Viral genetics articles within Nature Communications

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  • Article
    | Open Access

    Gut ecosystem colonization impacts lifelong health. Here, authors track mother-infant gut viruses over time, reveal feeding’s influence on early viral colonization, and demonstrate the co-transmission of bacteriophages and bacteria from mothers to infants.

    • Sanzhima Garmaeva
    • , Trishla Sinha
    •  & Alexandra Zhernakova

  • Article
    | Open Access

    Niche theory is often invoked to explain biodiversity, but it does not explain how species evolve to exploit unique niches. Using a combination of experimental and computational approaches, this study shows that resource competition can deform fitness landscapes, opening new pathways that promote ecological speciation.

    • Michael B. Doud
    • , Animesh Gupta
    •  & Justin R. Meyer

  • 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

    The serial interval (time between symptom onset in an infector and infectee) is usually estimated from contact tracing data, but this is not always available. Here, the authors develop a method for estimation of serial intervals using whole genome sequencing data and apply it data from clusters of SARS-CoV-2 in Victoria, Australia.

    • Jessica E. Stockdale
    • , Kurnia Susvitasari
    •  & Caroline Colijn

  • Article
    | Open Access

    Certain bats species have previously been identified as ancestral sources of coronaviruses that infect humans but there is limited data on the genomic diversity or zoonotic potential of viruses infecting bats in the UK. Here, the authors use deep sequencing and in vitro assays to characterise coronaviruses recovered from 48 bat faecal samples.

    • Cedric C. S. Tan
    • , Jahcub Trew
    •  & Vincent Savolainen

  • Article
    | Open Access

    Here, by sequencing viruses from individuals in multiple households, Bendall et al. find that SARS-CoV-2 transmission bottleneck does not vary between individuals infected with pre-variant lineages and those infected with highly transmissible Alpha, Delta, or Omicron variants, suggesting these tight bottlenecks will limit the spread of new mutations.

    • Emily E. Bendall
    • , Amy P. Callear
    •  & Adam S. Lauring

  • Article
    | Open Access

    Molnupiravir is an antiviral that forces lethal error catastrophe in SARS-CoV-2 RNAs. Here, the authors confirm the mechanism of action of molnupiravir in humans using samples obtained from the UK’s AGILE phase IIa clinical trial investigating the antiviral efficacy of the drug against SARS-CoV-2. No treatment-associated SARS-CoV-2 mutations were identified.

    • I’ah Donovan-Banfield
    • , Rebekah Penrice-Randal
    •  & Thomas Fletcher

  • Article
    | Open Access

    Previous bioinformatic analyses have indicated that bacteriophages can use genetic codes different from those of their host bacteria. Here, Peters et al. use metaproteomics to provide experimental evidence of reassignment of stop codon TAG to glutamine in phages found in the human gut microbiome.

    • Samantha L. Peters
    • , Adair L. Borges
    •  & Robert L. Hettich

  • Article
    | Open Access

    It is currently unknown how climate and land use changes could affect the endemic area of Lassa virus, a zoonotic pathogen responsible for Lassa fever. Here, the authors show that by 2070, new regions in Africa will likely become ecologically suitable for Lassa virus, drastically increasing the population living in conditions favourable for virus circulation.

    • Raphaëlle Klitting
    • , Liana E. Kafetzopoulou
    •  & Simon Dellicour

  • Article
    | Open Access

    Aotearoa New Zealand pursued a COVID-19 elimination strategy until October 2021 when it moved to a suppression strategy. In this genomic surveillance study, the authors describe spread of the virus during the transition between these strategies, with evidence of substantial undetected community transmission.

    • Lauren Jelley
    • , Jordan Douglas
    •  & Jemma L. Geoghegan

  • Article
    | Open Access

    Dog vaccination is an effective rabies prevention measure, but widespread vaccination campaigns are challenging in settings like India with large free-roaming dog populations. Here, the authors describe a One Health campaign in Goa state which led to a large reduction of cases in dogs and elimination in humans.

    • A. D. Gibson
    • , G. Yale
    •  & R. J. Mellanby

  • Article
    | Open Access

    Variants of concerns arise from SARS-CoV-2 mutations poise as severe public health threats. Here the authors chronicle SARS-CoV-2 mutations onset and immune parameters in an immunocompromised patient with continuous virus-shedding, thereby hinting potential intra-host viral evolution and escape facilitated by ineffective T cell immunity.

    • Sissy Therese Sonnleitner
    • , Martina Prelog
    •  & Gernot Walder

  • Article
    | Open Access

    Post-international travel quarantine has been widely implemented to mitigate SARS-CoV-2 transmission, but the impacts of such policies are unclear. Here, the authors used linked genomic and contact tracing data to assess the impacts of a 14-day quarantine on return to England in summer 2020.

    • Dinesh Aggarwal
    • , Andrew J. Page
    •  & Ewan M. Harrison

  • Article
    | Open Access

    In this study, Aggarwal and colleagues perform prospective sequencing of SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge. They identify important factors that contributed to within university transmission and onward spread into the wider community.

    • Dinesh Aggarwal
    • , Ben Warne
    •  & Ian G. Goodfellow

  • Article
    | Open Access

    In this study, the authors sequence 892 SARS-CoV-2 genomes from Saudi Arabia and describe population dynamics and importations into the country. They identify a nucleocapsid protein mutation associated with increased viral load and host interactions and characterise its role through biochemical analyses.

    • Tobias Mourier
    • , Muhammad Shuaib
    •  & Arnab Pain

  • 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

    Zika and dengue incidence in the Americas declined in 2017–2018, but dengue resurged in 2019 in Brazil. This study uses epidemiological, climatological and genomic data to show that the decline of dengue may be explained by protective immunity from pre-exposure to ZIKV and/or DENV in prior years.

    • Anderson Fernandes Brito
    • , Lais Ceschini Machado
    •  & Nathan D. Grubaugh

  • Article
    | Open Access

    Varicella-zoster virus (VZV) establishes lifelong neuronal latency in humans. Here, Ouwendijk and Depledge et al. identify a fusion transcript, VLT-ORF63, which is expressed during lytic and latent infection, and demonstrate a role for the translated fusion protein in induction of lytic gene expression from latent VZV genomes.

    • Werner J. D. Ouwendijk
    • , Daniel P. Depledge
    •  & Tomohiko Sadaoka

  • Article
    | Open Access

    Nanopore sequencing (ONT) has been used in SARS-CoV-2 studies, however adoption of ONT for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. Here, the authors perform a comprehensive evaluation of ONT analytical performance on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls.

    • Rowena A. Bull
    • , Thiruni N. Adikari
    •  & Ira W. Deveson

  • Article
    | Open Access

    Genome sequencing can be used to infer pathogen transmission dynamics and inform public health responses. Here, the authors sequence >1,200 SARS-CoV-2 samples from Victoria, Australia and find genomic support for the effectiveness of social restrictions in reducing transmission.

    • Torsten Seemann
    • , Courtney R. Lane
    •  & Benjamin P. Howden

  • 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

    CrAss-like phages are bacterial viruses often found in the human gut. Here, Siranosian et al. analyze gut metagenomic data to evaluate the patterns of acquisition, transmission and strain diversity of these phages in mother-infant pairs and in patients undergoing fecal microbiota transplantation.

    • Benjamin A. Siranosian
    • , Fiona B. Tamburini
    •  & Ami S. Bhatt

  • 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

    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

    It is thought that CRISPR-Cas systems, which confer acquired immunity to phage and archaeal viruses, are widespread among bacteria and archaea. Here, Burstein et al.show that entire lineages of uncultivated microorganisms are essentially devoid of CRISPR-Cas systems.

    • David Burstein
    • , Christine L. Sun
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Mutations allow RNA virus to adapt fast but also entail fitness costs. Geller et al. show that, in HIV-1, mutations occur three times less often in the most external domains of the envelope, and that this is due to changes in RNA sequence context and structure, which control viral and host-encoded mutational mechanisms.

    • Ron Geller
    • , Pilar Domingo-Calap
    •  & Rafael Sanjuán

  • Article
    | Open Access

    The Ljungan virus is a picornavirus that lacks the internal coat protein VP4, and the packaging of its RNA genome is poorly understood. Here, the authors use cryo-electron microscopy to visualize this virus and suggest that it uses a different mechanism to other viruses for encapsidation of its genome.

    • Ling Zhu
    • , Xiangxi Wang
    •  & David I. Stuart

  • Article
    | Open Access

    Horizontal gene transfer from retroviruses to mammals is rare between unrelated viruses. Here the authors show the convergent acquisition by herpesviruses of a virulence gene of ancient retroviruses, which occurred at least twice from different donor lineages, to distinct herpesviruses that infect mammals.

    • Amr Aswad
    •  & Aris Katzourakis

  • Article
    | Open Access

    Understanding the factors that enable some bird flu viruses to infect humans is important for the identification of circulating viruses with higher potential to infect us. Here, Taft et al.identify novel mutations in the polymerase of an avian H5N1 virus that help the virus to replicate in human cells and in mice

    • Andrew S. Taft
    • , Makoto Ozawa
    •  & Yoshihiro Kawaoka

  • Article |

    Understanding influenza evolution is challenging. Here, the authors determine the timing and order of critical amino acid changes that contributed to a world-wide predominance of oseltamivir-resistant H1N1 influenza viruses and show the role of epistasis in the emergence of novel influenza phenotypes.

    • Susu Duan
    • , Elena A. Govorkova
    •  & Richard J. Webby

  • Article |

    The Gag precursor protein recognizes the HIV-1 genomic RNA among hundreds of other viral and cellular RNAs during assembly of viral particles. Here, the authors identify the primary binding site of Gag on the HIV-1 RNA, and show that other RNA regions enhance or inhibit Gag binding.

    • Ekram W. Abd El-Wahab
    • , Redmond P. Smyth
    •  & Roland Marquet

  • Article |

    The potential evolutionary advantage associated with genome segmentation in multipartite viruses is not well established. Here Sicard et al. demonstrate that genome segmentation can allow a differential regulation of the copy number of each gene in a multipartite plant nanovirus during host infection.

    • Anne Sicard
    • , Michel Yvon
    •  & Stéphane Blanc

  • Article |

    RNA viruses are known to rapidly evolve new features through errors in replication and reshuffling of genomic segments. These authors report another strategy used by the measles virus to improve infectivity; the cooperation between wild-type and mutant fusion proteins in the same viral particle.

    • Yuta Shirogane
    • , Shumpei Watanabe
    •  & Yusuke Yanagi

  • Article |

    Lamivudine treatment of hepatitis B is associated with drug-resistance mutations in the virus’ DNA polymerase. In this study, 11 patients with drug resistance are investigated and the primary mutation in the DNA polymerase shown to be essential but not sufficient for establishing drug resistance.

    • Hong Thai
    • , David S. Campo
    •  & Yury Khudyakov

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