Suchergebnisse

Several decades after the discovery of the human norovirus, with thousands of lives and billions of dollars lost, the lack of a robust cell culture system still severely hampers development of vaccines and therapeutics. This is likely in large part as a result of our limited understanding of the immune responses against an infection with the virus. Here, the presence of a RIG-I/STING-dependent innate response pathway that restricts the replication of noroviruses is described, and an attempt by the murine norovirus to subvert it through expression of an accessory protein is demonstrated. We show that both RIG-I and STING are required for a robust interferon response to infection with MNV1 in primary BMDMs and RAW264.7 cells, with a significant increase in viral titres following infection in RIG-I- and STING-deficient cells. We also show that STING is non-canonically activated in MNV1-infected cells partly in a RIG-I dependent manner. Furthermore, our data indicate that the MNV VF1 protein binds to STING and can inhibit interferon induction downstream of RIG-I. Secondly, while exploring the mechanisms for the differential induction of interferon sub- types, we show that depletion of MED23 leads to a reduction in expression of both types I and III IFNs in human and mouse cell lines. We also show that Med23 knockout cells undergo genetic compensation, suggesting a critical role for MED23 in this pathway. Mechanistically, we show that MED23 interacts with IRF3, and is required for recruitment of RNA Polymerase II to promoters of IRF3-dependent genes. Taken together, our data indicate that MED23 plays a central role in antiviral responses by coupling IRF3 activation and RNA Pol II recruitment. ; Presidential Special Scholarship Scheme for Innovation and Development (Nigerian Government)

Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.

Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses. ; This work was funded by COG-UK, supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute;

Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics. ; DA is a Wellcome Clinical PhD Fellow and gratefully supported by the Wellcome Trust (Grant number: 222903/Z/21/Z). BW receives funding from the University of Cambridge and the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre (BRC) at the Cambridge University Hospitals NHS Foundation Trust. IG is a Wellcome Senior Fellow and is supported by the Wellcome Trust (Grant number: 207498/Z/17/Z and 206298/B/17/Z). EMH is supported by a UK Research and Innovation (UKRI) Fellowship: MR/S00291X/1. CJRI acknowledges Medical Research Council (MRC) funding (ref: MC_UU_00002/11). NJM is supported by the MRC (CSF MR/P008801/1) and NHSBT (WPA15-02). AJP gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352, also Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). LdP and OGP were supported by the Oxford Martin School. This research was supported by the NIHR Cambridge BRC. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care. The COVID-19 Genomics UK Consortium is supported by funding from the MRC part of UK Research & Innovation (UKRI), the National Institute of Health Research and Genome Research Limited, operating as the Wellcome Sanger Institute. The Cambridge Covid-19 testing Centre is funded by the Department of Health and Social Care, UK Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. For the purpose of Open Access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.

Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.

Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics. ; DA is a Wellcome Clinical PhD Fellow and gratefully supported by the Wellcome Trust (Grant number: 222903/Z/21/Z). BW receives funding from the University of Cambridge and the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre (BRC) at the Cambridge University Hospitals NHS Foundation Trust. IG is a Wellcome Senior Fellow and is supported by the Wellcome Trust (Grant number: 207498/Z/17/Z and 206298/B/17/Z). EMH is supported by a UK Research and Innovation (UKRI) Fellowship: MR/S00291X/1. CJRI acknowledges Medical Research Council (MRC) funding (ref: MC_UU_00002/11). NJM is supported by the MRC (CSF MR/P008801/1) and NHSBT (WPA15-02). AJP gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352, also Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). LdP and OGP were supported by the Oxford Martin School. This research was supported by the NIHR Cambridge BRC. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health and Social Care. The COVID-19 Genomics UK Consortium is supported by funding from the MRC part of UK Research & Innovation (UKRI), the National Institute of Health Research and Genome Research Limited, operating as the Wellcome Sanger Institute. The Cambridge Covid-19 testing Centre is funded by the Department of Health and Social Care, UK Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. For the purpose of Open Access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.