Virus research最新文献

{"title":"Infectivity in full-term placenta of Zika viruses with different lipid profiles","authors":"Eva Mazzetto ,&nbsp;Alessio Bortolami ,&nbsp;Davide Bovo ,&nbsp;Matteo Stocchero ,&nbsp;Elisa Mazzacan ,&nbsp;Alessandra Napolitan ,&nbsp;Valentina Panzarin ,&nbsp;Maria Rosa Tran ,&nbsp;Gianpiero Zamperin ,&nbsp;Adelaide Milani ,&nbsp;Andrea Fortin ,&nbsp;Michela Bigolaro ,&nbsp;Paola Pirillo ,&nbsp;Matteo Pagliari ,&nbsp;Claudia Zanardello ,&nbsp;Giuseppe Giordano ,&nbsp;Maria Teresa Gervasi ,&nbsp;Eugenio Baraldi ,&nbsp;Calogero Terregino ,&nbsp;Carlo Giaquinto ,&nbsp;Francesco Bonfante","doi":"10.1016/j.virusres.2024.199518","DOIUrl":"10.1016/j.virusres.2024.199518","url":null,"abstract":"<div><div>Among flaviviruses, Zika virus (ZIKV) is the only arbovirus officially recognized as a teratogenic agent, as a consequence of its ability to infect and cross the placental barrier causing congenital malformation in the fetus. While many studies have focused on understanding ZIKV pathogenesis during pregnancy, the viral mechanisms affecting fetal development remain largely unclear. In this study, we investigated ZIKV virulence in placental trophoblasts, using viruses with distinct lipid profiles. Firstly, we propagated a ZIKV strain belonging to the Asian lineage in either mammalian or mosquito cells, obtaining two viral stocks, which were purified and analyzed to determine their genetic and lipid composition. Successively, we assessed the infectivity of the two stocks in placental cells using both immortalized cell lines and explants. We found that the two viral stocks displayed identical consensus sequences with homogeneous quasispecies composition. However, the lipid composition of their envelope significantly varied depending on the cell of origin, with the mammalian-derived viral stock characterized by a higher content of phosphatidylcholines compared to the virions originating from mosquito cells. Notably, ZIKV stock derived from mammalian cells showed a higher infectivity in immortalized villous trophoblasts and full-term placental explants of human origin. This increased infectivity was linked to enhanced fusion efficiency during the viral uncoating phase in trophoblast cells, as demonstrated using a lipophilic probe. Collectively, our data suggest a potential role of viral lipids as determinants of ZIKV infectivity in full-term placenta, underscoring the importance of lipidomic research in virology.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"352 ","pages":"Article 199518"},"PeriodicalIF":2.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142903617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomics-based investigation of resistance differences to swine fever between large white pigs and min pigs","authors":"Jia Li ,&nbsp;Deming Ren ,&nbsp;Xiangxu Meng ,&nbsp;Yiyun He ,&nbsp;Lixian Wang ,&nbsp;Xihui Sheng ,&nbsp;Ligang Wang","doi":"10.1016/j.virusres.2025.199536","DOIUrl":"10.1016/j.virusres.2025.199536","url":null,"abstract":"<div><div>The genetic foundations underlying the observed disease resistance in certain indigenous pig breeds, notably the Min pigs of China, present a compelling underexplored subject of study. Exploring the mechanisms of disease resistance in these breeds could lay the groundwork for genetic improvements in pig immunity, potentially augmenting overall pig productivity. In this study, whole blood samples were collected from pre- and post- swine fever vaccinated Min and Large White pigs for transcriptome sequencing. The mRNA and lncRNA in both pig breeds were analyzed, and intra-group and inter-group comparisons were also conducted. The results indicated that a greater number of immune-related pathways such as the JAK-STAT and PI3K-AKT signaling were enriched in Min pigs. Furthermore, genes involved in inflammation and antiviral responses, including IL16, IL27, USP18, and DHX58, were upregulated in post-vaccination Min pigs compared to post-vaccination Large White pigs. This heightened immune responsiveness could contribute to the observed differences in disease resistance between Min pigs and Large White pigs.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199536"},"PeriodicalIF":2.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143060869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging the gap: Phage manufacturing processes from laboratory to agri-food industry","authors":"Elham Mohammadi ,&nbsp;Mohammadreza Rahimian ,&nbsp;Bahman Panahi","doi":"10.1016/j.virusres.2025.199537","DOIUrl":"10.1016/j.virusres.2025.199537","url":null,"abstract":"<div><div>Interest in bacteriophages (phages) as sustainable biocontrol agents in the agri-food industry has increased because of growing worries about food safety and antimicrobial resistance (AMR). The phage manufacturing process is examined in this review, with particular attention paid to the crucial upstream and downstream processes needed for large-scale production. Achieving large phage yields requires upstream procedures, including fermentation and phage amplification. In the meantime, downstream procedures, including purification, endotoxin removal, and formulation, is essential for guaranteeing product quality and regulatory compliance. Despite advances in upstream and downstream process optimization of phage production processes, these methods are not effectively utilized in manufacturing processes. Additionally, the commercialization of phage products is hindered by fragmented rules and inconsistent regulations. Emerging technologies such as enhanced chromatography, continuous processing, and encapsulating techniques provide prospects for increased stability, efficiency, and scalability to fill these gaps. Furthermore, by facilitating real-time process optimization, predictive quality control (QC), and unique phage product creation, the integration of artificial intelligence (AI) and machine learning has the potential to transform the phage manufacturing industry completely. In order to provide consistent standards, encourage innovation, and bridge the gap between academic research and commercial applications, this review identifies gaps and highlights the necessity of cooperation between academia, industry, and regulatory agencies. To effectively utilize phages' potential to improve food safety, fight AMR, and promote sustainable agricultural practices, the agri-food industry must advance phage manufacturing techniques and harmonize regulatory frameworks.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199537"},"PeriodicalIF":2.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143068312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic evolution of SARS-CoV-2 in Morocco: Insights from whole genome sequences collected from 2020 to 2024","authors":"Hamza GHAMMAZ ,&nbsp;Marouane MELLOUL ,&nbsp;Ahlam MBARKI ,&nbsp;Mouhssine HEMLALI ,&nbsp;Taha CHOUATI ,&nbsp;Hicham EL ANNAZ ,&nbsp;Nadia TOUIL ,&nbsp;Mostafa ELOUENNASS ,&nbsp;Khalid ENNIBI ,&nbsp;Elmostafa EL FAHIME","doi":"10.1016/j.virusres.2025.199530","DOIUrl":"10.1016/j.virusres.2025.199530","url":null,"abstract":"<div><div>This study investigates the evolution and genetic diversity of SARS-CoV-2 strains circulating in Morocco to track the spread, clade distributions and mutations of the virus across various regions from February 2020 to June 2024. The genome sequences were retrieved from the GISAID database. A total of 2630 SARS-CoV-2 genome sequences were analyzed using bioinformatic tools such as Nextclade, followed by phylogenetic and statistical analyses. The study highlights the predominance of the GRA clade (Omicron variant) since November 2021, while clades such as G, GH, GR, and GRY were identified earlier. The GRA clade exhibited the highest number of non-synonymous mutations, particularly in the Spike (S) gene, suggesting strong evolutionary pressure. The correlation analysis between structural and non-structural proteins revealed key interactions between S and NSP5, providing insights into the viral replication and assembly processes. This work gives new insights to the dynamics of SARS-CoV-2 in Morocco and underscores the importance of ongoing genomic surveillance to respond to emerging variants and potential future outbreaks.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199530"},"PeriodicalIF":2.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A cell-penetrating bispecific antibody suppresses hepatitis B virus replication and secretion","authors":"Chongwei Xie ,&nbsp;Bing Zhou ,&nbsp;Da Yao ,&nbsp;Xin Wang ,&nbsp;Lihong Zhong ,&nbsp;Chuanghua Qiu ,&nbsp;Junfang Zhang","doi":"10.1016/j.virusres.2025.199531","DOIUrl":"10.1016/j.virusres.2025.199531","url":null,"abstract":"<div><div>Hepatitis B virus (HBV) represents one of the major pathogenic factor that leads to chronic liver diseases and the development of hepatocellular carcinoma (HCC). The currently approved anti-HBV drugs cannot eradicate the virus or block the development of HCC. HBV nucleocapsid consists of the hepatitis B core antigen (HBcAg) and the HBV relaxed-circular partially double-stranded DNA (rcDNA), indispensable in virus replication. The present study reported a cell-penetrating bispecific antibody targeting HBcAg and preS1, fused with the cell-penetrating peptide R9TAT, named Anti-preS1 × Anti-HBcAg-R9TAT. The antibody could recognize preS1 and HBcAg and internalize into living cells efficiently, suppressing the extracellular hepatitis B surface antigen (HBsAg) and hepatitis B envelope antigen, and the intracellular HBsAg and HBcAg <em>in vitro</em>. This cell-penetrating bispecific antibody is a novel approach to suppressing HBV replication and secretion and is a promising anti-HBV therapeutic antibody candidate.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199531"},"PeriodicalIF":2.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143041678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of feline caliciviruses isolated from several adult cats with atypical infection showing severe flu-like symptoms on a remote island in Ehime, Japan","authors":"Yuki Nishisaka ,&nbsp;Hikaru Fujii ,&nbsp;Fumiko Ono ,&nbsp;Sho Kadekaru ,&nbsp;Hiroyuki Kogiku ,&nbsp;Yumi Une ,&nbsp;Shione Takeguchi ,&nbsp;Naomi Ohta ,&nbsp;Masumi Eto ,&nbsp;Chiharu Takeuchi ,&nbsp;Seigou Takeuchi ,&nbsp;Tetsuko Miki ,&nbsp;Akihiko Tokuda ,&nbsp;Keiko Ookawa ,&nbsp;Yukinobu Tohya ,&nbsp;Keita Ishijima ,&nbsp;Akiko Okutani ,&nbsp;Ken Maeda ,&nbsp;Shumpei Watanabe ,&nbsp;Shigeru Morikawa","doi":"10.1016/j.virusres.2025.199535","DOIUrl":"10.1016/j.virusres.2025.199535","url":null,"abstract":"<div><div>In November 2020, a volunteer group reported an outbreak of an infectious disease with a high fatality rate and flu-like symptoms among stray cats in Aoshima, a remote island in Ehime, Japan. Nine adult cats with severe symptoms were hospitalized. Feline calicivirus (FCV) was isolated from pharyngeal swabs of six hospitalized cats. An outbreak of virulent systemic FCV (VS-FCV) infection was initially suspected because of obvious flu-like symptoms in adult cats; however, no symptoms typically associated with VS-FCV, such as skin ulcers on the limbs, edema, or viremia, were observed. Notably, two of the hospitalized cats that showed severe disease had diarrhea and anemia, and died or had a prolonged illness. These cases reveal atypical symptoms of FCV infection that have not been previously reported. We further isolated typical strains from western Japan (Osaka, Kumamoto, and Ehime) and analyzed the viral genes along with virulent strains from Aoshima. Phylogenetic analysis showed that the Aoshima strain formed a new lineage distinct from known FCVs. The Aoshima strains isolated in the initial outbreak before December 5, 2020, and those isolated after the end of the outbreak, which are suspected pathogenic and typical non-pathogenic strains, respectively, were located in the same cluster and shown to be very similar in sequence. The virulent Aoshima strain, which causes atypical FCV infections in cats, may have been derived by acquiring several mutations from a typical strain that chronically infects cats on a remote island.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199535"},"PeriodicalIF":2.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143068315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of synonymous codon usage bias of Lassa virus","authors":"Siddiq Ur Rahman ,&nbsp;Yikui Hu ,&nbsp;Hassan Ur Rehman ,&nbsp;May M. Alrashed ,&nbsp;Kotb A. Attia ,&nbsp;Ubaid Ullah ,&nbsp;Huiying Liang","doi":"10.1016/j.virusres.2025.199528","DOIUrl":"10.1016/j.virusres.2025.199528","url":null,"abstract":"<div><div>Lassa virus genome consists of two single-stranded, negative-sense RNA segments that lie in the genus <em>Arenavirus</em>. The disease associated with the Lassa virus is distributed all over the world, with approximately 3,000,000–5,000,000 infections diagnosed annually in West Africa. It shows high health risks to the human being. Previous research used the evolutionary time scale and adaptive evolution to describe the Lassa virus population pattern. However, it is still unclear how the Lassa virus takes advantage of synonymous codons. In this study, we analyzed the codon usage bias in 162 Lassa virus strains by calculating and comparing the nucleotide contents, effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and others. The results disclosed that LASV strains are rich in A/T. The average ENC value indicated a low codon usage bias in LASVs. The ENC-plot, neutrality plot and parity rule 2 plot demonstrated that, besides mutational pressure, other factors like natural selection also contributed to codon usage bias. This study is significant because it described the pattern of codon usage in the genomes of the Lassa viruses and provided the information needed for a fundamental evolutionary study of them.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199528"},"PeriodicalIF":2.5,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143012481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a water-dispersible antimicrobial lipid mixture to inhibit African swine fever virus and other enveloped viruses","authors":"Joshua A. Jackman ,&nbsp;Roza Izmailyan ,&nbsp;Rafayela Grigoryan ,&nbsp;Tun Naw Sut ,&nbsp;Abel Taye ,&nbsp;Hovakim Zakaryan ,&nbsp;Charles C. Elrod","doi":"10.1016/j.virusres.2024.199516","DOIUrl":"10.1016/j.virusres.2024.199516","url":null,"abstract":"<div><div>Medium-chain antimicrobial lipids are promising antiviral agents to inhibit membrane-enveloped viruses such as African swine fever virus (ASFV) and influenza A virus (IAV) in livestock applications. However, current uses are limited to feed pathogen mitigation due to low aqueous solubility and the development of water-dispersible lipid formulations is needed for broader application usage. In this study, we report a water-dispersible antimicrobial lipid mixture of monoglycerides and lactylates that can inhibit ASFV and IAV and exhibits antiviral properties in drinking water and feed matrices. The lipid mixture reduced the viral infectivity of membrane-enveloped ASFV and IAV in aqueous solution in a dose-dependent manner but was inactive against non-enveloped encephalomyocarditis virus (EMCV). Additional ASFV experiments supported that the lipid mixture is virucidal, which was corroborated by polymerase chain reaction (PCR) experiments. Feed mitigation experiments demonstrated that the lipid mixture can also inhibit ASFV infectivity and affected the conformational properties of ASFV p72 structural protein in virus-spiked feed. Mechanistic experiments identified that the lipid mixture rapidly disrupted phospholipid membranes in a micelle-dependent manner, which aligns with the virological data while higher concentrations were needed for virucidal activity than for the onset of membrane disruption. These findings support that water-dispersible antimicrobial lipid mixtures can effectively inhibit ASFV and IAV and have practical advantages for drinking water applications compared to existing medium-chain antimicrobial lipid mitigant options that are formulated as dry powders or oils for in-feed applications.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"351 ","pages":"Article 199516"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11731633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Achieving chronic hepatitis B functional cure: Factors and potential mechanisms","authors":"Jiarui Zheng,&nbsp;Zilong Wang,&nbsp;Linxiang Huang,&nbsp;Zixuan Qiu,&nbsp;Yandi Xie,&nbsp;Suzhen Jiang,&nbsp;Bo Feng","doi":"10.1016/j.virusres.2024.199507","DOIUrl":"10.1016/j.virusres.2024.199507","url":null,"abstract":"<div><div>Chronic hepatitis B (CHB) is a significant global health issue affecting approximately 254 million individuals worldwide. Achieving the loss of hepatitis B surface antigen (HBsAg), either with or without seroconversion to hepatitis B surface antibody (HBsAb), is regarded as a functional cure and the optimal goal for addressing CHB, and can be achieved through various approaches, including induction with nucleos(t)ide analogues (NAs), induction with pegylated interferon alpha (PegIFNα), and spontaneous clearance of HBsAg. Spontaneous clearance of HBsAg is rare, while NAs can directly inhibit HBV DNA, they are unable to act on covalently closed circular DNA (cccDNA), hence inhibiting HBsAg production or clearing HBsAg is extremely challenging. On the other hand, functional cure based on PegIFNα shows good long-term durability, but over 10 % of patients still experience relapse, mostly within 48 weeks after functional cure. Factors related to CHB functional cure with antiviral therapy are complex, including host factors, viral factors, environmental factors, etc. The integration of HBV DNA into liver cells, persistence of HBV cccDNA, insufficient B cell responses and compromised T cell function pose significant barriers to HBV clearance. Therefore, this study systematically reviewed the relevant factors and potential mechanisms influencing functional cure CHB, which can provide a basis for personalized treatment, help predict treatment outcomes and assess prognosis, and provide theoretical support for the advancement of novel treatment strategies and medications.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"351 ","pages":"Article 199507"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11699463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders","authors":"Filipe Zimmer Dezordi ,&nbsp;José Valter Joaquim Silva Júnior ,&nbsp;Terimar Facin Ruoso ,&nbsp;Angela Giovana Batista ,&nbsp;Pedro Mesquita Fonseca ,&nbsp;Larissa Paim Bernardo ,&nbsp;Richard Steiner Salvato ,&nbsp;Tatiana Schäffer Gregianini ,&nbsp;Thaísa Regina Rocha Lopes ,&nbsp;Eduardo Furtado Flores ,&nbsp;Rudi Weiblen ,&nbsp;Patrícia Chaves Brites ,&nbsp;Mônica de Medeiros Silva ,&nbsp;João Batista Teixeira da Rocha ,&nbsp;Gustavo de Lima Barbosa ,&nbsp;Lais Ceschini Machado ,&nbsp;Alexandre Freitas da Silva ,&nbsp;Marcelo Henrique Santos Paiva ,&nbsp;Matheus Filgueira Bezerra ,&nbsp;Tulio de Lima Campos ,&nbsp;Gabriel da Luz Wallau","doi":"10.1016/j.virusres.2024.199500","DOIUrl":"10.1016/j.virusres.2024.199500","url":null,"abstract":"<div><div>Brazil's COVID-19 response has faced challenges due to the continuous emergence of variants of concern (VOCs), emphasizing the need for ongoing genomic surveillance and retrospective analyses of past epidemic waves to reassess and fine tune containment protocols. Rio Grande do Sul (RS), Brazil's southernmost state, has international borders and trades with Argentina and Uruguay, along with significant domestic connections within Brazil. The identification of source and sink transmission chains at national and international scales can identify main hubs and pathways to target future interventions. In this study we investigated the RS state role in the national and international SARS-CoV-2 transmission chains, which has not been fully explored. Nasopharyngeal samples from various municipalities in RS were collected between June 2020 and July 2022. SARS-CoV-2 whole genome amplification and sequencing were performed using high-throughput Illumina sequencing. Bioinformatics analysis encompassed the development of scripts and tools to perform subsampling taking into account epidemiological information to reduce sequencing disparities bias among the regions/countries, genome assembly, and large-scale alignment and phylogenetic reconstruction. We sequenced a total of 1,480 SARS-CoV-2 genomes from RS, covering all major regions. Sequences predominantly represented Gamma (April-June 2021) and Omicron (January-July 2022) lineages. Phylogenetic analysis revealed a regional pattern for transmission dynamics, particularly with Southeast Brazil for Gamma, and a range of inter-regional connections for Delta and Omicron within the country. On the other hand, international and cross-border transmission with Argentina and Uruguay was rather limited. We evaluated the three VOCs circulation over two years in RS using a new subsampling strategy based on the number of cases in each state during the circulation of each VOC. In summary, the retrospective analysis of genomic surveillance data demonstrated that virus transmission was less intense between country borders than within the country. These findings suggest that while non-pharmacological interventions were effective to mitigate transmission across international RS land borders, they were insufficient to contain transmission at the domestic level.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"351 ","pages":"Article 199500"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11720880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}