PREDAC-CNN: predicting antigenic clusters of seasonal influenza A viruses with convolutional neural network.

Vaccination stands as the most effective and economical strategy for prevention and control of influenza. The primary target of neutralizing antibodies is the surface antigen hemagglutinin (HA). However, ongoing mutations in the HA sequence result in antigenic drift. The success of a vaccine is contingent on its antigenic congruence with circulating strains. Thus, predicting antigenic variants and deducing antigenic clusters of influenza viruses are pivotal for recommendation of vaccine strains. The antigenicity of influenza A viruses is determined by the interplay of amino acids in the HA1 sequence. In this study, we exploit the ability of convolutional neural networks (CNNs) to extract spatial feature representations in the convolutional layers, which can discern interactions between amino acid sites. We introduce PREDAC-CNN, a model designed to track antigenic evolution of seasonal influenza A viruses. Accessible at http://predac-cnn.cloudna.cn, PREDAC-CNN formulates a spatially oriented representation of the HA1 sequence, optimized for the convolutional framework. It effectively probes interactions among amino acid sites in the HA1 sequence. Also, PREDAC-CNN focuses exclusively on physicochemical attributes crucial for the antigenicity of influenza viruses, thereby eliminating unnecessary amino acid embeddings. Together, PREDAC-CNN is adept at capturing interactions of amino acid sites within the HA1 sequence and examining the collective impact of point mutations on antigenic variation. Through 5-fold cross-validation and retrospective testing, PREDAC-CNN has shown superior performance in predicting antigenic variants compared to its counterparts. Additionally, PREDAC-CNN has been instrumental in identifying predominant antigenic clusters for A/H3N2 (1968-2023) and A/H1N1 (1977-2023) viruses, significantly aiding in vaccine strain recommendation.

Dynamics of the Emerging Genogroup of Infectious Bursal Disease Virus Infection in Broiler Farms in South Korea: A Nationwide Study.

Infectious bursal disease (IBD), caused by IBD virus (IBDV), threatens the health of the poultry industry. Recently, a subtype of genogroup (G) 2 IBDV named G2d has brought a new threat to the poultry industry. To determine the current status of IBDV prevalence in South Korea, active IBDV surveillance on 167 randomly selected broiler farms in South Korea from August 2020 to July 2021 was conducted. The bursas of Fabricius from five chickens from each farm were independently pooled and screened for IBDV using virus-specific RT-PCR. As a result, 86 farms were found to be infected with the G2d variant, 13 farms with G2b, and 2 farms with G3. Current prevalence estimation of IBDV infection in South Korea was determined as 17.8% at the animal level using pooled sampling methods. G2d IBDV was predominant compared to other genogroups, with a potentially high-risk G2d infection area in southwestern South Korea. The impact of IBDV infection on poultry productivity or Escherichia coli infection susceptibility was also confirmed. A comparative pathogenicity test indicated that G2d IBDV caused severe and persistent damage to infected chickens compared with G2b. This study highlights the importance of implementation of regular surveillance programs and poses challenges for the comprehensive prevention of IBDV infections.

Rabies Virus Variants Detected from Cougar (Puma concolor) in Mexico 2000-2021.

In 2019, the World Health Organization (WHO) and the Pan-American Health Organization (PAHO) recognized Mexico as a country free of human rabies transmitted by dogs. Nevertheless, the sylvatic cycle remains as a public health concern in the country. Although cougars (Puma concolor) are not reservoirs of any rabies virus variant (RVV), these felines could act as vectors at the top of the food chain, and their relationships with other organisms must be considered important for the regulatory effect on their prey's populations. In this study, genetic and antigenic characterization was performed on all cougar rabies cases diagnosed at the Rabies Laboratory Network of the Ministry of Health (RLNMH) in Mexico from 2000 to 2021. Samples from other species, a skunk, a horse (Equus caballus) (attacked by a cougar), and a gray fox (Urocyon cineroargenteus), were included as reference. Rabies cases in cougars were restricted to two Northern states of Mexico (Sonora and Chihuahua). Five out of six samples of cougars were RVV7 (Arizona gray fox RVV) and one from Sonora was RVV1. Interestingly, there is no evidence of RVV1 in dogs in the Northern states since the 1990s but skunk species now harbor this RVV1 in this region of the country.

Evidence of Circulation of Several HAV Genetic Variants and Emergence of Potential Antigenic Variants in an Endemo-Epidemic Country before Vaccine Introduction.

Similar to several other countries in the world, the epidemiology of hepatitis A virus changed from high to intermediate endemicity level in Tunisia, which led to the occurrence of outbreaks. This study aimed to determine the genetic and antigenic variability of HAV strains circulating in Tunisia during the last few years. Genotyping using complete VP1 gene and VP1-2A junction confirmed the predominance of genotype IA, with co-circulation of several genetic and antigenic variants. Phylogenetic analysis including Tunisian and strains from other regions of the world showed the presence of at least two IA-variants within IA subgenotype. Amino-acid analysis showed several mutations in or close to epitope regions in the VP1-region. This study provides a baseline on the genetic and antigenic variability of HAV circulating strains before the introduction of vaccination into the national immunization schedule.

Characterization of antigenic variant infectious bursal disease virus strains identified in South Korea.

Infectious bursal disease (IBD) is one of the most important immunosuppressive diseases of young chickens, causing considerable economic losses to the poultry industry. More than 30 years ago, an antigenic variant (av) pathotype of the IBD virus (IBDV) was reported to originate in, and subsequently spread among, poultry farms in the USA. Recently, a novel avIBDV lineage was identified in China and was shown to exhibit clear differences in its pathogenicity as well as molecular characteristics compared with the previously isolated variant strains. In this study, we conducted a passive surveillance of chicken carcasses submitted to our research division from June-December 2019, and detected the IBDV strains by reverse transcription PCR. Five avIBDV strains were isolated, and their pathogenicity was determined by necropsy and molecular analysis. Additionally, a coinfection field case involving an avIBDV strain and a very virulent IBDV (vvIBDV) strain was identified. Multiple sequence alignment and phylogenetic analysis of partial viral protein 1 (VP1) and hypervariable region (hv) VP2 genes revealed that those strains originated from two different avIBDV lineages. The co-occurrence of two sub-groups of avIBDVs in South Korea confirms for the first time the evolution of antigenic variant IBDV strains, and highlights the urgency for the development of new strategies for IBDV intervention in South Korea.RESEARCH HIGHLIGHTS Five avIBDV strains were identified in South Korea by passive surveillance test in 2019.A coinfection between two IBDV strains from different genogroups was reported in a field case.By phylogenetic analysis, Korean avIBDVs belonged to two distinct lineages of antigenic variant genogroup.

Antigenic changes among the predominantly circulating C/Sao Paulo lineage strains of influenza C virus in Yamagata, Japan, between 2015 and 2018.

Influenza C virus is a pathogen that causes acute respiratory illness in children and results in the hospitalization of infants. The antigenicity of the hemagglutinin esterase (HE) glycoprotein is highly stable, and it is not yet known whether antigenic changes contribute to the worldwide transmission and the occurrence of outbreaks of influenza C virus. Here, we performed antigenic analysis of 84 influenza C viruses isolated in Yamagata, Japan, during a 4-year period from 2015 to 2018 and analyzed sequence data for strains of the virus from Japan and many other parts of the world. Antigenic and phylogenetic analyses revealed that 83 strains belonged to the C/Sao Paulo lineage, and two sublineage strains, the Aichi99 sublineage and Victoria2012 sublineage, cocirculated between 2016 and 2018. Aichi99 sublineage strains exhibiting decreased reactivity with the monoclonal antibody YA3 became predominant after 2016, and these strains possessed the K190N mutation. Residue 190 is located in the 190-loop on the top side of the HE protein within a region that is known to show variation that does not impair the biological activity of the protein. The Aichi99 sublineage strains possessing the K190N mutation were detected after 2012 in Europe, Australia, the USA, and Asia as well as Japan. These observations suggest that antigenic variants with K190N mutations have circulated extensively around the world and caused outbreaks in Japan between 2016 and 2018. Our study indicated that the 190-loop is an important antigenic region, and the results suggested that changes in the 190-loop have contributed to the extensive transmission of the virus.

Canine parvovirus types 2a and 2c detection from dogs with suspected parvoviral enteritis in Peru.

Canine parvovirus type 2 (CPV-2) has been reported worldwide as the main agent related to acute hemorrhagic enteritis of high morbidity and variable mortality in puppies. The detection and characterization of this virus is essential to understand the etiology of the disease and to develop control measures. To characterize the virus circulating in Peruvian dogs and to provide new insights into the local diversity of CPV-2, rectal swabs from 39 puppies with clinical symptoms and with no history of previous vaccinations were analyzed. Total DNA was extracted by fast boiling method, and PCR and sequencing were performed using specific primers that amplify a 1316 bp fragment corresponding to the VP2 gene of CPV-2. CPV-2 was detected in 62% of the analyzed samples. The sequencing of PCR product was possible in 9 samples, which were identified as type 2a (4 samples) and type 2c (5 samples). A phylogenetic analysis of both variants circulating in Peruvian dogs showed similarities to Equatorian and Uruguayan strains. This work constitutes the first report about genetic characterization of CPV-2 in Peru.

Prevalence and molecular epidemiology of Canine parvovirus 2 in diarrheic dogs in Colombia, South America: A possible new CPV-2a is emerging?

Since its identification in 1978, Canine parvovirus type 2 (CPV-2) has been considered a pathogen of great importance in the canine population because it causes severe enteritis with high mortality rates in pups. CPV-2 is a virus belonging to the family Parvoviridae. Currently, there are three described antigenic variants (CPV-2a, CPV-2b, and CPV-2c). CPV-2c is an emerging virus that is seen as a global health hazard. The objective of this work was to confirm the presence of CPV-2 in dogs with acute gastroenteritis compatible with parvovirus and to molecularly characterize the antigenic variants circulating in two regions of Colombia. An analytical cross-sectional study was conducted with fecal samples collected from 71 dogs showing signs of acute diarrhea. The samples were processed and polymerase chain reaction (PCR), restriction fragment length polymorphism analysis (RFLP), sequencing and phylogenetic analysis was performed to detect and characterize CPV. A total of 70.42% of the individuals were confirmed positive for CPV-2. Statistically differences were found in the presentation of CPV-2 between the evaluated regions. Phylogenetic analyses confirmed the presence of the antigenic variants CPV-2a/2b. Moreover, we found the presence of two conserved substitutions Asn428Asp and Ala514Ser in the VP2 protein suggesting the presence of a possible new CPV-2a variant circulating in Colombia. This study demonstrates the importance of the CPV 2a/2b in the region and highlights the importance of performing molecular studies for the early detection of new antigenic variants of CPV-2.

Virus mutations and their impact on vaccination against infectious bursal disease (Gumboro disease). / Les mutations virales et leur impact sur la vaccination contre la bursite infectieuse (maladie de Gumboro).

Infectious bursal disease (also known as Gumboro disease) is an immunosuppressive viral disease specific to chickens. In spite of all the information amassed on the antigenic and immunological characteristics of the virus, the disease has not yet been brought fully under control. It is still prevalent in properly vaccinated flocks carrying specific antibodies at levels normally high enough to prevent the disease. Common causes apart, failure of vaccination against infectious bursal disease is associated mainly with early vaccination in flocks of unknown immune status and with the evolution of viruses circulating in the field, leading to antigenic drift and a sharp rise in pathogenicity. Various highly sensitive molecular techniques have clarified the viral determinants of antigenicity and pathogenicity of the infectious bursal disease virus. However, these markers are not universally recognised and tend to be considered as evolutionary markers. Antigenic variants of the infectious bursal disease virus possess modified neutralising epitopes that allow them to evade the action of maternally-derived or vaccine-induced antibodies. Autogenous or multivalent vaccines are required to control antigenic variants in areas where classical and variant virus strains coexist. Pathotypic variants (very virulent viruses) remain antigenically related to classical viruses. The difficulty in controlling pathotypic variants is linked to the difficulty of eliciting an early immune response, because of the risk of the vaccine virus being neutralised by maternal antibodies. Mathematical calculation of the optimal vaccination time and the use of vaccines resistant to maternally-derived antibodies have improved the control of very virulent viruses.

La bursite infectieuse (maladie de Gumboro) est une pathologie virale immunodépressive spécifique du poulet. En dépit des informations accumulées sur les caractères antigéniques et immunologiques du virus, la maladie reste imparfaitement contrôlée. Elle sévit aujourd'hui dans des cheptels correctement vaccinés et porteurs d'anticorps spécifiques à des niveaux habituellement suffisants pour prévenir la maladie. Au-delà des causes triviales, les échecs de la vaccination contre la maladie de Gumboro sont essentiellement liés aux vaccinations précoces de cheptels au statut immunitaire inconnu et à l'évolution des virus qui circulent sur le terrain, se traduisant par une dérive antigénique et une hausse sensible de la pathogénicité. Diverses techniques moléculaires hautement sensibles ont permis d'identifier les déterminants viraux d'antigénicité et de pathogénicité du virus. Ces marqueurs ne sont cependant pas unanimement reconnus et sont pour la plupart considérés comme des marqueurs évolutionnaires. Les virus variants antigéniques possèdent des épitopes neutralisants modifiés qui leur permettent de se soustraire à l'action des anticorps résiduels ou vaccinaux. Leur contrôle passe par l'utilisation d'autovaccins ou de vaccins multivalents dans les régions où coexistent virus classiques et variants. Les variants pathotypiques (virus hypervirulents) restent antigéniquement apparentés aux virus classiques. La difficulté de contrôler ce type de variant est liée à celle d'obtenir une réponse immune précoce, en raison du risque de neutralisation du virus vaccinal par les anticorps d'origine maternelle. Le calcul mathématique de la date optimale de vaccination et l'utilisation de vaccins insensibles aux anticorps résiduels ont permis un meilleur contrôle des virus hypervirulents.

La bursitis infecciosa (enfermedad de Gumboro) es una patología viral específica del pollo, en el que provoca inmunodeficiencia. Pese al acervo de datos existentes sobre los caracteres antigénicos e inmunológicos del virus, la enfermedad no está aún del todo controlada. Hoy en día afecta a bandadas que están correctamente vacunadas y presentan niveles de anticuerpos específicos que en general son suficientes para prevenir la enfermedad. Más allá de las causas corrientes, el fracaso de las vacunaciones contra la enfermedad de Gumboro tiene que ver esencialmente con la vacunación precoz de bandadas cuyo estado inmunológico se desconoce y con la evolución de los virus circulantes sobre el terreno, que se traduce en una deriva antigénica y un sensible aumento de la patogenicidad. Gracias a diversas técnicas moleculares de gran sensibilidad se han podido discernir los determinantes de antigenicidad y patogenicidad del virus, aunque se trata de marcadores no reconocidos unánimemente y considerados en su mayor parte marcadores evolutivos. Los virus que representan variantes antigénicas poseen epitopos neutralizantes modificados que les permiten escapar a la acción de los anticuerpos residuales o inducidos por vacunación. Para combatirlos es preciso utilizar autovacunas o vacunas polivalentes allí donde coexisten los virus clásicos y las variantes. Las variantes patotípicas (virus hipervirulentos) no dejan de estar emparentadas antigénicamente con los virus clásicos. La dificultad de luchar contra este tipo de variante está ligada a la de obtener una respuesta inmunitaria precoz, en razón del riesgo de neutralización del virus vacunal por acción de los anticuerpos de origen materno. El cálculo matemático de la fecha idónea de vacunación y el uso de vacunas insensibles a los anticuerpos residuales han permitido luchar más eficazmente contra los virus hipervirulentos.

Detection of influenza antigenic variants directly from clinical samples using polyclonal antibody based proximity ligation assays.

Identification of antigenic variants is the key to a successful influenza vaccination program. The empirical serological methods to determine influenza antigenic properties require viral propagation. Here a novel quantitative PCR-based antigenic characterization method using polyclonal antibody and proximity ligation assays, or so-called polyPLA, was developed and validated. This method can detect a viral titer that is less than 1000 TCID50/mL. Not only can this method differentiate between different HA subtypes of influenza viruses but also effectively identify antigenic drift events within the same HA subtype of influenza viruses. Applications in H3N2 seasonal influenza data showed that the results from this novel method are consistent with those from the conventional serological assays. This method is not limited to the detection of antigenic variants in influenza but also other pathogens. It has the potential to be applied through a large-scale platform in disease surveillance requiring minimal biosafety and directly using clinical samples.

Complete genome sequence of a clinical Bordetella pertussis isolate from Brazil

There has been a resurgence in the number of pertussis cases in Brazil and around the world. Here, the genome of a clinical Bordetella pertussis strain (Bz181) that was recently isolated in Brazil is reported. Analysis of the virulence-associated genes defining the pre- and post-vaccination lineages revealed the presence of the prn2-ptxS1A-fim3B-ptxP3 allelic profile in Bz181, which is characteristic of the current pandemic lineage. A putative metallo-β-lactamase gene presenting all of the conserved zinc-binding motifs that characterise the catalytic site was identified, in addition to a multidrug efflux pump of the RND family that could confer resistance to erythromycin, which is the antibiotic of choice for treating pertussis disease.

Using multiple linear regression and physicochemical changes of amino acid mutations to predict antigenic variants of influenza A/H3N2 viruses.

Among human influenza viruses, strain A/H3N2 accounts for over a quarter of a million deaths annually. Antigenic variants of these viruses often render current vaccinations ineffective and lead to repeated infections. In this study, a computational model was developed to predict antigenic variants of the A/H3N2 strain. First, 18 critical antigenic amino acids in the hemagglutinin (HA) protein were recognized using a scoring method combining phi (ϕ) coefficient and information entropy. Next, a prediction model was developed by integrating multiple linear regression method with eight types of physicochemical changes in critical amino acid positions. When compared to other three known models, our prediction model achieved the best performance not only on the training dataset but also on the commonly-used testing dataset composed of 31878 antigenic relationships of the H3N2 influenza virus.

Prostate cancer biomarker annexin A3 detected in urines obtained following digital rectal examination presents antigenic variability.

OBJECTIVES: Annexin A3 (ANXA3) is a potential marker for prostate cancer (PCa). We aimed to develop robust immunoassays suitable for quantifying ANXA3 in urine samples obtained following digital rectal examination (DRE) in order to facilitate the diagnostic performance evaluation of this marker. DESIGN AND METHODS: Anti-ANXA3 monoclonal antibodies were generated and their epitopes mapped. Two different ANXA3 assay prototypes were established on the VIDAS® automated immunoanalyser and analytical validation was carried out using post-DRE urine samples obtained from patients with PCa (n=23) or benign prostate hyperplasia (n=31). RESULTS: The assays had the same capture antibody (TGC44) but different detection antibodies (13A12 or 5C5), recognizing novel distinct epitopes. Both had a lower limit of quantification <1ng/mL and were highly specific for ANXA3, not cross-reacting with other annexins. Interassay imprecision was ≤11% and ≤15% for 13A12 and 5C5 assays, respectively. Surprisingly, a total lack of correlation was observed between ANXA3 levels measured by these two assays in post-DRE urines, indicating detection of distinct antigenic variants. Two freeze-thaw cycles did not affect analyte stability in either assay, whereas a lack of stability of antigenic variants was observed when samples were stored at -80°C for 1month. CONCLUSIONS: Two different antigenic variants of ANXA3 are present in post-DRE urines and their clinical significance for diagnosis of prostate cancer should be further investigated. These variants are not stable over time in samples preserved at -80°C. Until this issue is resolved, ANXA3 should only be measured in freshly collected samples.

Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses.

Two distinct antigenic clusters were previously identified among the H3N2 swine influenza A viruses (IAVs) and were designated H3N2SIV-alpha and H3N2SIV-beta (Feng et al., 2013. Journal of Virology 87 (13), 7655-7667). A consistent mutation was observed at the position 189 of hemagglutinin (R189K) between H3N2SIV-alpha and H3N2SIV-beta fair isolates. To evaluate the contribution of R189K mutation to the antigenic drift from H3N2SIV-alpha to H3N2SIV-beta, four reassortant viruses with 189R or 189K were generated. The antigenic cartography demonstrated that the R189K mutation in the hemagglutinin of H3N2 IAV contributed to the antigenic drift, separating these viruses into H3N2SIV-alpha to H3N2SIV-beta. This R189K mutation was also found to contribute to the cross-reaction with several ferret sera raised against historical human IAVs with hemagglutinin carrying 189K. This study suggests that the R189K mutation plays a vital role in the antigenicity of swine and human H3N2 IAVs and identification of this antigenic determinant will help us rapidly identify antigenic variants in influenza surveillance.

Rabia en Chile: 1989-2005 / Rabies in Chile: 1989-2005

A retrospective epidemiological study about epidemiology of rabies in Chile between years 1989 and 2005 was done. A data base of 39793 national registries of rabies samples was analyzed by means of statistical packages. Out of 39793 analyzed cases, 719 bats, 7 dogs, 7 cats, 1 bovine and 1 human were positive to rabies throughout the 17 years of this study. The statistical analysis established a significant increase in the proportions of positivity in bats, with predominance of variant 4 between the reservoirs. Given the complexity of the wild cycle of the rabies in Chile, it is necessary to maintain a program control of rabies, directed to educate people for a responsible possession of domestic animals, due to the risk of rabies transmission from bat to the susceptible species.

Se realizó este estudio para actualizar el conocimiento epidemiológico de la rabia en Chile, entre los años 1989 y 2005. Se trabajó con una base de datos de 39.793 registros históricos nacionales de muestras para el diagnóstico de rabia que mantiene el Instituto de Salud Pública de Chile, analizando los datos mediante paquetes estadísticos. De los 39.793 casos analizados se detectaron positivos a rabia en murciélagos (n: 719), perros (n: 7), gatos (n: 7), bovino (n: 1) y humano (n:l) a lo largo de los 17 años de estudio; estos representan el total de casos confirmados en Chile durante ese período. El análisis estadístico determinó un aumento lento pero significativo de positividad a rabia en murciélagos con un predominio de la variante 4 entre los reservónos circulantes. Dada la complejidad del ciclo silvestre de la rabia en Chile, es necesario mantener un programa de control de rabia dirigido a la educación de la población en pro de la tenencia responsable de los animales domésticos; existe riesgo de transmisión de la rabia desde murciélago a las especies susceptibles.