Virus Evolution最新文献

{"title":"Major change in swine influenza virus diversity in France owing to emergence and widespread dissemination of a newly introduced H1N2 1C genotype in 2020.","authors":"Gautier Richard, Séverine Hervé, Amélie Chastagner, Stéphane Quéguiner, Véronique Beven, Edouard Hirchaud, Nicolas Barbier, Stéphane Gorin, Yannick Blanchard, Gaëlle Simon","doi":"10.1093/ve/veae112","DOIUrl":"10.1093/ve/veae112","url":null,"abstract":"<p><p>Swine influenza A viruses (swIAVs) are a major cause of respiratory disease in pigs worldwide, presenting significant economic and health risks. These viruses can reassort, creating new strains with varying pathogenicity and cross-species transmissibility. This study aimed to monitor the genetic and antigenic evolution of swIAV in France from 2019 to 2022. Molecular subtyping revealed a marked increase in H1_avN2 cases from 2020 onwards, altering the previously stable subtypes' distribution. Whole-genome sequencing and phylogenetic analyses of H1_av (1C) strains identified 10 circulating genotypes, including 5 new genotypes. The most predominant genotype from 2020 onwards, denominated H1_avN2#E, was characterized by an HA-1C.2.4, an N2-Gent/84, and internal protein-encoding genes belonging to a newly defined subclade within the Eurasian avian-like (EA) lineage termed EA-DK. H1_avN2#E emerged in Brittany, the country's most pig-dense region, and rapidly became the most frequently detected swIAV genotype across France. This drastic change in the swIAV lineage proportions at a national scale was unprecedented, making H1_avN2#E a unique case for understanding swIAV evolution and spreading patterns. Phylogenetic analyses suggested an introduction of the H1_avN2#E genotype from a restricted source, likely originating from Denmark. It spread rapidly with low genetic diversity at the start of the epizootic in 2020, showing increasing diversification in 2021 and 2022 as the inferred population size grew and stabilized, and exhibited reassortments with other enzootic genotypes. Amino acid sequence alignments of H1_avN2#E antigenic sites revealed major mutations and deletions compared to commercial vaccine 1C strain (HA-1C.2.2) and previously predominant H1_avN1 strains (HA-1C.2.1). Antigenic cartography confirmed significant antigenic distances between H1_avN2#E and other 1C strains, suggesting that the new genotype has escaped the pre-existing immunity of the swine population. Epidemiologically, the H1_avN2#E virus exhibited epizootic hallmarks with more severe clinical outcomes compared to H1_avN1 viruses. These factors likely contributed to the spread of H1_avN2#E within the pig population. The rapid rise of H1_avN2#E highlighted the dynamic nature of swIAV genetic and antigenic diversity, underscoring the importance of tailored surveillance programs to support risk assessment during potential new outbreaks. It also demonstrates the need to strengthen biosecurity measures when introducing pigs into a herd, including swIAV positivity assessment followed by quarantine, and restrict the trade of swIAV-excreting live swine between European countries.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veae112"},"PeriodicalIF":5.5,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Increase of niche filling with increase of host richness for plant-infecting mastreviruses.","authors":"Sélim Ben Chéhida, Heemee Devi Bunwaree, Murielle Hoareau, Oumaima Moubset, Charlotte Julian, Laurence Blondin, Denis Filloux, Christophe Lavergne, Philippe Roumagnac, Arvind Varsani, Darren P Martin, Jean-Michel Lett, Pierre Lefeuvre","doi":"10.1093/ve/veae107","DOIUrl":"10.1093/ve/veae107","url":null,"abstract":"<p><p>Now that it has been realized that viruses are ubiquitous, questions have been raised on factors influencing their diversity and distribution. For phytoviruses, understanding the interplay between plant diversity and virus species richness and prevalence remains cardinal. As both the amplification and the dilution of viral species richness due to increasing host diversity have been theorized and observed, a deeper understanding of how plants and viruses interact in natural environments is needed to explore how host availability conditions viral diversity and distributions. From a unique dataset, this study explores interactions of <i>Mastrevirus</i> species (family <i>Geminiviridae</i>) with Poales order hosts across 10 sites from three contrasting ecosystems on La Réunion. Among 273 plant pools, representing 61 Poales species, 15 <i>Mastrevirus</i> species were characterized from 22 hosts. The analysis revealed a strong association of mastreviruses with hosts from agroecosystems, the rare presence of viruses in coastal grasslands, and the absence of mastreviruses in subalpine areas, areas dominated by native plants. This suggests that detected mastreviruses were introduced through anthropogenic activities, emphasizing the role of humans in shaping the global pathobiome. By reconstructing the realized host-virus infection network, besides revealing a pattern of increasing viral richness with increasing host richness, we observed increasing viral niche occupancies with increasing host species richness, implying that virus realized richness at any given site is conditioned on the global capacity of the plant populations to host diverse mastreviruses. Whether this tendency is driven by synergy between viruses or by an interplay between vector population and plant richness remains to be established.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae107"},"PeriodicalIF":5.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On modes of disease transmission and the hidden shape of pandemics: A review of <i>Asymptomatic</i> by Joshua Weitz.","authors":"C Brandon Ogbunugafor","doi":"10.1093/ve/veae109","DOIUrl":"10.1093/ve/veae109","url":null,"abstract":"<p><p>The importance of asymptomatic transmission was a key discovery in our efforts to study and intervene in the COVID-19 pandemic. In <i>Asymptomatic</i> (Johns Hopkins University Press, 2024), Joshua Weitz uses this aspect of SARS-CoV-2 natural history to discuss many counterintuitive characteristics of the pandemic. In this essay, I engage the arguments in the book, and discuss why asymptomatic transmission is such a critical dimension of the study of infectious diseases. I explore ideas contained within <i>Asymptomatic</i> and connect them to related issues in evolutionary virology and disease ecology, including epistemic uncertainty and the evolution of virulence. Furthermore, I comment on the broader messages in the text, including the gap between scientific knowledge and social understanding.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae109"},"PeriodicalIF":5.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HIV-1 Vif global diversity and possible APOBEC-mediated response since 1980.","authors":"Eric Lewitus, Yifan Li, Morgane Rolland","doi":"10.1093/ve/veae108","DOIUrl":"10.1093/ve/veae108","url":null,"abstract":"<p><p>HIV-1 Vif's principal function is to counter the antiretroviral activities of DNA-editing APOBEC3 cytidine deaminases. Unconstrained APOBEC3 activity introduces premature stop codons in HIV-1 genes and can lead to viral inactivation. To investigate the evolution and diversification of Vif over the HIV-1 pandemic and document evidence of APOBEC3-mediated pressure, we analyzed 4612 publicly available sequences derived from 10 dominant subtypes and circulating recombinant forms (CRFs) using the Hervé platform. We found widespread evidence of diversifying selection that was convergent across subtypes and CRFs, but remarkable stability in consensus sequences over time. Divergence and selection did not favor APOBEC3-interacting sites. We furthermore found that APOBEC3-induced substitutions in <i>env</i> and <i>gag-pol</i> genes increased over time and were positively associated with <i>vif</i> diversity. These results suggest that APOBEC3-driven adaptation in Vif is relatively rare and that permissiveness to human APOBEC3-induced substitution as a mechanism for generating diversity may be advantageous to HIV-1 evolution.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veae108"},"PeriodicalIF":5.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Origin, spread, and interspecies transmission of a dominant genotype of BJ/94 lineage H9N2 avian influenza viruses with increased threat.","authors":"Yong Zhou, Yudong Li, Hongzhuang Chen, Sicheng Shu, Zhixin Li, Honglei Sun, Yipeng Sun, Jinhua Liu, Lu Lu, Juan Pu","doi":"10.1093/ve/veae106","DOIUrl":"10.1093/ve/veae106","url":null,"abstract":"<p><p>The H9N2 subtype of avian influenza viruses (AIVs) is widely prevalent in poultry and wild birds globally, with occasional transmission to humans. In comparison to other H9N2 lineages, the BJ/94 lineage has raised more public health concerns; however, its evolutionary dynamics and transmission patterns remain poorly understood. In this study, we demonstrate that over three decades (1994-2023), BJ/94 lineage has undergone substantial expansion in its geographical distribution, interspecies transmission, and viral reassortment with other AIV subtypes, increasing associated public health risks. These changes were primarily driven by the emergence of a dominant genotype G57. In the first decade, G57 emerged in East China and rapidly adapted to chickens and spread across China. Since 2013, the G57 genotype has expanded beyond China into eight other countries and reassorted with various AIV subtypes to form new zoonotic reassortants. Chickens have played a key role in the generation and circulation of the G57 viruses, with ducks and other poultry species likely assuming an increasingly importantly role. Over the past decade, G57 has been more frequently detected in wild birds, mammals, and humans. Additionally, Vietnam has emerged as a new hotspot for the international spread of G57. Our results suggest that the BJ/94 lineage H9N2 virus may continue to overcome geographical and species barriers, with potentially more severe consequences.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae106"},"PeriodicalIF":5.5,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11673197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A meta-analysis highlights the idiosyncratic nature of tradeoffs in laboratory models of virus evolution.","authors":"Ketty Kabengele, Wendy C Turner, Paul E Turner, C Brandon Ogbunugafor","doi":"10.1093/ve/veae105","DOIUrl":"10.1093/ve/veae105","url":null,"abstract":"<p><p>Different theoretical frameworks have been invoked to guide the study of virus evolution. Three of the more prominent ones are (i) the evolution of virulence, (ii) life history theory, and (iii) the generalism-specialism dichotomy. All involve purported tradeoffs between traits that define the evolvability and constraint of virus-associated phenotypes. However, as popular as these frameworks are, there is a surprising paucity of direct laboratory tests of the frameworks that support their utility as broadly applicable theoretical pillars that can guide our understanding of disease evolution. In this study, we conduct a meta-analysis of direct experimental evidence for these three frameworks across several widely studied virus-host systems: plant viruses, fungal viruses, animal viruses, and bacteriophages. We extracted 60 datasets from 28 studies and found a range of relationships between traits in different analysis categories (e.g., frameworks, virus-host systems). Our work demonstrates that direct evidence for relationships between traits is highly idiosyncratic and specific to the host-virus system and theoretical framework. Consequently, scientists researching viral pathogens from different taxonomic groups might reconsider their allegiance to these canons as the basis for expectation, explanation, or prediction. Future efforts could benefit from consistent definitions, and from developing frameworks that are compatible with the evidence and apply to particular biological and ecological contexts.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae105"},"PeriodicalIF":5.5,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics.","authors":"Adriana Lucia-Sanz, Shengyun Peng, Chung Yin Joey Leung, Animesh Gupta, Justin R Meyer, Joshua S Weitz","doi":"10.1093/ve/veae104","DOIUrl":"10.1093/ve/veae104","url":null,"abstract":"<p><p>The enormous diversity of bacteriophages and their bacterial hosts presents a significant challenge to predict which phages infect a focal set of bacteria. Infection is largely determined by complementary-and largely uncharacterized-genetics of adsorption, injection, cell take-over, and lysis. Here we present a machine learning approach to predict phage-bacteria interactions trained on genome sequences of and phenotypic interactions among 51 <i>Escherichia coli</i> strains and 45 phage λ strains that coevolved in laboratory conditions for 37 days. Leveraging multiple inference strategies and without <i>a priori</i> knowledge of driver mutations, this framework predicts both who infects whom and the quantitative levels of infections across a suite of 2,295 potential interactions. We found that the most effective approach inferred interaction phenotypes from independent contributions from phage and bacteria mutations, accurately predicting 86% of interactions while reducing the relative error in the estimated strength of the infection phenotype by 40%. Feature selection revealed key phage λ and <i>Escherchia coli</i> mutations that have a significant influence on the outcome of phage-bacteria interactions, corroborating sites previously known to affect phage λ infections, as well as identifying mutations in genes of unknown function not previously shown to influence bacterial resistance. The method's success in recapitulating strain-level infection outcomes arising during coevolutionary dynamics may also help inform generalized approaches for imputing genetic drivers of interaction phenotypes in complex communities of phage and bacteria.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae104"},"PeriodicalIF":5.5,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11666707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing.","authors":"Carla Julia S P Vieira, Michael B Onn, Martin A Shivas, Damien Shearman, Jonathan M Darbro, Melissa Graham, Lucas Freitas, Andrew F van den Hurk, Francesca D Frentiu, Gabriel L Wallau, Gregor J Devine","doi":"10.1093/ve/veae103","DOIUrl":"10.1093/ve/veae103","url":null,"abstract":"<p><p>Arbovirus surveillance of wild-caught mosquitoes is an affordable and sensitive means of monitoring virus transmission dynamics at various spatial-temporal scales, and emergence and re-emergence during epidemic and interepidemic periods. A variety of molecular diagnostics for arbovirus screening of mosquitoes (known as xeno-monitoring) are available, but most provide limited information about virus diversity. Polymerase chain reaction (PCR)-based screening coupled with RNA sequencing is an increasingly affordable and sensitive pipeline for integrating complete viral genome sequencing into surveillance programs. This enables large-scale, high-throughput arbovirus screening from diverse samples. We collected mosquitoes in CO₂-baited light traps from five urban parks in Brisbane from March 2021 to May 2022. Mosquito pools of ≤200 specimens were screened for alphaviruses and flaviviruses using virus genus-specific primers and reverse transcription quantitative PCR (qRT-PCR). A subset of virus-positive samples was then processed using a mosquito-specific ribosomal RNA depletion method and then sequenced on the Illumina NextSeq. Overall, 54,670 mosquitoes representing 26 species were screened in 382 pools. Thirty detections of arboviruses were made in 28 pools. Twenty of these positive pools were further characterized using RNA sequencing generating 18 full-length genomes. These full-length sequences belonged to four medically relevant arboviruses: Barmah Forest, Ross River, Sindbis-like, and Stratford viruses. Phylogenetic and evolutionary analyses revealed the evolutionary progression of arbovirus lineages over the last 100 years, demonstrating that different epidemiological, immunological, and evolutionary processes may actively shape the evolution of Australian arboviruses. These results underscore the need for more genomic surveillance data to explore the complex evolutionary pressures acting on arboviruses. Overall, our findings highlight the effectiveness of our methodology, which can be applied broadly to enhance arbovirus surveillance in various ecological contexts and improve understanding of transmission dynamics.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"0"},"PeriodicalIF":5.5,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11646120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142831031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endogenous viral elements: insights into data availability and accessibility.","authors":"Muriel Ritsch, Nadja Brait, Erin Harvey, Manja Marz, Sebastian Lequime","doi":"10.1093/ve/veae099","DOIUrl":"10.1093/ve/veae099","url":null,"abstract":"<p><p>Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR ('findable, accessible, interoperable, and reusable') principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"10 1","pages":"veae099"},"PeriodicalIF":5.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive molecular epidemiology of influenza viruses in Brazil: insights from a nationwide analysis.","authors":"Isabela Carvalho Brcko, Vinicius Carius de Souza, Gabriela Ribeiro, Alex Ranieri Jeronimo Lima, Antonio Jorge Martins, Claudia Renata Dos Santos Barros, Eneas de Carvalho, James Siqueira Pereira, Loyze Paola Oliveira de Lima, Vincent Louis Viala, Simone Kashima, Debora Glenda Lima de La Roque, Elaine Vieira Santos, Evandra Strazza Rodrigues, Juliana Almeida Nunes, Leandro Spalato Torres, Luiz Artur Vieira Caldeira, Melissa Palmieri, Caio Genovez Medina, Raphael Augusto de Arruda, Renata Beividas Lopes, Geraldo Reple Sobrinho, Daniel Macedo de Melo Jorge, Eurico Arruda, Eladja Christina Bezerra da Silva Mendes, Hazerral de Oliveira Santos, Arabela Leal E Silva de Mello, Felicidade Mota Pereira, Marcela Kelly Astete Gómez, Vanessa Brandão Nardy, Brenno Henrique, Lucas Luiz Vieira, Mariana Matos Roll, Elaine Cristina de Oliveira, Júlia Deffune Profeta Cidin Almeida, Stephanni Figueiredo da Silva, Gleissy Adriane Lima Borges, Katia Cristina de Lima Furtado, Patricia Miriam Sayuri Sato Barros da Costa, Shirley Moreira da Silva Chagas, Esper G Kallás, Daniel Larh, Marta Giovanetti, Svetoslav Nanev Slavov, Sandra Coccuzzo Sampaio, Maria Carolina Elias","doi":"10.1093/ve/veae102","DOIUrl":"10.1093/ve/veae102","url":null,"abstract":"<p><p>Influenza A and B viruses represent significant global health threats, contributing substantially to morbidity and mortality rates. However, a comprehensive understanding of the molecular epidemiology of these viruses in Brazil, a continental-size country and a crucial hub for the entry, circulation, and dissemination of influenza viruses within South America, still needs to be improved. This study addresses this gap by consolidating data and samples across all Brazilian macroregions, as part of the Center for Viral Surveillance and Serological Assessment project, together with an extensive number of other Brazilian sequences provided by a public database during the epidemic seasons spanning 2021-23. Phylogenetic analysis of the hemagglutinin segment of influenza A/H1N1pdm09, A/H3N2, and influenza B/Victoria-lineage viruses revealed that in 2021 and in the first semester of 2022, the A/H3N2 2a.3 strain was the predominant circulating strain. Subsequently, the A/H3N2 2b became the prevalent strain until October, when it was substituted by A/H1N1pdm09 5a.2a and 5a.2a.1 lineages. This scenario was maintained during the year of 2023. B/Victoria emerged and circulated at low levels between December 2021 and September 2022 and then became coprevalent with A/H1N1pdm09 5a.2a and 5a.2a.1 lineages. The comparison between the vaccine strain A/Darwin/9/2021 and circulating viruses revealed shared mutations to aspartic acid at residues 186 and 225 across all A/H3N2 lineages from 2021 to 2023, altering the charge in the receptor-binding domain. For A/H1N1pdm09, the 2022 consensus of 5a.2a.1 and the vaccine strain A/Victoria/2570/2019 showed 14 amino acid substitutions. Key residues H180, D187, K219, R223, E224, and T133 are involved in hydrogen interactions with sialic acids, while N130, K142, and D222 may contribute to distance interactions based on docking analyses. Importantly, distinct influenza A lineage frequency patterns were observed across Brazil's macroregions, underscoring the regional variations in virus circulation. This study characterizes influenza A and B viruses circulating in Brazil, providing insights into their circulation patterns and dynamics across Brazilian macroregions. These findings hold significant implications for public health interventions, informing strategies to mitigate transmission risks, optimize vaccination efforts, and enhance outbreak control measures.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"11 1","pages":"veae102"},"PeriodicalIF":5.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11711486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}