Viral evolution articles within Nature Communications

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  • Article
    | Open Access

    In this study, the authors identify genetic insertions in the population of hepatitis E virus analyzed in serum samples of a patient with ribavirin treatment failure. They show that these genomic rearrangements promote viral replication without affecting ribavirin sensitivity.

    • Michael Hermann Wißing
    • , Toni Luise Meister
    •  & Daniel Todt

  • Article
    | Open Access

    This study presents a machine learning model that accurately predicts seasonal antigenic changes of influenza A H3N2 using genetic data. The model’s predictions can aid influenza surveillance, vaccine strain selection, and public health management.

    • Syed Awais W. Shah
    • , Daniel P. Palomar
    •  & Matthew R. McKay

  • Article
    | Open Access

    In this study, the authors report the case of a patient who underwent lung transplantation and subsequently developed COVID-19 that resulted in persistent infection. Following antiviral treatment, SARS-CoV-2 (BA.5) showed dynamic genetic diversity with remdesivir resistant mutations leading to enhanced fusogenicity.

    • Hidetoshi Igari
    • , Seiichiro Sakao
    •  & Eiji Ido

  • Article
    | Open Access

    Non-pharmaceutical interventions for COVID-19 also impacted the transmission of other viruses including respiratory syncytial virus (RSV). Here the authors describe the changing epidemiology, clinical severity, and genetic diversity of RSV in Chicago, Illinois, from July 2010 to April 2023.

    • Estefany Rios-Guzman
    • , Lacy M. Simons
    •  & Judd F. Hultquist

  • Article
    | Open Access

    The Omicron BA.2.86 subvariant differs from previous variants by over 30 spike mutations. Here, the authors report that BA.2.86 likely evolved in Southern Africa and that its immune escape is not larger than recently circulating SARS-CoV-2 strains. Neither its replication nor its pathogenicity are enhanced in vitro.

    • Khadija Khan
    • , Gila Lustig
    •  & Alex Sigal

  • Article
    | Open Access

    Non-retroviral endogenous viral elements are widely dispersed in eukaryotic genomes, but their functions remain largely unknown. Here, Huang et al show that one such element in planthoppers has been co-opted and contributes to insect fitness..

    • Hai-Jian Huang
    • , Yi-Yuan Li
    •  & Jun-Min Li

  • Article
    | Open Access

    This study examines the biogeography and functional gene repertoires of marine eukaryote-infecting large and giant DNA viruses. It shows a clear divide in the viral communities between polar and nonpolar environments, with recurrent evolutionary adaptations to the polar environment likely driven by alterations of their genomic functions.

    • Lingjie Meng
    • , Tom O. Delmont
    •  & Hiroyuki Ogata

  • Article
    | Open Access

    Despite their essentiality, human ANP32A and ANP32B are redundant host factors for influenza virus genome replication. In this work, authors show that an influenza virus grown in cells lacking ANP32A and ANP32B evolved to use ANP32E. They explore the polymerase mutations that enable this, and demonstrate increased virulence in mice.

    • Carol M. Sheppard
    • , Daniel H. Goldhill
    •  & Wendy S. Barclay

  • Article
    | Open Access

    Ongoing retroviral invasion into vertebrates has been rarely documented. Here the authors have identified 412 endogenous retroviruses that are invading the genomes of over a hundred vertebrate species. This may be relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.

    • Jianhua Wang
    •  & Guan-Zhu Han

  • Article
    | Open Access

    RNA viruses are defined by linear RNA genomes encoding an RNA-dependent RNA polymerase, while viroid-like elements consist of small, single-stranded, circular RNA genomes that, in some cases, encode self-cleaving catalytic RNAs. Here, the authors identify over 20,000 candidate viroid-like elements, and show that infectious agents of fungi display hybrid features of viroid-like RNAs and RNA viruses.

    • Marco Forgia
    • , Beatriz Navarro
    •  & Marcos de la Peña

  • Article
    | Open Access

    Antibodies against SARS-CoV-2 can be used to treat infections but there is a risk of driving viral resistance to antibodies. Here the authors characterise SARS-CoV-2 escape mutants from an immunocompromised patient treated with anti-SARS-CoV-2 antibodies using mouse protection studies and structural prediction.

    • Lena Jaki
    • , Sebastian Weigang
    •  & Jonas Fuchs

  • Article
    | Open Access

    There is limited data on within-host SARS-CoV-2 genetic diversity and how it is affected by vaccination. The authors analysed intra-host sequence diversity and found that VOCs may have more sequence variations than non-VOCs and that breakthrough infections in vaccinated individuals do not seem to increase non-silent mutations.

    • Haogao Gu
    • , Ahmed Abdul Quadeer
    •  & Leo L. M. Poon

  • Article
    | Open Access

    Until today, genetic tools have been lacking to enable manipulation of amoebal giant viruses (GVs) by CRISPR/Cas9 technology. Here, Bisio et al. apply S. pyogenes Cas9 together with pU6- driven guide RNAs to investigate the replication of pandoravirus, a GV replication in the nucleus. Using this tool, they provide evidence for stepwise evolution and genetic expansion of viral gigantism.

    • Hugo Bisio
    • , Matthieu Legendre
    •  & Chantal Abergel

  • Article
    | Open Access

    Structural biology investigation of conserved capsid proteins facilitates the study of virus evolution. Here, characterization of the lipid-containing ssDNA bacteriophage ΦCjT23 suggests that this phage may serve as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae.

    • Nejc Kejzar
    • , Elina Laanto
    •  & Juha T. Huiskonen

  • Article
    | Open Access

    Evolution of the SARS-CoV-2 spike protein is likely driven by many factors, including immune escape and receptor binding. Here, by measuring the binding affinity of more than 30,000 variants of the SARS-CoV-2 RBD to its receptor ACE2, Moulana et al. show that the evolution of the Omicron BA.1 variant was driven by interactions between mutations.

    • Alief Moulana
    • , Thomas Dupic
    •  & Michael M. Desai

  • Article
    | Open Access

    This study presents data from the REACT-1 SARS-CoV-2 community sampling study in England from November 2021 to March 2022. They show that the Omicron variant peaked in January with a prevalence of ~7% and that the BA.2 sublineage had a 1.5x higher reproduction number compared to other Omicron sublineages.

    • Oliver Eales
    • , Leonardo de Oliveira Martins
    •  & Marc Chadeau-Hyam

  • Article
    | Open Access

    Genetic recombination can confound standard phylogenetic approaches. Here, the authors present a method to reconstruct virus recombination networks, and show the importance of recombination in shaping the ongoing evolution of SARS-like, MERS and 3 human seasonal coronaviruses.

    • Nicola F. Müller
    • , Kathryn E. Kistler
    •  & Trevor Bedford

  • Article
    | Open Access

    Transmission of influenza A viruses (IAV) between hosts and replication within host impose genetic bottlenecks, constraining viral diversity and adaptation. Here, Amato et al. perform site-specific inoculation of barcoded IAV of ferrets and track viral diversity as infection spreads to the lower respiratory tract and conclude that narrow population bottlenecks are an important feature of the within-host infection dynamics.

    • Katherine A. Amato
    • , Luis A. Haddock III
    •  & Andrew Mehle

  • Article
    | Open Access

    For archival pathogens, like pH1N1 Influenza A virus the causative agent of 1918/19 pandemic, only few whole genome sequences exist. Here, Patrono et al. provide one complete and two partial genomes from Germany and find variation in two sites in the nucleoprotein gene in pandemic samples compared to pre-pandemic samples, that are associated with resistance to host antiviral response, pointing at a possible viral adaptation to humans.

    • Livia V. Patrono
    • , Bram Vrancken
    •  & Sébastien Calvignac-Spencer

  • Article
    | Open Access

    The SARS-CoV-2 spike has been evolving in the human population. The variants of concern alpha and beta evolved to optimise spike openness and so ability to bind its receptor ACE2, the affinity towards the receptor, and stability upon receptor binding.

    • Antoni G. Wrobel
    • , Donald J. Benton
    •  & Steven J. Gamblin

  • Article
    | Open Access

    MERS-CoV is enzootic in dromedary camels, can spread to humans but undergoes limited onward transmission. Here, Schroeder et al. compare clinical isolates of MERS-CoV in vitro and show that the predominantly circulating recombinant lineage 5 possess a fitness advantage over parental lineage 3 and 4 due to reduced activation of innate immune signaling.

    • Simon Schroeder
    • , Christin Mache
    •  & Christian Drosten

  • Article
    | Open Access

    Respiratory syncytial virus (RSV) is a common infection in children and older adults but little is known about within-host viral population diversity. Here, the authors perform deep sequencing and find that RSV subgroup B exhibited more diversity than subgroup A, with implications for development of therapeutics and vaccines.

    • Gu-Lung Lin
    • , Simon B. Drysdale
    •  & Andrew J. Pollard

  • Article
    | Open Access

    The COVID-19 epidemic began later in Russia than many European countries, possibly due to restrictions on travel from China. Here, the authors analyze whole genome sequences sampled early in the epidemic in Russia, and find that most strains were not linked to China.

    • Andrey B. Komissarov
    • , Ksenia R. Safina
    •  & Georgii A. Bazykin

  • Article
    | Open Access

    Highly pathogenic avian influenza viruses (HPAIV) can evolve via acquisition of polybasic cleavage sites, but the contribution of other mutations remains unclear. Here, the authors combine phylogenetic, statistical and structural approaches, and identify parallel mutations that are associated with HPAIV phenotype.

    • Marina Escalera-Zamudio
    • , Michael Golden
    •  & Oliver G. Pybus

  • Article
    | Open Access

    Human coronavirus-HKU1 contains two surface projections called spike and haemagglutinin-esterase (HE), with the latter acting as a receptor-destroying enzyme. Here, the authors use cryo-EM and mass spectrometry to characterise the small, heavily glycosylated HKU1 HE, revealing a vestigial lectin domain covered with a putative glycan shield; and they discuss these features in the context of host adaptation.

    • Daniel L. Hurdiss
    • , Ieva Drulyte
    •  & Raoul J. de Groot

  • Article
    | Open Access

    Metagenomics allows virus genome discovery, but the viral hosts are often not identified. Here, Kinsella et al. use recombination events between virus genomes, statistical association of viruses to hosts in clinical samples, and analysis of endogenous viral elements in host genomes to identify probable hosts of three CRESS virus families.

    • Cormac M. Kinsella
    • , Aldert Bart
    •  & Lia van der Hoek

  • Article
    | Open Access

    Bacteriophages and their hosts are involved in a constant evolutionary arms race that should lead to divergence between phage genes over time. Here, the authors recruit metagenomic reads to virus reference genomes and genome fragments in samples from cryoconite holes and show that phages with near-identical core genomes maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants.

    • Christopher M. Bellas
    • , Declan C. Schroeder
    •  & Alexandre M. Anesio

  • Article
    | Open Access

    The mechanism underlying packaging of the 8 segments of the influenza virus genome into virions is not well understood. Here, the authors use a multiplexed FISH assay to monitor the 8 segments in parallel in infected cells suggesting bundling routes during the packaging process.

    • Ivan Haralampiev
    • , Simon Prisner
    •  & Andreas Herrmann

  • Article
    | Open Access

    Bats are a likely reservoir of zoonotic coronaviruses (CoVs). Here, analyzing bat CoV sequences in China, the authors find that alpha-CoVs have switched hosts more frequently than betaCoVs, identify a bat family and genus that are highly involved in host-switching, and define hotspots of CoV evolutionary diversity.

    • Alice Latinne
    • , Ben Hu
    •  & Peter Daszak

  • Article
    | Open Access

    Astroviruses are common human pathogens and their genomes contain three known protein-coding genes. Here, Lulla et al. report a fourth, previously overlooked gene encoding protein XP which has a viroporin-like activity that is important for efficient production and/or release of virus particles.

    • Valeria Lulla
    •  & Andrew E. Firth

  • Article
    | Open Access

    DNA methylation is an epigenetic marker in all domains of life. Here, Jeudy et al., using single-molecule realtime sequencing, determine DNA methylation patterns in giant viruses and evolutionary analysis of virus encoded DNA methyltransferases suggests that they affect viral fitness.

    • Sandra Jeudy
    • , Sofia Rigou
    •  & Matthieu Legendre

  • Article
    | Open Access

    Antigenic site B in influenza A virus hemagglutinin (HA) is immunodominant in circulating human H3N2 strains. Using deep mutational scanning, Wu et al. here define the local fitness landscapes of HA antigenic site B in six human H3N2 strains, providing insights into evolvability of influenza antigenicity.

    • Nicholas C. Wu
    • , Jakub Otwinowski
    •  & Ian A. Wilson

  • Article
    | Open Access

    Poliovirus has a higher mutation rate than HIV, yet has been almost eradicated by vaccination while an effective vaccine against HIV does not exist. Here, the authors develop a fitness model for poliovirus viral protein 1 to show that it is subject to stringent evolutionary constraints that limit its ability to avoid vaccine-induced immune responses.

    • Ahmed A. Quadeer
    • , John P. Barton
    •  & Matthew R. McKay

  • Article
    | Open Access

    The genome of influenza is often incomplete in infected cells, but the implications for infection remain unclear. Here, Jacobs et al. show that an average of 3.6 particles is necessary for productive infection and that coinfection supports efficient complementation within a host but not upon transmission to a new host.

    • Nathan T. Jacobs
    • , Nina O. Onuoha
    •  & Anice C. Lowen

  • Article
    | Open Access

    Polymorphisms in the avian influenza A virus (IAV) polymerase restrict its host range during transmission from birds to mammals. Here, the authors investigate differences in the host chromatin regulator ANP32A regarding IAV polymerase adaptation, and profile ANP32A splicing to predict avian species associated with pre-adaptive human-signatures in the virus.

    • Patricia Domingues
    • , Davide Eletto
    •  & Benjamin G. Hale

  • Article
    | Open Access

    The dynamics of HIV-1 DNA sequences early after HIV-1 transmission remains poorly characterized. Here, the authors perform a longitudinal evaluation of HIV-1 DNA sequences in subtype C-infected individuals during acute infection, providing a landscape of the nature and evolution of the very early viral genome.

    • Guinevere Q. Lee
    • , Kavidha Reddy
    •  & Mathias Lichterfeld

  • Article
    | Open Access

    Here, the authors present the cryo-EM structure of the archaeal virus SH1 at 3.8 Å resolution and show how the major capsid proteins assemble into hetero-hexamers, providing insights into the assembly process of this and related PRD1-adeno lineage viruses.

    • Luigi De Colibus
    • , Elina Roine
    •  & David I. Stuart

  • Article
    | Open Access

    Viruses are potential vectors for horizontal gene transfer. Here, studying viral infection of sugar beet plants, the authors report the generation of virus-host circular DNA hybrids and provide a picture of the initial steps in virus-mediated horizontal transfer of chromosomal DNA between plant species.

    • Marco Catoni
    • , Emanuela Noris
    •  & Gian Paolo Accotto

  • Article
    | Open Access

    Current influenza vaccine approaches largely focus on highly variable epitopes with high immunogenicity or epitopes of low variability that often have low immunogenicity. Here, Thompson et al. identify a highly immunogenic epitope of limited variability in the head domain of the H1 haemagglutinin and show protection from diverse H1N1 strains in mice.

    • Craig P. Thompson
    • , José Lourenço
    •  & Sunetra Gupta

  • Article
    | Open Access

    Giant viruses are visible by light microscopy and have unusually long genomes. Here, the authors report three new members of the Pandoraviridae family and investigate their evolution and diversity.

    • Matthieu Legendre
    • , Elisabeth Fabre
    •  & Jean-Michel Claverie

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