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Chigor VN, Digwo DC, Adediji A, Chidebelu PE, Chigor CB, Ugwu KO, Ibangha IAI, Street R, Farkas K. Epidemiology of norovirus infection in Nigeria: a systematic review and meta-analysis. Arch Virol 2024; 169:138. [PMID: 38847856 DOI: 10.1007/s00705-024-06056-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/23/2024] [Indexed: 06/13/2024]
Abstract
Human norovirus (HuNoV) is responsible for most cases of gastroenteritis worldwide, but information about the prevalence and diversity of HuNoV infections in lower-income settings is lacking. In order to provide more information about the burden and distribution of norovirus in Nigeria, we systematically reviewed original published research articles on the prevalence of HuNoV in Nigeria by accessing databases, including PubMed, Web of Science, ScienceDirect, Google Scholar, and African Journals Online (AJOL). The protocol for the review was registered on PROSPERO (registration number CRD42022308857). Thirteen relevant articles were included in the review, and 10 of them were used for meta-analysis. The pooled prevalence of HuNoV-associated gastroenteritis among children below 5 years of age in Nigeria, determined using the random-effects model, was 10.9% (95% CI, 6.7-16.7%). Among children below the age of 5 presenting with HuNoV infections, the highest prevalence was in children ≤2 years old (n = 127, 83%). The prevalence of HuNoV infections was seen to decrease with increasing age. In addition, HuNoV was detected in asymptomatic food handlers, bats, and seafoods. A total of 85 sequences of HuNoV isolates from Nigeria have been determined, and based on those sequences, the most prevalent norovirus genogroup was GII (84%). Genotypes GII.4 and GI.3 were the most frequently identified genotypes, with GII.4 constituting 46% of all of the HuNoVs identified in Nigeria. These results suggest a risk associated with cocirculation of emerging variants with known genotypes because of their recombination potential. Larger molecular epidemiological studies are still needed to fully understand the extent and pattern of circulation of HuNoVs in Nigeria.
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Affiliation(s)
- Vincent N Chigor
- Water and Public Health Research Group (WPHRG), Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria.
| | - Daniel C Digwo
- Water and Public Health Research Group (WPHRG), Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria
| | - Adedapo Adediji
- Water and Public Health Research Group (WPHRG), Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria
| | - Paul E Chidebelu
- Water and Public Health Research Group (WPHRG), Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria
| | - Chinyere B Chigor
- Water and Public Health Research Group (WPHRG), Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria
| | - Kenneth O Ugwu
- Water and Public Health Research Group (WPHRG), Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria
| | - Ini-Abasi I Ibangha
- Water and Public Health Research Group (WPHRG), Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria
| | - Renee Street
- South African Medical Research Council, Environment & Health Research Unit, Durban, KwaZulu-Natal, South Africa
| | - Kata Farkas
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, United Kingdom
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2
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Characterization of a Novel RNA Virus Causing Massive Mortality in Yellow Catfish, Pelteobagrus fulvidraco, as an Emerging Genus in Caliciviridae ( Picornavirales). Microbiol Spectr 2022; 10:e0062422. [PMID: 35924844 PMCID: PMC9431444 DOI: 10.1128/spectrum.00624-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An emerging disease in farmed yellow catfish (Pelteobagrus fulvidraco) causing massive mortality broke out in 2020 in Hubei, China. Histopathological examination indicated significant changes in kidneys and spleens of diseased fish. Electron microscopy revealed large numbers of viral particles in the kidneys and spleens. These particles were spherical with a diameter of approximately 35 nm. By using RNA sequencing and rapid identification of cDNA ends, the full nucleotide sequence of the virus was identified. The viral genome comprises 7,432 bp and contains three open reading frames sharing no nucleotide sequence similarity with other viruses; however, the amino acid sequence partially matched that of the nonstructural (NS) proteins from viruses in the order Picornavirales. Combined with the phylogenetic analysis, the conserved amino acid motifs and the domains of the viral genome predict a genome order typical of a calicivirus. Therefore, this virus was tentatively named yellow catfish calicivirus (YcCV). Cell culture showed that YcCV could cause a cytopathic effect in the channel catfish kidney cell line (CCK) at early passages. In artificial infection, this virus could infect healthy yellow catfish and led to clinical symptoms similar to those that occurred naturally. In situ hybridization analysis detected positive signals of the virus in kidney, spleen, liver, heart, and gill tissues of diseased fish. This study represents the first report of calicivirus infection in yellow catfish and provides a solid basis for future studies on the control of this viral disease. IMPORTANCE Caliciviruses are rapidly evolving viruses that cause pandemic outbreaks associated with significant morbidity and mortality globally. A novel calicivirus identified from yellow catfish also causes substantial mortality. Using an RNA sequencing (RNA-seq) and rapid amplification of cDNA ends (RACE) method, the full nucleotide sequence was identified and characterized, and this virus was tentatively named yellow catfish calicivirus (YcCV). A nucleotide sequence similarity search found no match with other viruses, and an amino acid sequence comparison indicated approximately 23.3% amino acid homology with the viruses in the order Picornavirales. These findings may represent a new avenue to explain virus evolution and suggest a need to further study the pathogenesis of calicivirus and characterize possible interactions among interspecific viruses in the aquaculture environment.
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3
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Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck's Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family. Microorganisms 2022; 10:microorganisms10081540. [PMID: 36013958 PMCID: PMC9416405 DOI: 10.3390/microorganisms10081540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular genetics and bioinformatics methods can shed light on their genetic architecture and evolutionary relationships. Here, we present and characterize the complete genome sequence of calicivirus isolated from a sandpiper-Temminck's stint (Calidris temminckii), preliminarily named Temminck's stint calicivirus (TsCV). Its genome is a linear, non-segmented, single-stranded (+sense) RNA with genome organization typical of avian caliciviruses. Comparative studies have shown significant divergence of the nucleotide sequence of the TsCV genome, as well as the amino acid sequence of the major capsid protein from all publicly available genomic and protein sequences, with the highest genome sequence similarity to unclassified Ruddy turnstone calicivirus A (43.68%) and the lowest pairwise divergence of the major capsid protein with unclassified goose calicivirus (57.44%). Phylogenetic analysis, as well as a comparative analysis of the homologous proteins, showed evidence of another separate genus within the Caliciviridae family-previously proposed, but not yet accepted by International Committee on Taxonomy of Viruses (ICTV)-the Sanovirus genus, which combines seven previously unclassified genomic sequences of avian caliciviruses, including the newly discovered TsCV, which we propose to consider as a separate species.
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4
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Wang J, Li L, Xu Y, Mao T, Ma Y, Sun X, Liu X, Wang Y, Duan Z. Identification of a novel norovirus species in fox. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105214. [PMID: 35051652 DOI: 10.1016/j.meegid.2022.105214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
A novel Norovirus (NoV) was identified by viral metagenomic analysis in fox fecal samples from the Xinjiang Uygur Autonomous Region of China. The virus exhibited typical genomic characteristics of NoVs. It was closely related to the canine NoV GVII strains with 86.0-86.2% and 91.9% amino acid identities in the capsid protein VP1 and RNA-dependent RNA polymerase (RdRp), respectively. The fox NoV clustered phylogenetically with the two canine NoV GVII strains, and it was distant from other NoVs. According to the new classification criteria of NoVs, the new fox NoV belongs to the same genotype as GVII, similar to canine GVII NoVs. Moreover, key amino acid residues in the Histo-blood group antigen (HBGA) binding sites and the HBGA binding pattern of the fox NoV differed significantly from those of human and canine GVII NoVs. This study identified a new GVII norovirus from wild foxes in China. These findings enrich our understanding of the diversity of NoVs and provide further evidence regarding the genetic heterogeneity of NoVs in carnivores.
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Affiliation(s)
- Jindong Wang
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lili Li
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yalong Xu
- Shaanxi Provincial Centre for Disease Control and Prevention, Xi'an 710054, China
| | - Tongyao Mao
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yalin Ma
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiaoman Sun
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiafei Liu
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yuanzhi Wang
- School of Medicine, Shihezi University, Shihezi 832000, China.
| | - Zhaojun Duan
- National Institute for Viral Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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5
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Bonny P, Schaeffer J, Besnard A, Desdouits M, Ngang JJE, Le Guyader FS. Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams. Front Microbiol 2021; 12:770385. [PMID: 34917052 PMCID: PMC8669915 DOI: 10.3389/fmicb.2021.770385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.
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Affiliation(s)
- Patrice Bonny
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France.,Département de Microbiologie, Université de Yaoundé I, Yaoundé, Cameroon.,Centre de Recherche en Alimentation et Nutrition, IMPM, Yaoundé, Cameroon
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Alban Besnard
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Marion Desdouits
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
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6
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Albery GF, Becker DJ, Brierley L, Brook CE, Christofferson RC, Cohen LE, Dallas TA, Eskew EA, Fagre A, Farrell MJ, Glennon E, Guth S, Joseph MB, Mollentze N, Neely BA, Poisot T, Rasmussen AL, Ryan SJ, Seifert S, Sjodin AR, Sorrell EM, Carlson CJ. The science of the host-virus network. Nat Microbiol 2021; 6:1483-1492. [PMID: 34819645 DOI: 10.1038/s41564-021-00999-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/18/2021] [Indexed: 01/21/2023]
Abstract
Better methods to predict and prevent the emergence of zoonotic viruses could support future efforts to reduce the risk of epidemics. We propose a network science framework for understanding and predicting human and animal susceptibility to viral infections. Related approaches have so far helped to identify basic biological rules that govern cross-species transmission and structure the global virome. We highlight ways to make modelling both accurate and actionable, and discuss the barriers that prevent researchers from translating viral ecology into public health policies that could prevent future pandemics.
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Affiliation(s)
- Gregory F Albery
- Department of Biology, Georgetown University, Washington DC, USA.
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Liam Brierley
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Cara E Brook
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tad A Dallas
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Evan A Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Anna Fagre
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maxwell J Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Emma Glennon
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Maxwell B Joseph
- Earth Lab, Cooperative Institute for Research in Environmental Science, University of Colorado Boulder, Boulder, CO, USA
| | - Nardus Mollentze
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,MRC - University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Benjamin A Neely
- National Institute of Standards and Technology, Charleston, SC, USA
| | - Timothée Poisot
- Québec Centre for Biodiversity Sciences, Montréal, Québec, Canada.,Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sadie J Ryan
- Department of Geography, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Stephanie Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Anna R Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Erin M Sorrell
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA.,Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA. .,Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA.
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7
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Noroviruses-The State of the Art, Nearly Fifty Years after Their Initial Discovery. Viruses 2021; 13:v13081541. [PMID: 34452406 PMCID: PMC8402810 DOI: 10.3390/v13081541] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/06/2021] [Accepted: 07/31/2021] [Indexed: 12/11/2022] Open
Abstract
Human noroviruses are recognised as the major global cause of viral gastroenteritis. Here, we provide an overview of notable advances in norovirus research and provide a short recap of the novel model systems to which much of the recent progress is owed. Significant advances include an updated classification system, the description of alternative virus-like protein morphologies and capsid dynamics, and the further elucidation of the functions and roles of various viral proteins. Important milestones include new insights into cell tropism, host and microbial attachment factors and receptors, interactions with the cellular translational apparatus, and viral egress from cells. Noroviruses have been detected in previously unrecognised hosts and detection itself is facilitated by improved analytical techniques. New potential transmission routes and/or viral reservoirs have been proposed. Recent in vivo and in vitro findings have added to the understanding of host immunity in response to norovirus infection, and vaccine development has progressed to preclinical and even clinical trial testing. Ongoing development of therapeutics includes promising direct-acting small molecules and host-factor drugs.
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8
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Cuéllar-Cruz M. The histo-blood group antigens of the host cell may determine the binding of different viruses such as SARS-CoV-2. Future Microbiol 2021; 16:107-118. [PMID: 33459559 PMCID: PMC7842250 DOI: 10.2217/fmb-2020-0158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Viruses have caused the death of millions of people worldwide. Specifically, human viruses are grouped into 21 families, including the family of coronaviruses (CoVs). In December 2019, in Wuhan, China, a new human CoV was identified, SARS-CoV-2. The first step of the infection mechanism of the SARS-CoV-2 in the human host is adhesion, which occurs through the S glycoprotein that is found in diverse human organs. Another way through which SARS-CoV-2 could possibly attach to the host's cells is by means of the histo-blood group antigens. In this work, we have reviewed the mechanisms by which some viruses bind to the histo-blood group antigens, which could be related to the susceptibility of the individual and are dependent on the histo-blood group.
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Affiliation(s)
- Mayra Cuéllar-Cruz
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta, C.P. 36050, Guanajuato, Guanajuato, México
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9
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Human Noroviruses Attach to Intestinal Tissues of a Broad Range of Animal Species. J Virol 2021; 95:JVI.01492-20. [PMID: 33115870 DOI: 10.1128/jvi.01492-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/26/2020] [Indexed: 11/20/2022] Open
Abstract
Human noroviruses are the most common nonbacterial cause of gastroenteritis outbreaks, with new variants and genotypes frequently emerging. The origin of these new viruses is unknown; however, animals have been proposed as a potential source, as human noroviruses have been detected in animal species. Here, we investigated the potential of animals to serve as a reservoir of human noroviruses by testing norovirus attachment to formalin-fixed intestinal tissues of a range of potential reservoir animals. We set up a novel method to study norovirus binding using fluorescein isothiocyanate (FITC)-labeled virus-like particles (VLPs). In humans, noroviruses interact with histo-blood group antigens (HBGAs), carbohydrates that are expressed, among others, on the epithelial lining of the gastrointestinal tract. In animals, this interaction is not well understood. To test if virus binding depends on HBGAs, we characterized the HBGA phenotype in animal tissues by immunohistochemistry. With the exception of the black-headed gull and the straw-colored fruitbat, we observed the attachment of several human norovirus genotypes to the intestinal epithelium of all tested animal species. However, we did not find an association between the expression of a specific HBGA phenotype and virus-like particle (VLP) attachment. We show that selected human noroviruses can attach to small-intestinal tissues across species, supporting the hypothesis that human noroviruses can reside in an animal reservoir. However, whether this attachment can subsequently lead to infection needs to be further assessed.IMPORTANCE Noroviruses are a major cause of acute gastroenteritis in humans. New norovirus variants and recombinants (re)emerge regularly in the human population. From animal experiments and surveillance studies, it has become clear that at least seven animal models are susceptible to infection with human strains and that domesticated and wild animals shed human noroviruses in their feces. As virus attachment is an important first step for infection, we used a novel method utilizing FITC-labeled VLPs to test for norovirus attachment to intestinal tissues of potential animal hosts. We further characterized these tissues with regard to their HBGA expression, a well-studied norovirus susceptibility factor in humans. We found attachment of several human strains to a variety of animal species independent of their HBGA phenotype. This supports the hypothesis that human strains could reside in an animal reservoir.
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10
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Ruis C, Lindesmith LC, Mallory ML, Brewer-Jensen PD, Bryant JM, Costantini V, Monit C, Vinjé J, Baric RS, Goldstein RA, Breuer J. Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence. Virus Evol 2020; 6:veaa067. [PMID: 33381305 PMCID: PMC7751145 DOI: 10.1093/ve/veaa067] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The control of re-occurring pandemic pathogens requires understanding the origins of new pandemic variants and the factors that drive their global spread. This is especially important for GII.4 norovirus, where vaccines under development offer promise to prevent hundreds of millions of annual gastroenteritis cases. Previous studies have hypothesized that new GII.4 pandemic viruses arise when previously circulating pandemic or pre-pandemic variants undergo substitutions in antigenic regions that enable evasion of host population immunity, as described by conventional models of antigenic drift. In contrast, we show here that the acquisition of new genetic and antigenic characteristics cannot be the proximal driver of new pandemics. Pandemic GII.4 viruses diversify and spread over wide geographical areas over several years prior to simultaneous pandemic emergence of multiple lineages, indicating that the necessary sequence changes must have occurred before diversification, years prior to pandemic emergence. We confirm this result through serological assays of reconstructed ancestral virus capsids, demonstrating that by 2003, the ancestral 2012 pandemic strain had already acquired the antigenic characteristics that allowed it to evade prevailing population immunity against the previous 2009 pandemic variant. These results provide strong evidence that viral genetic changes are necessary but not sufficient for GII.4 pandemic spread. Instead, we suggest that it is changes in host population immunity that enable pandemic spread of an antigenically preadapted GII.4 variant. These results indicate that predicting future GII.4 pandemic variants will require surveillance of currently unsampled reservoir populations. Furthermore, a broadly acting GII.4 vaccine will be critical to prevent future pandemics.
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Affiliation(s)
- Christopher Ruis
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Lisa C Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Josephine M Bryant
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Veronica Costantini
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christopher Monit
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Richard A Goldstein
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.,Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children, London, UK
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11
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Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2. Sci Rep 2020; 10:14502. [PMID: 32879332 PMCID: PMC7468141 DOI: 10.1038/s41598-020-71303-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
Rabbit haemorrhagic disease is a viral disease that emerged in the 1980s and causes high mortality and morbidity in the European rabbit (Oryctolagus cuniculus). In 2010, a new genotype of the rabbit haemorrhagic disease virus emerged and replaced the former circulating Lagovirus europaeus/GI.1 strains. Several recombination events have been reported for the new genotype Lagovirus europaeus/GI.2, with pathogenic (variants GI.1a and GI.1b) and benign (genotype GI.4) strains that served as donors for the non-structural part while GI.2 composed the structural part; another recombination event has also been described at the p16/p23 junction involving GI.4 strains. In this study, we analysed new complete coding sequences of four benign GI.3 strains and four GI.2 strains. Phylogenetic and recombination detection analyses revealed that the first GI.2 strains, considered as non-recombinant, resulted from a recombination event between GI.3 and GI.2, with GI.3 as the major donor for the non-structural part and GI.2 for the structural part. Our results indicate that recombination contributed to the emergence, persistence and dissemination of GI.2 as a pathogenic form and that all described GI.2 strains so far are the product of recombination. This highlights the need to study full-genomic sequences of lagoviruses to understand their emergence and evolution.
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12
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Abdollahi A, Mahmoudi-Aliabadi M, Mehrtash V, Jafarzadeh B, Salehi M. The Novel Coronavirus SARS-CoV-2 Vulnerability Association with ABO/Rh Blood Types. IRANIAN JOURNAL OF PATHOLOGY 2020; 15:156-160. [PMID: 32754209 PMCID: PMC7354076 DOI: 10.30699/ijp.2020.125135.2367] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/05/2020] [Indexed: 11/30/2022]
Abstract
Background & Objective: Coronavirus disease 2019 (COVID-19) is the most recent emerging viral disease. Defining the epidemiological aspects and factors influencing the susceptibility of the patients to COVID-19 has been an ongoing struggle. In the present study, we have investigated the connection between ABO histo-blood group phenotypes and the COVID-19. Methods: This study was conducted on 397 patients with confirmed diagnoses of COVID-19 admitted to our center. Also, 500 individuals were selected to form the controls, all of whom had been disclosed to the same medical center in June 2019, before the onset of the outbreak. Results: Our results demonstrated ABO histo-blood phenotypes are correlated with patients’ susceptibility to the infection. A higher rate of infection was observed among patients with the AB histo-blood group, while patients with the O histo-blood group have shown a lower rate of infection. The Rh blood group phenotype was not statistically significant in determining a patient’s vulnerability. Conclusion: Similar to several previous studies about other viral diseases’ association with ABO histo-blood groups, we have concluded that an individual’s ABO histo-blood group phenotype and his/her susceptibility to COVID-19 are indeed connected. So far, only one research has been conducted about this association. Interestingly, while we observed a decreased vulnerability to the disease among patients with an O histo-blood group, we have reached discordant results regarding the increased susceptibility among individuals with an AB histo-blood group, unlike A histo-blood group in the previous study.
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Affiliation(s)
- Alireza Abdollahi
- Department of Pathology, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Maedeh Mahmoudi-Aliabadi
- Department of Laboratory, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Mehrtash
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Bita Jafarzadeh
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Salehi
- Department of Infectious Diseases and Tropical Medicine, School of Medicine, Imam Hospital complex, Tehran University of Medical Sciences, Tehran, Iran
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GII.13/21 Noroviruses Recognize Glycans with a Terminal β-Galactose via an Unconventional Glycan Binding Site. J Virol 2019; 93:JVI.00723-19. [PMID: 31118252 PMCID: PMC6639292 DOI: 10.1128/jvi.00723-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/17/2023] Open
Abstract
Evidence from both phenotypic binding assay and structural study support the observed interactions of human noroviruses (huNoVs) with histo-blood group antigens (HBGAs) as receptors or attachment factors, affecting their host susceptibility. GII.13 and GII.21 genotypes form a unique genetic lineage that differs from the mainstream GII huNoVs in their unconventional glycan binding site. Unlike the previous findings that GII.13/21 genotypes recognize only Lea antigen, we found in this study that they can interact with a group of glycans with a common terminal β-Gal, including Lec, lactose, and mucin core 2. However, this wide glycan binding spectrum in a unique binding mode of the GII.13/21 huNoVs appears not to increase their prevalence, probably due to the existence of decoy glycan receptors in human gastrointestinal tract limiting their infection. Our findings shed light on the host interaction and epidemiology of huNoVs, which would impact the strategy of huNoV control and prevention. Human noroviruses (huNoVs) recognize histo-blood group antigens (HBGAs) as host susceptibility factors. GII.13 and GII.21 huNoVs form a unique genetic lineage that emerged from mainstream GII NoVs via development of a new, nonconventional glycan binding site (GBS) that binds Lea antigen. This previous finding raised the question of whether the new GII.13/21 GBS really has such a narrow glycan binding spectrum. In this study, we provide solid phenotypic and structural evidence indicating that this new GBS recognizes a group of glycans with a common terminal β-galactose (β-Gal). First, we found that P domain proteins of GII.13/21 huNoVs circulating at different times bound three glycans sharing a common terminal β-Gal, including Lec, lactose, and mucin core 2. Second, we solved the crystal structures of the GII.13 P dimers in complex with Lec and mucin core 2, which showed that β-Gal is the major binding saccharide. Third, nonfat milk and lactose blocked the GII.13/21 P domain-glycan binding, which may explain the low prevalence of GII.13/21 viruses. Our data provide new insight into the host interactions and epidemiology of huNoVs, which would help in the control and prevention of NoV-associated diseases. IMPORTANCE Evidence from both phenotypic binding assay and structural study support the observed interactions of human noroviruses (huNoVs) with histo-blood group antigens (HBGAs) as receptors or attachment factors, affecting their host susceptibility. GII.13 and GII.21 genotypes form a unique genetic lineage that differs from the mainstream GII huNoVs in their unconventional glycan binding site. Unlike the previous findings that GII.13/21 genotypes recognize only Lea antigen, we found in this study that they can interact with a group of glycans with a common terminal β-Gal, including Lec, lactose, and mucin core 2. However, this wide glycan binding spectrum in a unique binding mode of the GII.13/21 huNoVs appears not to increase their prevalence, probably due to the existence of decoy glycan receptors in human gastrointestinal tract limiting their infection. Our findings shed light on the host interaction and epidemiology of huNoVs, which would impact the strategy of huNoV control and prevention.
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14
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Animals as Reservoir for Human Norovirus. Viruses 2019; 11:v11050478. [PMID: 31130647 PMCID: PMC6563253 DOI: 10.3390/v11050478] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 01/12/2023] Open
Abstract
Norovirus is the most common cause of non-bacterial gastroenteritis and is a burden worldwide. The increasing norovirus diversity is currently categorized into at least 10 genogroups which are further classified into more than 40 genotypes. In addition to humans, norovirus can infect a broad range of hosts including livestock, pets, and wild animals, e.g., marine mammals and bats. Little is known about norovirus infections in most non-human hosts, but the close genetic relatedness between some animal and human noroviruses coupled with lack of understanding where newly appearing human norovirus genotypes and variants are emerging from has led to the hypothesis that norovirus may not be host restricted and might be able to jump the species barrier. We have systematically reviewed the literature to describe the diversity, prevalence, and geographic distribution of noroviruses found in animals, and the pathology associated with infection. We further discuss the evidence that exists for or against interspecies transmission including surveillance data and data from in vitro and in vivo experiments.
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15
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Desselberger U. Caliciviridae Other Than Noroviruses. Viruses 2019; 11:v11030286. [PMID: 30901945 PMCID: PMC6466229 DOI: 10.3390/v11030286] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/24/2022] Open
Abstract
Besides noroviruses, the Caliciviridae family comprises four other accepted genera: Sapovirus, Lagovirus, Vesivirus, and Nebovirus. There are six new genera proposed: Recovirus, Valovirus, Bavovirus, Nacovirus, Minovirus, and Salovirus. All Caliciviridae have closely related genome structures, but are genetically and antigenically highly diverse and infect a wide range of mammalian host species including humans. Recombination in nature is not infrequent for most of the Caliciviridae, contributing to their diversity. Sapovirus infections cause diarrhoea in pigs, humans and other mammalian hosts. Lagovirus infections cause systemic haemorrhagic disease in rabbits and hares, and vesivirus infections lead to lung disease in cats, vesicular disease in swine, and exanthema and diseases of the reproductive system in large sea mammals. Neboviruses are an enteric pathogen of cattle, differing from bovine norovirus. At present, only a few selected caliciviruses can be propagated in cell culture (permanent cell lines or enteroids), and for most of the cultivatable caliciviruses helper virus-free, plasmid only-based reverse genetics systems have been established. The replication cycles of the caliciviruses are similar as far as they have been explored: viruses interact with a multitude of cell surface attachment factors (glycans) and co-receptors (proteins) for adsorption and penetration, use cellular membranes for the formation of replication complexes and have developed mechanisms to circumvent innate immune responses. Vaccines have been developed against lagoviruses and vesiviruses, and are under development against human noroviruses.
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Affiliation(s)
- Ulrich Desselberger
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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16
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Thompson AJ, de Vries RP, Paulson JC. Virus recognition of glycan receptors. Curr Opin Virol 2019; 34:117-129. [PMID: 30849709 PMCID: PMC6476673 DOI: 10.1016/j.coviro.2019.01.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/24/2019] [Indexed: 01/17/2023]
Abstract
Attachment of viruses to cell-surface receptors is the initial step in infection. Many mammalian viruses have evolved to recognize receptors that are glycans on cell-surface glycoproteins or glycolipids. Although glycans are a ubiquitous component of mammalian cells, the types of terminal structures expressed vary among different cell-types and tissues, and even between comparable cells and tissues from different species, frequently leading to specific tissue and species tropisms as a direct consequence of glycan receptor recognition. Covering the majority of known virus families, this review provides an overview of mammalian viruses that use glycans as receptors, and their roles in determining in host recognition and tropism.
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Affiliation(s)
- Andrew J Thompson
- Departments of Molecular Medicine, Immunology & Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - James C Paulson
- Departments of Molecular Medicine, Immunology & Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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17
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Viruses in bats and potential spillover to animals and humans. Curr Opin Virol 2019; 34:79-89. [PMID: 30665189 PMCID: PMC7102861 DOI: 10.1016/j.coviro.2018.12.007] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/17/2022]
Abstract
Bats are a very important source of emerging viruses. Bat coronavirus, filovirus, paramyxovirus and reovirus are known zoonotic viruses. Many of the emergent bat viruses are highly lethal in livestock and humans. Past incidents and viral genetic features predict bat coronaviruses as the highest risk.
In the last two decades, several high impact zoonotic disease outbreaks have been linked to bat-borne viruses. These include SARS coronavirus, Hendra virus and Nipah virus. In addition, it has been suspected that ebolaviruses and MERS coronavirus are also linked to bats. It is being increasingly accepted that bats are potential reservoirs of a large number of known and unknown viruses, many of which could spillover into animal and human populations. However, our knowledge into basic bat biology and immunology is very limited and we have little understanding of major factors contributing to the risk of bat virus spillover events. Here we provide a brief review of the latest findings in bat viruses and their potential risk of cross-species transmission.
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18
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Yang Y, Xia M, Wang L, Arumugam S, Wang Y, Ou X, Wang C, Jiang X, Tan M, Chen Y, Li X. Structural basis of host ligand specificity change of GII porcine noroviruses from their closely related GII human noroviruses. Emerg Microbes Infect 2019; 8:1642-1657. [PMID: 31711377 PMCID: PMC6853222 DOI: 10.1080/22221751.2019.1686335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/20/2019] [Indexed: 02/07/2023]
Abstract
Diverse noroviruses infect humans and animals via the recognition of host-specific glycan ligands. Genogroup II (GII) noroviruses consist of human noroviruses (huNoVs) that generally bind histo-blood group antigens (HBGAs) as host factors and three porcine norovirus (porNoV) genotypes (GII.11/18/19) that form a genetic lineage lacking HBGA-binding ability. Thus, these GII porNoVs provide an excellent model to study norovirus evolution with host ligand specificity changes. Here we solved the crystal structures of a native GII.11 porNoV P protein and a closely-related GII.3 huNoV P protein complexed with an HBGA, focusing on the HBGA-binding sites (HBSs) compared with the previously known ones to understand the structural basis of the host ligand specificity change. We found that the GII.3 huNoV binds HBGAs via a conventional GII HBS that uses an arginine instead of the conserved aromatic residue for the required Van der Waals interaction, while the GII.11 porNoV HBS loses its HBGA-binding function because of two mutations (Q355/V451). A mutant that reversed the two mutated residues back to the conventional A355/Y451 restored the HBGA-binding function of the GII.11 porNoV P protein, which validated our observations. Similar mutations are also found in GII.19 porNoVs and a GII.19 P protein mutant with double reverse mutations restored the HBS function. This is the first reconstruction of a functional HBS based on one with new host specificity back to its parental one. These data shed light on the molecular basis of structural adaptation of the GII porNoVs to the pig hosts through mutations at their HBSs.
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Affiliation(s)
- Yang Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ming Xia
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Leyi Wang
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Sahaana Arumugam
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Yajing Wang
- College of Life Science, Nankai University, Tianjin, People’s Republic of China
| | - Xianjin Ou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Chenlong Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xi Jiang
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ming Tan
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yutao Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xuemei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
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