalent serotypes seen each year were different. G1 (54.9%, 45/82) was the major serotype in 2001 followed by G3 (14.6%, 12/82). In 2003, the major serotype was G3 (43.0%, 63/146) and followed by G1 (29.5%, 43/146). The reliability of ELISA was confirmed by RT-PCR, gene sequencing and homology analysis., Conclusion: The main prevalent serotypes of VP7 of rotavirus were G1 and G3. The dominant serotypes of rotavirus varied in Hangzhou area from 2001 to 2003.

Of five globally important VP7 (G) serotypes (G1-4 and 9) of group A rotaviruses (the single most important etiologic agents of infantile diarrhea worldwide), G9 continues to attract considerable attention because of its unique natural history. Serotype G9 rotavirus was isolated from a child with diarrhea first in the United States in 1983 and subsequently in Japan in 1985. Curiously, soon after their detection, G9 rotaviruses were not detected for about a decade in both countries and then reemerged in both countries in the mid-1990s. Unexpectedly, however, such reemerged G9 strains were distinct genetically and molecularly from those isolated in the 1980s. Thus, the origin of the reemerged G9 viruses remains an enigma. Sequence analysis has demonstrated that the G9 rotavirus VP7 gene belongs to one of at least three phylogenetic lineages: lineage 1 (strains isolated in the 1980s in the United States and Japan), lineage 2 (strains first isolated in 1986 and exclusively in India thus far), and lineage 3 (strains that emerged/reemerged in the mid-1990s). Currently, lineage 3 G9 viruses are the most frequently detected G9 strains globally. We characterized a porcine rotavirus (A2 strain) isolated in the United States that was known to belong to the P[7] genotype but had not been serotyped by neutralization. The A2 strain was found to bear serotype G9 and P9 specificities as well as NSP4 [B] and subgroup I characteristics. By VP7-specific neutralization, the porcine G9 strain was more closely related to lineage 3 viruses than to lineage 1 or 2 viruses. Furthermore, by sequence analysis, the A2 VP7 was shown to belong to lineage 3 G9. These findings raise intriguing questions regarding possible explanations for the emergence of variations among the G9 strains.

The present study was undertaken to antigenically characterize the buffalopox virus (BPV). Six monoclonal antibodies (MAbs) against the BP4 strain of BPV have been produced and characterized. All six MAbs appeared to be specific to BPV, as none of them showed cross-reactivity with other poxviruses in antigen capture ELISA. Only two MAbs (20AB8 and 20CD11) bound significantly with different BPV isolates in antigen capture ELISA, whereas the remaining four MAbs bound weakly with the BPV. In Western blot analysis with purified BPV-BP4, the rabbit hyperimmune serum against purified BPV-BP4 reacted with 15 immunodominant polypeptides (100 kDa to 25 kDa), whereas two MAbs (21CB6, 21DB11) reacted with 42 kDa and 45 kDa polypeptides, respectively. However, three MAbs (20AB8, 20CD11, 21CB5) reacted with three degraded polypeptides (100 kDa, 40 kDa and 87 kDa) of BPV-BP4. In radioimmunoprecipitation assay (RIPA) with the rabbit hyperimmune serum to BPV-BP4, three virus specific polypeptides (69 kDa, 34 kDa, 32 kDa) were recognized in BPV-BP4, whereas two polypeptides (69 kDa, 34 kDa) were recognized in other BPV isolates (BPV-Bly, BPV-Vij96, BPV-Vij97). In virus neutralization test, none of the six MAbs tested showed any significant neutralizing ability to infection with different BPV isolates. However, the hyperimmune serum showed weak neutralizing ability to BPV infection.

Hemorrhagic fever with renal syndrome (HVRS) has been for decades a topical problem for healthcare systems of many countries in the Eurasian continent. Viruses triggering HVRS alongside with other related viruses (but not pathogenic to man) were discovered in 70-80-ies and formed a new genus Hantavirus of the Bunyaviridae family. The study results of a severe outbreak of the respiratory disease with the mortality rate of 60% (South-West of the USA, 1933) showed that hantaviruses were also among the causative agents. Later, the disease was designated as hantavirus cardio-pulmonary syndrome. By now, it has been established that hantaviruses are wide spread with different rodents being their carriers. The discussed viruses cause, in rodents, a chronic asymptomatic infection and are transferred, later, to man by the aerogenic path through excretions of infected animals. Studies of hantaviruses have been restricted for a long time due to their high pathogenicity (protection equipment not below than the P-3 level is needed), because of a lack of a laboratory model of infected animals and because of a low growth in cell cultures. With the rapid development and application of molecular biological techniques of the recent years, substantial progress has been made in studies of hantaviruses. Different aspects of hantavirus ecology, molecular biology, morphology, pathogenesis and diagnostics are discussed in the offered survey.

Since the emergence of Canine parvovirus (CPV-2) in the late 1970s, CPV-2 has evolved consecutively new antigenic types, CPV-2a and 2b. Although CPV-2 did not have a feline host range, CPV-2a and 2b appear to have gained the ability to replicate in cats. Recent investigations demonstrate the prevalence of CPV-2a and 2b infection in a wide range of cat populations. We illustrate the pathogenic potential of CPV in cats and assess the risk caused by CPV variants.

Nine monoclonal antibodies (MAB) against nucleocapsid protein (NP) of Newcastle disease virus (NDV) have been prepared and characterized. All the MABs were classified into three groups by means of the competitive binding assay. At least three antigenic sites were delineated on the NP. The 1st site includes two closely located epitopes; the 2nd site includes two related and two distinct epitopes; the 3rd site includes two closely related and one distinct epitopes.

The sequences of the antigenically relevant capsid proteins VP1-3 of 10 isolates obtained during an epizootic of serotype A foot-and-mouth disease virus in Iran, and collected within two and a half years, were found to be highly similar. However, each isolate differed by at least one amino acid from all others. This prompted us to analyze the immunological reactivity of the isolates. To this end, monoclonal antibodies (mAbs) against one isolate were generated and characterized with regard to neutralizing activity and reactivity with trypsinized virus. These mAbs as well as others raised against A22 virus were used for antigen profiling. This distinguished four antigenic conditions among the isolates and 16 reactivities among the mAbs. These findings, together with the observed sequence differences indicated the location of several epitopes. Many mAbs recognized the minor antigenic sites on VP2 and 3 and some the major site, the GH-loop of VP1. One epitope was composed of residues of the capsid proteins VP1 and 2.

Antigenic properties between new Japanese field isolates and vaccine strains of canine distemper virus (CDV) have been compared using four monoclonal antibodies (MAbs) (JD-5, JD-7, JD-11 and d-7) against the hemagglutinin (H) proteins of CDV. JD-5, JD-7 and JD-11 are newly established antibodies. Three MAbs, namely d-7, JD-5 and JD-11, reacted similarly to all the CDV strains examined. However, JD-7 reacted much more strongly with the vaccine strains and an old field isolate than the recent field isolates in immunofluorescence, radio immunoprecipitation and virus neutralization assays. These results indicate that an antigenic region in the H protein, concerned with neutralization and recognized by JD-7, has been altered in the recent field isolates.

A comprehensive phylogenetic study based on the hemagglutinin (H) protein of all known African measles virus (MV) isolates is presented. The study includes 64 new H gene sequences from Ghana. Nigeria and South Africa as well as viruses from Zambia and The Gambia for which only incomplete sequencing data were available and that have previously not been genotyped. The results provide further support to the tentative assignment of the Nigerian and Ghanaian viruses to a new genotype B3 within clade B. A distinct geographic distribution pattern emerged with clade B viruses circulating exclusively in African countries north of the equator. All MV strains from southern Africa grouped in clades A and D with the majority of viruses belonging to genotype D4. The viruses considerably differed by their sensitivity to neutralization by monoclonal antibodies (mAb), but three selected antibodies were sufficient to distinguish between African MVs representing four different genotypes.

Partial sequences of the G protein gene of 33 isolates from antigenic group B of human respiratory syncytial virus were determined. Phylogenetic analysis indicated that the evolutionary pattern of group B viruses is similar to that previously described for isolates of antigenic group A, including worldwide distribution of related viruses and co-circulation of viruses from different lineages during the same epidemic. Dominance of AG+GA over UC+CU transitions was observed when G sequences of group B viruses were compared, as previously found in viruses from antigenic group A. Interestingly, differences in protein length, determined by the usage of alternative termination codons, were more pronounced in group B than in group A viruses. Changes in protein length correlated with the classification of viruses in different lineages. Thus, mutations that determined termination codon usage seem to have played an important role in the diversification of group B viruses.

We isolated three strains of canine distemper virus (CDV)--the Ueno, Hamamatsu, and Yanaka strains--from dogs in Japan and analysed the molecular properties of their haemagglutinin (H) proteins. Immunoprecipitation of all three strains with a monoclonal antibody revealed H proteins with molecular masses of 84 kDa, which differs from the molecular mass (78 kDa) of the H protein of the Onderstepoort vaccine strain. However, after tunicamycin treatment immunoprecipitation identified H proteins of identical molecular mass (68 kDa) for all three field isolates and the vaccine strain. Sequence analysis showed nine potential sites for asparagine-linked glycosylation in the H proteins of the new isolates, in contrast to four in the H protein of the Onderstepoort strain. Thus, variation in glycosylation of the H proteins of the isolates and the vaccine strain may cause differences in antigenicity of the viruses. Sequences of the H genes showed that the new Japanese isolates have 99% identity with each other, 95% with other European and American isolates (from seals, a German dog, a ferret and large felids) and 90% with the vaccine strain. Phylogenetically, the new Japanese isolates form one cluster which is separate from recent European or American isolates, all of which are distinct from vaccine strains.

Western equine encephalomyelitis (WEE) virus (Togaviridae: Alphavirus) was shown previously to have arisen by recombination between eastern equine encephalomyelitis (EEE)- and Sindbis-like viruses (C. S. Hahn, S. Lustig, E. G. Strauss, and J. H. Strauss, Proc. Natl. Acad. Sci. USA 85:5997-6001, 1988). We have now examined the recombinational history and evolution of all viruses belonging to the WEE antigenic complex, including the Buggy Creek, Fort Morgan, Highlands J, Sindbis, Babanki, Ockelbo, Kyzylagach, Whataroa, and Aura viruses, using nucleotide sequences derived from representative strains. Two regions of the genome were examined: sequences of 477 nucleotides from the C terminus of the E1 envelope glycoprotein gene which in WEE virus was derived from the Sindbis-like virus parent, and 517 nucleotide sequences at the C terminus of the nsP4 gene which in WEE virus was derived from the EEE-like virus parent. Trees based on the E1 region indicated that all members of the WEE virus complex comprise a monophyletic group. Most closely related to WEE viruses are other New World members of the complex: the Highlands J, Buggy Creek, and Fort Morgan viruses. More distantly related WEE complex viruses included the Old World Sindbis, Babanki, Ockelbo, Kyzylagach, and Whataroa viruses, as well as the New World Aura virus. Detailed analyses of 38 strains of WEE virus revealed at least 4 major lineages; two were represented by isolates from Argentina, one was from Brazil, and a fourth contained isolates from many locations in South and North America as well as Cuba. Trees based on the nsP4 gene indicated that all New World WEE complex viruses except Aura virus are recombinants derived from EEE- and Sindbis-like virus ancestors. In contrast, the Old World members of the WEE complex, as well as Aura virus, did not appear to have recombinant genomes. Using an evolutionary rate estimate (2.8 x 10(-4) substitutions per nucleotide per year) obtained from E1-3' sequences of WEE viruses, we estimated that the recombination event occurred in the New World 1,300 to 1,900 years ago. This suggests that the alphaviruses originated in the New World a few thousand years ago.

Virus infection has been proposed as an initiating factor in the aetiology of insulin-dependent diabetes mellitus (IDDM). We have examined lymphocyte proliferation to virus proteins which demonstrate sequence similarity to the beta-cell autoantigen glutamic acid decarboxylase (GAD)65. The magnitude and frequency of response to coxsackie B viruses and adenovirus in a T-cell proliferation assay was significantly higher in a group of recently diagnosed IDDM subjects than in non-diabetic control subjects. The frequency of positive response to the coxsackie B viruses was also significantly higher in IDDM subjects expressing the DRB 1*04 major histocompatibility complex (MHC) haplotype than the DRB 1*03 haplotype. There was no evidence that non-aspartate residue at position 57 of DQB 1 genes influenced virus responses in the IDDM group. The coxsackie homology was in amino acids 258-266 and the adenovirus homology was in amino acids 509-524 of GAD65. Both these regions are suspected to be T-cell epitopes in IDDM. These results indicate a disease and MHC class II association between coxsackie B virus infection and IDDM and an association between adenovirus infection and IDDM.