Retrovirus articles within Nature Communications

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  • Article
    | Open Access

    There is limited data on drug resistance in South African communities strongly affected by HIV. In this study, the authors observed low levels of resistance to newer drugs but widespread resistance to older HIV medications in a South African community. Resistance to rilpivirine was detected even in untreated individuals.

    • Steven A. Kemp
    • , Kimia Kamelian
    •  & Ravindra K. Gupta

  • Article
    | Open Access

    HIV remission has been seen in people living with HIV after the cessation of antiretroviral therapy and is termed post treatment control. Here Passaes and colleagues present an SIV model that shows early initiation of antiretroviral therapy after SIV infection is linked to improved post treatment control upon cessation of antiviral therapy and associates with the expansion of an enhanced memory pool of CD8 + T cells‘.

    • Caroline Passaes
    • , Delphine Desjardins
    •  & Asier Sáez-Cirión

  • Article
    | Open Access

    A defining feature of retroviruses compared to other +ssRNA viruses is reverse transcription. Here, Köppke et al. show that retroviruses (e.g. HIV-1) can produce viral proteins even in the absence of reverse transcription.

    • Julia Köppke
    • , Luise-Elektra Keller
    •  & Oya Cingöz

  • Article
    | Open Access

    It is still unclear why HIV-1 vaccines targeting MPER induce antibodies that fail to bind HIV. Here, the authors show that antibodies targeting membrane-proximal linear epitopes of virion spike proteins must generate relevant antibody paratopes and approach angles to ligate their quarry in a topologically restricted site.

    • Kemin Tan
    • , Junjian Chen
    •  & Mikyung Kim

  • Article
    | Open Access

    Here the authors use biochemical assays and single molecule imaging to show that DNA breaks and single-stranded gaps modulate dynamic PFV retroviral intasome interactions with target DNA and encourage site-specific integration.

    • Gayan Senavirathne
    • , James London
    •  & Kristine E. Yoder

  • Article
    | Open Access

    HIV-1 assembles and buds from the host cell membrane of infected T lymphocytes. Here, Dibsy et al. characterise the role of cortical actin, viral Gag and host factor Arpin in virion assembly and release.

    • Rayane Dibsy
    • , Erwan Bremaud
    •  & Delphine Muriaux

  • Article
    | Open Access

    The authors used mathematical modeling of human data to study how HIV persists despite suppressive antiretroviral therapy. They found that when latently infected CD4+ T cells proliferate or differentiate, they can create HIV DNA and passage it into other subsets. More mature CD4 cell subsets then clear HIV DNA faster.

    • Daniel B. Reeves
    • , Charline Bacchus-Souffan
    •  & Peter W. Hunt

  • Article
    | Open Access

    Yoth et al. report that some mobile retrovirus-like genetic elements, errantiviruses, pose a threat to genome integrity when reactivated in somatic gonadal tissue, showing that they can infect the oocyte and transpose into the germline genome.

    • Marianne Yoth
    • , Stéphanie Maupetit-Méhouas
    •  & Emilie Brasset

  • Article
    | Open Access

    The hexagonal immature capsid lattice of human endogenous retrovirus K is determined at 3.2 Å resolution, which is an assembly of small molecule-stabilized hexamers via dimer and trimer interfaces, a highly conserved mechanism among retroviruses.

    • Anna-Sophia Krebs
    • , Hsuan-Fu Liu
    •  & Peijun Zhang

  • Article
    | Open Access

    Endogenous retroviruses, or genomic relics of ancient viral infection, have been associated with certain neurodegenerative diseases. Here, Liu et al. report a pathway by which reactivated viral gene products contribute to intercellular protein aggregate spreading.

    • Shu Liu
    • , Stefanie-Elisabeth Heumüller
    •  & Ina M. Vorberg

  • Article
    | Open Access

    Multicolor imaging employing genetically-encodable fluorescent proteins permits spatiotemporal live cell imaging of multiple cues. Here, authors use multicolor lifetime imaging to visualize quadruple-labelled human immunodeficiency viruses within cellular contexts.

    • Tobias Starling
    • , Irene Carlon-Andres
    •  & Sergi Padilla-Parra

  • Article
    | Open Access

    Envelope glycoproteins from Asia prevalent HIV-1 subtypes, CRF01_AE and CRF07_BC, remain less explored. Here, the authors reveal the unique features of their V1 regions, associate them with the resistance to certain broad neutralising antibodies (bNAbs), and unravel the epitope and mechanism of a bNAb from CRF01_AE infected individuals.

    • Jun Niu
    • , Qi Wang
    •  & Bei Yang

  • Article
    | Open Access

    Nuclear import of the HIV-1 capsid (CA) is mediated through direct interactions with components of the nuclear pore complexes. Here, the authors identify Nup35 and POM121 as HIV-1 CA interacting factors regulating nuclear entry and further demonstrate regulation of the process by soluble factors Cyclophilin A and CPSF6.

    • Guangai Xue
    • , Hyun Jae Yu
    •  & Vineet N. KewalRamani

  • Article
    | Open Access

    In this study, Henderson and Zhou et al. visualize the development of a HIV-1 broadly neutralizing antibody (bnAb) from germline to maturity by determining cryo-EM structures of HIV-1 Envelope (Env) proteins bound to Fab fragments of antibodies at different stages of development of a Env V3-glcyan supersite targeting bnAb clone.

    • Rory Henderson
    • , Ye Zhou
    •  & Priyamvada Acharya

  • Article
    | Open Access

    Here the authors present an HIV-1 vaccine strategy that combines Env stabilization, nanoparticle display, and glycan trimming, which improves neutralizing antibody responses, frequency of vaccine responders, and germinal center reactions in animal models.

    • Yi-Nan Zhang
    • , Jennifer Paynter
    •  & Jiang Zhu

  • Article
    | Open Access

    Some HIV-infected cells persist during antiretroviral therapies (ART) but their phenotype is less clear. Dufour et al. show that HIV-infected cells that persist in people receiving ART are phenotypically diverse and that CD4+ T cells expressing the integrin VLA-4 are highly enriched in replication-competent HIV.

    • Caroline Dufour
    • , Corentin Richard
    •  & Nicolas Chomont

  • Article
    | Open Access

    Acute graft versus host disease is a rare but deadly complication following liver transplantation. Author show here, upon screening a large cohort of liver transplanted patients and detailed immune phenotyping of samples from the 7 affected individuals and appropriate controls, that human T cell lymphotropic virus type I infection of donor immune cells appear to correlate with the occurrence of acute graft versus host disease.

    • Chuan Shen
    • , Yiyang Li
    •  & Qiang Xia

  • Article
    | Open Access

    Host proteins CPSF6, NUP153, and SEC24C are vital for HIV-1 infection. They bind to the viral capsid protein and contribute to shuttling of virions through the cytoplasm (SEC24C), import into the nucleus (NUP153 and CPSF6) and subsequent trafficking to preferred integration sites (CPSF6). Here, Wei et al. combine structural, biochemical and virological assays to emphasize the importance of prion-like low complexity domains surrounding short phenylalanine-glycine regions in binding and increasing the avidity when interacting with viral capsid.

    • Guochao Wei
    • , Naseer Iqbal
    •  & Mamuka Kvaratskhelia

  • Article
    | Open Access

    SIVmac239 infection of macaques is a favored model of human HIV infection, but antibody-mediated protection for SIVmac239 is insufficiently understood. Here, Zhao and Berndsen et al isolated nAbs and confirmed protection against SIVmac239 infection in passive transfer studies in macaques. The nAb was used to provide the first high-resolution structure of a rhesus SIV trimer by CryoEM. Analysis of the glycosylation pattern of this SIV trimer suggests a denser glycan shield on Env for rhesus SIV compared to chimpanzee SIV or HIV-1, which partially explains the poor nAb response of rhesus macaques to SIVmac239 infection.

    • Fangzhu Zhao
    • , Zachary T. Berndsen
    •  & Devin Sok

  • Article
    | Open Access

    Although antiretroviral therapy (ART) is able to successfully suppress plasma viremia in most people living with HIV, ART withdrawal typically results in viral replication and rebound. Authors investigate the effect, in terms of delay in viral replication, and immune cell dynamics in lymphoid tissue, of fingolimod (FTY720) administration at the time of ART initiation in SIV-infected rhesus macaques.

    • Maria Pino
    • , Amélie Pagliuzza
    •  & Mirko Paiardini

  • Article
    | Open Access

    Human T-cell leukemia virus type 1 (HTLV-1) is an oncogenic virus with constantly active antisense transcription from the proviral genome. Here, Matsuo et al. perform proviral DNA-capture followed by high-throughput sequencing and identify a yet unknown viral enhancer in the middle of the HTLV-1 provirus.

    • Misaki Matsuo
    • , Takaharu Ueno
    •  & Yorifumi Satou

  • Article
    | Open Access

    The authors determined high-resolution cryo-EM structures of the lentiviral intasome — the nucleoprotein complex that inserts viral DNA into a host chromosome — and show that the architecture comprising 16 integrase subunits is critical for its function.

    • Allison Ballandras-Colas
    • , Vidya Chivukula
    •  & Peter Cherepanov

  • Article
    | Open Access

    SERINC5 is a host-restriction factor preventing HIV progeny entry, which is counteracted by interactions with HIV Nef. Here, Li et al. show that E3 ubiquitin ligase Cullin 3 polyubiquitinates SERINC5 at Lys 130 via K48- and K33-linked ubiquitin chains and provide evidence that this modification is not only required for its membrane localization and anti-viral activity but also relevant for Nef counteractive activity.

    • Sunan Li
    • , Rongrong Li
    •  & Yong-Hui Zheng

  • Article
    | Open Access

    HIV-1 integration sites are biased towards actively transcribed genes, likely mediated by binding of the viral integrase (IN) protein to host factors. Here, Winans et al. show that the K258R point mutation in IN eredirects viral DNA integration to the centromeres of host chromosomes, which may affect HIV latency.

    • Shelby Winans
    • , Hyun Jae Yu
    •  & Stephen P. Goff

  • Article
    | Open Access

    The human silencing hub (HUSH) complex, which includes TASOR, deposits repressive marks on HIV proviruses, resulting in gene repression. Here, Matkovic et al. show that TASOR interacts with RNA Polymerase II, predominantly under its elongating state, and RNA degradation proteins to repress HIV provirus expression.

    • Roy Matkovic
    • , Marina Morel
    •  & Florence Margottin-Goguet

  • Article
    | Open Access

    SAMHD1 is a cellular dNTPase proposed to inhibit HIV-1 reverse transcription in non-cycling immune cells by limiting dNTP substrate supply; its anti-viral but not dNTPase function is downregulated by phosphorylation of T592. Here, Martinat et al. describe an additional SUMOylation at residue K595, which promotes the dNTPase-independent restriction activity.

    • Charlotte Martinat
    • , Arthur Cormier
    •  & Alessia Zamborlini

  • Article
    | Open Access

    Current HIV cure-focused clinical trials rely on analytic treatment interruption (ATI) to evaluate post-treatment control (PTC). Here, combining untargetted metabolomics and glycomics in two HIV clinical cohorts, in vitro assays, and machine learning, the authors identify and validate metabolic and glycomic biomarkers linked to inflammatory pathways and HIV latency reactivation associated with PTC, suggesting non-invasive biomarkers as an alternative to predict HIV remission.

    • Leila B. Giron
    • , Clovis S. Palmer
    •  & Mohamed Abdel-Mohsen

  • Article
    | Open Access

    Inositol hexakisphosphate (IP6) is a known assembly cofactor for HIV-1. Here, the authors show the role of IP6 in the assembly of the Rous sarcoma virus (RSV). Reported cryo-ET structures of mature capsid-like particles (CLPs) suggest that IP6 modulates the formation of capsid polyhedrons of variable shape.

    • Martin Obr
    • , Clifton L. Ricana
    •  & Robert A. Dick

  • Article
    | Open Access

    HIV-1 integrase (IN) binds the host factor INI1/SMARCB1, which is required at multiple stages of HIV-1 replication. Here, the authors show that the same IN residues are involved in INI1 and RNA binding and in influencing particle morphogenesis and suggest that the IN-binding INI1 domain is structurally similar to HIV TAR RNA.

    • Updesh Dixit
    • , Savita Bhutoria
    •  & Ganjam V. Kalpana

  • Article
    | Open Access

    DEAD-box polypeptide 3 (DDX3) is a host protein belonging to the family of ATP-dependent RNA helicases. Here, the authors demonstrate that DDX3 inhibitors reverse HIV-1 latency and selectively induce cell death in HIV-1-infected cell lines, primary CD4+ T cells and in CD4+ T cells from cART-suppressed people living with HIV-1.

    • Shringar Rao
    • , Cynthia Lungu
    •  & Tokameh Mahmoudi

  • Article
    | Open Access

    Epithelial tissue mononuclear phagocytes (MNP) can transmit HIV to CD4 T cells, but less is known about sub-epithelial cells. Here, the authors describe MNPs in human anogenital and colorectal tissues and find that CD14+CD1c+ monocyte-derived dendritic cells and langerin-expressing conventional dendritic cells 2 preferentially take up and transmit HIV.

    • Jake W. Rhodes
    • , Rachel A. Botting
    •  & Andrew N. Harman

  • Article
    | Open Access

    Koalas are susceptible to neoplasms, which are related to infection with the Koala retrovirus. Here, the authors use DNA sequencing to show that the retroviral insertion sites cluster near known cancer genes and demonstrate a high mutational load associated with the germline invasion of the virus.

    • Gayle K. McEwen
    • , David E. Alquezar-Planas
    •  & Alex D. Greenwood

  • Article
    | Open Access

    NK cells control SIV infection in secondary lymphoid tissues in the natural host that typically doesn’t progress toward disease. Here the authors show that this control is associated with terminal NK cell differentiation and improved MHC-E-dependent activity lacking in pathogenic SIV infection.

    • Nicolas Huot
    • , Philippe Rascle
    •  & Michaela Müller-Trutwin

  • Article
    | Open Access

    It is unknown whether capsulized fecal microbiota transplantation (FMT) can modify the microbiota of people with HIV. Here, the authors report the results of a pilot double-blind study, where 30 HIV-infected subjects on ART were randomized to either weekly oral FMT capsules or placebo for 8 weeks, and show that transplanted microbiota successfully engrafts and is able to attenuate HIV-associated dysbiosis.

    • Sergio Serrano-Villar
    • , Alba Talavera-Rodríguez
    •  & Santiago Moreno

  • Article
    | Open Access

    Here the authors combine next generation sequencing on plasma from participants of the ADVANCE clinical trial with virological and follow-up data to investigate the impact of pre-treatment drug resistance (PDR) to non-nucleoside reverse transcriptase inhibitors (NNRTIs) on the efficacy of second-generation integrase inhibitors and find an association between NNRTI resistance prior to treatment and long-term treatment.

    • Mark J. Siedner
    • , Michelle A. Moorhouse
    •  & Ravindra K. Gupta

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