Virus Evolution最新文献

{"title":"Continuous <i>in silico</i> screening of fish, amphibians, reptiles, and birds expands the diversity of bornavirids and reveals unexpected genomic architectures.","authors":"Mirette I Y Eshak, Sakiho Imai, Junna Kawasaki, Mai Kishimoto, Miguel Vences, Andolalao Rakotoarison, Martin Beer, Dennis Rubbenstroth, Masayuki Horie, Florian Pfaff","doi":"10.1093/ve/veag033","DOIUrl":"10.1093/ve/veag033","url":null,"abstract":"<p><p>Using an <i>in silico</i> data mining approach, we previously expanded the known diversity within the family <i>Bornaviridae</i> by identifying novel bornavirids in publicly available sequence datasets from bony and cartilaginous fish. Building on this discovery, we systematically screened numerous additional sequence datasets from fish, amphibians, reptiles, and birds in the Sequence Read Archive and a new RNA-seq dataset to further explore bornaviral diversity and evolutionary history. Our analysis identified nearly complete and partial bornaviral genomes across multiple host taxa, that represented either new viral variants, previously known viruses detected in so far unreported hosts/sources, or novel viruses. Several novel orthobornaviral genomes were identified in snake and lizard datasets. Sequences of the species <i>Orthobornavirus alphapsittaciforme</i> and <i>Orthobornavirus serini</i> were identified in avian datasets. We also found sequences of both known and possibly new species in the genus <i>Cultervirus</i>, which were detected in bony fish and, for the first time, in reptile and amphibian datasets. The identification of culterviruses in reptiles and amphibians suggests that this group of viruses, which was previously only known to be associated with fish, has a much wider host range. A genetically divergent bornaviral genome was discovered in the gold-striped salamander (<i>Chioglossa lusitanica</i>), possessing the genomic architecture of orthobornaviruses but likely representing a new genus within the family <i>Bornaviridae</i>. Interestingly, multiple distinct viral genomes identified in passerine birds were classified as carboviruses based on sequence similarities, but they exhibited distinct genomic features and lacked the genes that code for glycoprotein (G) and, in some cases, the accessory protein (X) and/or matrix protein (M). Subsequent screening of samples from passerine birds further confirmed these findings and showed that these carboviral sequences likely represent genuine viruses rather than endogenous bornaviral elements. Interestingly, these carboviruses appear to co-occur with enveloped viruses in potential co-infection or helper virus scenarios. These findings contribute substantially to our understanding of <i>Bornaviridae</i> diversity, their evolutionary adaptation as well as modes of transcriptional regulation.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag033"},"PeriodicalIF":3.8,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148334612","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":"Genomic epidemiology and evolutionary analysis of Lassa virus from small mammals suggest bidirectional viral movement across humans and animals.","authors":"Anise N Happi, Olusola A Ogunsanya, Ayotunde E Sijuwola, Femi M Saibu, Kazeem Akano, Akeemat O Ayinla, Richard O Daodu, Brady Page, Testimony J Olumade, Judith U Oguzie, Paul E Oluniyi, Oluwatobi A Adedokun, John Fadele, Cecilia Nwofoke, Obineche T Elias, Kehinde E Ogundana, Omolola Z Lawal, Iguosadolo Nosamiefan, Johnson Okolie, Ademola Adelabu, Kara Lombardi, Leigh A Eller, Erica Broach, Petra A Prins, Jonathan L Heeney, Kayvon Modjarrad, Thierry L F A Njatou, Zahra F Parker, Melanie McCauley, Sandhya Vasan, Edyth Parker, Natalie D Collins, Nelson L Michael, Christian T Happi","doi":"10.1093/ve/veag032","DOIUrl":"10.1093/ve/veag032","url":null,"abstract":"<p><p>Lassa fever is a viral haemorrhagic fever that poses a persistent public health threat in several West African countries, particularly Nigeria. The scarcity of Lassa virus (LASV) sequences isolated from small mammal reservoirs limits our knowledge and understanding of LASV genomic diversity and transmission dynamics. To address this knowledge gap, we sampled 1189 small mammals, including mice, rats, and shrews, from two LASV-endemic states in southern Nigeria (Ondo and Ebonyi States) and tested them for the presence of LASV RNA using reverse transcription-quantitative polymerase chain reaction. Selected quantitative polymerase chain reaction-positive samples were subjected to whole genome sequencing and small mammal speciation through next-generation sequencing outputs. We recorded an overall polymerase chain reaction positivity rate of 61.6%, with rat species demonstrating the highest LASV prevalence. We also conducted a serosurvey of 269 small rodents using indirect Enzyme-Linked Immunosorbent Assay (ELISA) and obtained an overall anti-LASV seroprevalence of 45%. Using the Nextera XT metagenomic sequencing protocol, we produced 55 LASV partial (<i>n</i> = 28) and full-length genomes (<i>n</i> = 27) from small mammals sampled, all of which clustered within sublineage 2g. LASV sequences generated from this study suggest that LASV variation is mostly driven by location, as isolates from this study tend to cluster more closely with other isolates collected from within the same region, rather than by collection date or host. However, samples collected from Ebonyi State were more closely related to isolates collected in Ondo State than to isolates from Edo, despite a larger physical distance. Overall, the data from this study suggest free movement of the virus across states in Nigeria, among humans and various non-human taxa. The finding of LASV in additional small mammal hosts suggests that the virus reservoir is vast and may include many small mammals not well-characterized.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag032"},"PeriodicalIF":3.8,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13285998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148310450","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":"Extending the temporal window of arbovirus evolutionary analysis through the recovery of a century-old bandavirus.","authors":"Udo Gieraths, Jörn Beheim-Schwarzbach, Matthew J Pickin, Annika Beyer, Lineke Begeman, Bernd Hoffmann, Kore Schlottau, Martin Beer, Rainer G Ulrich, Thomas Müller, Conrad M Freuling, Tiina Mauno, Marco van de Bildt, Vera C Mols, Victor M Corman, Friedemann Weber, Terry C Jones, Christian Drosten","doi":"10.1093/ve/veag034","DOIUrl":"10.1093/ve/veag034","url":null,"abstract":"<p><p>Arboviruses evolve under unique ecological constraints imposed by their dual replication cycles in vertebrate and arthropod hosts. This dual-host requirement results in markedly low substitution rates, which complicate molecular clock calibration, particularly when temporal sampling spans only narrow time windows. For RNA arboviruses, wide sampling windows are especially rare due to the intrinsic instability of RNA. Here, we demonstrate that ethanol-preserved museum specimens can help overcome these temporal limitations. We successfully recovered the coding-complete genome of a bandavirus, a negative-sense segmented RNA virus that clusters with the highly pathogenic human severe fever with thrombocytopenia syndrome virus. The virus was detected in a Common pipistrelle (<i>Pipistrellus pipistrellus)</i> bat collected in northern Germany in 1919, making it one of the oldest sequenced mammalian RNA viruses, only comparable to historic measles and influenza A viruses from 1912 and 1918. Screening 1086 contemporary bat samples revealed strains of the same virus species in nine Common pipistrelle bats (2010-2018) and one Serotine bat (<i>Eptesicus serotinus</i>, 1999) from Germany and the Netherlands. Coding-complete genomes indicate frequent genome segment reassortment and widespread circulation of reassortants of this understudied virus species (<i>Bandavirus zwieselense</i>). We detected an exceptionally low substitution rate (< 6.88 × 10^-5 substitutions/site/year) between the RdRp coding sequence of the ancient genome and its nearest modern counterpart. Additionally, functional assays demonstrated that the virus's non-structural (NSs) protein effectively inhibits interferon induction in human HEK-293T cells. Our findings highlight the feasibility and scientific value of extracting and analysing ancient viral RNA from ethanol-preserved museum specimens to substantially enhance our understanding of RNA arbovirus evolution.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag034"},"PeriodicalIF":3.8,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13317966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148364015","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":"Extreme GC3 codon bias in a novel brown seaweed virus results in pseudoambigrammatic characteristics.","authors":"Rob J Dekker, Wim C de Leeuw, Han Rauwerda, Marina F van Olst, Wim A Ensink, Selina M van Leeuwen, Job Cohen, Klaas Timmermans, Timo M Breit, Martijs J Jonker","doi":"10.1093/ve/veag030","DOIUrl":"10.1093/ve/veag030","url":null,"abstract":"<p><p>Although viruses are often studied in relation to disease, they can also offer valuable insights into RNA functionality. Due to their vast range of hosts and high mutation rates, viruses can quickly adapt to changing environments. It is therefore likely that viruses exploit a broad range of RNA functionalities to develop strategies for host infection and propagation. Our aim is to discover RNA viruses with survival strategies that reveal unknown RNA characteristics and functionalities. Here, we report a new, unclassified negative-sense single-stranded RNA virus from the large brown seaweed <i>Saccharina latissima</i> that showed a unique genome characteristic. The novel virus, designated SalaUV-NL1, possesses a bipartite genome. The small segment (2120 nt) encodes a putative 328-aa protein and possibly an additional protein of ≥315 aa. The large segment (7065 nt) encodes a putative RNA-dependent RNA polymerase (RdRp) of 2296 amino acids on the anti-genomic strand, but strikingly contains a similarly sized and largely overlapping open reading frame (reverse ORF; rORF) on the genomic strand that encodes a putative protein of 2317 aa. This raises the possibility that SalaUV-NL1 represents an ambigrammatic virus. However, the RdRp ORF exhibits an extreme GC3 codon bias (98%), far exceeding the typical codon constraints of ambigrammatic viruses that mostly reflect the avoidance of stop codons on the reverse strand. Therefore, the rORF is likely incidental because it is the result of the GC3 codon bias on the RdRp-coding anti-genomic strand. We therefore designate SalaUV-NL1 as pseudoambigrammatic. Several other viruses with a similar pseudoambigrammatic signature, characterized by unusually high GC3 codon bias, were identified in GenBank, most of which lack a discernible rORF. The codon bias of SalaUV-NL1 surpasses even that of its host, <i>S. latissima</i>, although other hosts of pseudoambigrammatic viruses do not display elevated GC3 levels. Comparative analysis of multiple SalaUV-NL1 variants further revealed exceptionally high nucleotide substitution rates, particularly silent A/U → G/C transitions, reaching frequencies of up to 81%. This novel virus, therefore, exemplifies a previously unrecognized survival strategy among RNA viruses, the functional implications of which remain unclear.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag030"},"PeriodicalIF":3.8,"publicationDate":"2026-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13262655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148254647","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":"Mapping the global distribution and spread of the <i>Plasmodium vivax</i>-associated virus MaRNAV-1.","authors":"Mary E Petrone, Justine Charon, Rhys H Parry, Matthew J Grigg, Kim A Piera, Jacob A F Westaway, Kayoko Shioda, Bruce Russell, Ric N Price, Timothy William, Enny Kenangalem, James S McCarthy, Bridget E Barber, Edward C Holmes, Nicholas M Anstey","doi":"10.1093/ve/veag031","DOIUrl":"10.1093/ve/veag031","url":null,"abstract":"<p><p>Matryoshka RNA virus 1 (MaRNAV-1) is a bi-segmented and single-stranded RNA virus associated with <i>Plasmodium vivax</i>, a cause of human malaria. Little has been uncovered about the epidemiology and ecology of this virus since its discovery in 2019. To address this, we used a combination of primary and publicly available metatranscriptomic data to map the geographic distribution and host associations of MaRNAV-1. We detected this virus throughout Southeast Asia, in parts of South America, and, for the first time, in Oceania. Despite its broad distribution, MaRNAV-1 was found exclusively in metatranscriptomes containing <i>P. vivax</i>, suggesting that there is a specific virus-host relationship that has shaped the evolutionary history of this virus. We were unable to estimate the emergence date of the MaRNAV-1 lineage; however, phylogeographic mapping analysis suggested that MaRNAV-1 is widely dispersed throughout Southeast Asia. Our findings have both evolutionary and public health implications and can serve as the basis for future investigations in these fields.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag031"},"PeriodicalIF":3.8,"publicationDate":"2026-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13271372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148273402","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":"Unravelling viral identity: avoiding the trap of endogenous sequences for viral surveillance of small ruminant oncogenic retroviruses.","authors":"Benjamin Riocreux-Verney, Marie Verneret, Christine Dolmazon, Shirin Ashraf, Stella A Atim, Vincent Navratil, Caroline Leroux, Jocelyn Turpin","doi":"10.1093/ve/veag028","DOIUrl":"10.1093/ve/veag028","url":null,"abstract":"<p><p>Small ruminants (sheep and goats) are one of the few mammals in which an exogenous retrovirus (XRV) and closely related endogenous retroviral (ERV) elements coexist within the same host genome. The betaretroviruses Jaagsiekte sheep retrovirus (JSRV) and Enzootic Nasal Tumour Virus (ENTV) cause pulmonary and nasal adenocarcinomas, respectively, and share extensive sequence similarity with their endogenous counterparts. Consequently, molecular surveillance must rely on assays that can unequivocally distinguish true exogenous infection from ERV-derived templates; failure to do so compromises diagnosis, phylogenetic inference, and epidemiological conclusions. We retrieved all complete JSRV, ENTV-1/2, and related ERV genomes deposited in public repositories and performed a comprehensive alignment. Only a limited number of genomic segments were capable of distinguishing exogenous from endogenous sequences. We refer to these as discriminating regions (DRs). Phylogenies built using DRs revealed that several entries annotated as XRV are, in fact, ERV-derived or chimeric artefacts generated by short-amplicon reconstruction. A systematic literature review of over 100 articles identified 286 distinct primers and probes used for the XRV amplification. <i>In-silico</i> mapping of each oligonucleotide onto the full alignment showed that only 28% reliably differentiate XRV from ERV. We experimentally validated the predictive power of this approach for 17 primer/probe sets, confirming that non-discriminating assays produce false-positive signals from endogenous templates. The misannotation of ERV sequences as exogenous viruses has resulted in the population of databases with dubious entries, fostering erroneous hypotheses such as vector-borne transmission of JSRV and ENTV. To address this issue, we propose a concise set of criteria for assay design, validation, and database annotation, emphasizing DR targeting, specificity testing against endogenous templates, and transparent reporting. Although this framework was developed for small ruminants, it is readily applicable to any host-virus system in which exogenous viruses coexist with endogenous viral elements. This will strengthen viral surveillance, phylogenetics, and the One Health initiatives.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag028"},"PeriodicalIF":3.8,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148058421","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":"The adaptive plasticity of temperate phage <i>λ</i>.","authors":"Sylvain Gandon, Tapan Goel, Joshua S Weitz, Sébastien Lion","doi":"10.1093/ve/veag026","DOIUrl":"10.1093/ve/veag026","url":null,"abstract":"<p><p>When the temperate phage [Formula: see text] infects its host, the bacterium <i>Escherichia coli</i>, it can either replicate to form new progeny (lytic growth) or integrate its genome into the host chromosome (lysogenization). Crucially, the probability of lysis or lysogeny is tightly regulated and varies with phage and host genotypes and the environment. In particular, the number of viruses coinfecting the same host cell is known to have a strong effect on the outcome of the infection, leading to phenotypic plasticity: the probability of lysogenization is higher when the cellular multiplicity of infection (MOI) increases. However, the selective forces driving the evolution of plasticity in phage [Formula: see text] remain unclear. Here, we analyze the evolution of the plasticity of lysogenization and show that a MOI-varying strategy is adaptive when the abundance of susceptible cells fluctuates periodically. We study how the speed of these fluctuations and various within-host decision rules affect the evolution of viral plasticity. Our results suggest that the complex genetic regulation of lysogeny in temperate phages can be shaped by natural selection allowing viruses to use the MOI as indirect information to persist in environments with fluctuating host densities.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag026"},"PeriodicalIF":3.8,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148152298","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":"Metaviromics reveals a high diversity of viruses belonging to the <i>Caliciviridae</i> family in seal feces.","authors":"Marion Desdouits, Julien Schaeffer, Cécile Le Mennec, Michèle Gourmelon, Françoise S Le Guyader","doi":"10.1093/ve/veag029","DOIUrl":"10.1093/ve/veag029","url":null,"abstract":"<p><p>Investigating potential zoonotic viruses in animal reservoirs is crucial to anticipate viral emergence. Seals can represent large populations of coastal mammals with unknown consequences on the microbiological quality of their surrounding environment. To assess this, we conducted a metaviromics analysis of feces collected from two species of seals in the North-Western Atlantic (Saint-Pierre et Miquelon archipelago). We focused on the <i>Caliciviridae</i> family, which regroups several genera with viruses infecting humans and other mammals, including marine mammals, but none identified in seals (<i>Phocidae</i>). Among the assembled sequences identified as <i>Caliciviridae</i>, there were four known genera (norovirus, sapovirus, vesivirus, and salovirus) and unknown, distantly related viruses. Complete or nearly-complete genomes could be assembled for each genus. Norovirus and sapovirus sequences from seals were diverse and likely represent several new genogroups or genotypes. Seal vesivirus formed a monophyletic group, representing a potential new species related to the canine vesivirus. Salovirus, which are fish viruses, were likely diet-derived, like the distant sequences which exhibited the hallmarks of caliciviruses and were more closely related to fish and reptile viruses. In conclusion, seals are a reservoir for a large diversity of <i>Caliciviridae</i>, some related to norovirus or sapovirus genotypes known to infect humans, and their impact on the quality of coastal water or shellfish should be further assessed. This study expands the knowledge on <i>Caliciviridae</i> genetic diversity and circulation in marine mammals.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag029"},"PeriodicalIF":3.8,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13200540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148037764","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":"Linkage-aware inference of fitness from short-read time-series genomic data.","authors":"Syed M U Abdullah, Muhammad Saqib Sohail, Raymond H Y Louie, Yanni Sun, John P Barton, Matthew R McKay","doi":"10.1093/ve/veag027","DOIUrl":"10.1093/ve/veag027","url":null,"abstract":"<p><p>Inferring the fitness effect of mutations is a basic problem in understanding the evolution of populations over time. When multiple mutations are present in a population simultaneously, genetic linkage comes into play, and the fate of an individual mutation depends on both its fitness as well as the background on which it occurs. Accurate inference of fitness effects for evolutionary systems with multiple competing mutations is therefore contingent on resolving the confounding effects of genetic linkage, captured by the covariance between allele-pairs. Increasingly, evolutionary studies are using short-read sequencing technologies to produce detailed snapshots of evolving populations. This presents a problem as the frequencies of allele-pairs are not known beyond the read-length, hampering any attempt to resolve the effects of genetic linkage between pairs of loci residing on different reads. Here we present a computationally efficient pipeline for inferring selection from short-read time-series data with partial allele-pair frequency information, whilst accounting for linkage. Simulation results show that the method has good performance and is scalable to systems with several thousand variants. Additionally, we demonstrate the pipeline's utility on real datasets of within-host human immunodeficiency virus and severe acute respiratory syndrome coronavirus 2 evolution, showcasing its applicability in resolving linkage effects from complex evolutionary histories.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag027"},"PeriodicalIF":3.8,"publicationDate":"2026-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13191327/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148018950","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":"Getting to the root of HIV transmitted founder virus sequences.","authors":"Bradley R Jones, Zabrina L Brumme, Eric Hunter, Jeffrey B Joy","doi":"10.1093/ve/veag025","DOIUrl":"10.1093/ve/veag025","url":null,"abstract":"<p><p>Determining the sequence of the transmitted founder virus, the virus that establishes infection in a new host, is critical for understanding early viral dynamics and evolution. Methods to estimate transmitted founder virus sequences using ancestral sequence reconstruction require either sequences collected early in infection or longitudinal samples that can capture the evolutionary history of the viral sequences, which can be challenging to collect. In human immunodeficiency virus infection, viral genomes are integrated into host cells which can persist, creating a proviral archive of the evolutionary history of the virus. We can potentially utilize these proviral sequences, which can be collected later during infection and while the individual is on therapy, to perform ancestral sequence reconstruction to estimate founder virus sequences. We analysed a previously described data set of 12 participants from Zambia who had human immunodeficiency virus sequences collected within months of infection and proviral sequences collected before and after suppressive therapy initiation. We investigated the accuracy of root placement and founder virus sequence reconstruction in these individuals from their proviral sequences using a variety of phylogenetic methods. We had limited success in reconstructing founder virus sequences across all ancestral sequence reconstruction and rooting methods. However, we observed lower error in founder virus sequence reconstruction with participants that had proviral sequences similar to their founder sequence. Our results highlight a need for new methods to be developed in order to effectively reconstruct founder virus sequences from proviral sequences.</p>","PeriodicalId":56026,"journal":{"name":"Virus Evolution","volume":"12 1","pages":"veag025"},"PeriodicalIF":3.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13155111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147870403","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}