101
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Drews SJ, O’Brien SF. Lessons Learned from the COVID-19 Pandemic and How Blood Operators Can Prepare for the Next Pandemic. Viruses 2022; 14:2126. [PMID: 36298680 PMCID: PMC9608827 DOI: 10.3390/v14102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/08/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Humans interact with virus-infected animal hosts, travel globally, and maintain social networks that allow for novel viruses to emerge and develop pandemic potential. There are key lessons-learned from the coronavirus diseases 2019 (COVID-19) pandemic that blood operators can apply to the next pandemic. Warning signals to the COVID-19 pandemic included outbreaks of Severe acute respiratory syndrome-related coronavirus-1 (SARS-CoV-1) and Middle East respiratory syndrome-related coronavirus (MERS-CoV) in the prior two decades. It will be critical to quickly determine whether there is a risk of blood-borne transmission of a new pandemic virus. Prior to the next pandemic blood operators should be prepared for changes in activities, policies, and procedures at all levels of the organization. Blood operators can utilize "Plan-Do-Study-Act" cycles spanning from: vigilance for emerging viruses, surveillance activities and studies, operational continuity, donor engagement and trust, and laboratory testing if required. Occupational health and donor safety issues will be key areas of focus even if the next pandemic virus is not transfusion transmitted. Blood operators may also be requested to engage in new activities such as the development of therapeutics or supporting public health surveillance activities. Activities such as scenario development, tabletop exercises, and drills will allow blood operators to prepare for the unknowns of the next pandemic.
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Affiliation(s)
- Steven J. Drews
- Canadian Blood Services, Microbiology, Donation and Policy Studies, Canadian Blood Services, Edmonton, AB T6G 2R8, Canada
- Division of Applied and Diagnostic Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Sheila F. O’Brien
- Epidemiology and Surveillance, Donation Policy and Studies, Canadian Blood Services, Ottawa, ON K1G 4J5, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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102
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Determinants of Virus Variation, Evolution, and Host Adaptation. Pathogens 2022; 11:pathogens11091039. [PMID: 36145471 PMCID: PMC9501407 DOI: 10.3390/pathogens11091039] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation.
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103
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Detection of human feces pecovirus in newly diagnosed HIV patients in Brazil. PLoS One 2022; 17:e0272067. [PMID: 36067165 PMCID: PMC9447917 DOI: 10.1371/journal.pone.0272067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
Circular single stranded DNA viruses (CRESS DNA) encoding a homologous replication-associated protein (REP) have been identified in most of eukaryotic groups. It is not clear yet the role in human diseases or details of the life cycle of these viruses. Recently, much interest has been raised in the evolutionary history of CRESS DNA owing to the increasing number of new sequences obtained by Next-Generation Sequencing (NGS) in distinct host species. In this study we describe two full-length CRESS DNA genomes obtained of two newly diagnosed HIV patients from São Paulo State, Brazil. The initial BLASTx search indicated that both sequences (named SP-FFB/2020 and SP-MJMS/2020) are highly similar (98%) to a previous CRESS DNA sequence detected in human fecal sample from Peru in 2016 and designated as pecovirus (Peruvian stool-associated circo-like virus). This study reported for the first time the Human feces pecovirus in the feces of two newly diagnosed HIV patients in Brazil. Our comparative analysis showed that although pecoviruses in South America share an identical genome structure they diverge and form distinct clades. Thus, we suggest the circulation of different species of pecoviruses in Latin America. Nevertheless, further studies must be done to examine the pathogenicity of this virus.
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104
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Franzo G, Faustini G, Legnardi M, Cecchinato M, Drigo M, Tucciarone CM. Phylodynamic and phylogeographic reconstruction of porcine reproductive and respiratory syndrome virus (PRRSV) in Europe: Patterns and determinants. Transbound Emerg Dis 2022; 69:e2175-e2184. [PMID: 35403349 PMCID: PMC9790212 DOI: 10.1111/tbed.14556] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/08/2022] [Accepted: 04/06/2022] [Indexed: 12/30/2022]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is among the most devastating diseases affecting the pig industry. Despite vaccines having been available for decades, the remarkable genetic variability of this virus, leading to poor cross-protection, has limited their efficacy, and other measures must be adopted to effectively control the viral circulation. Some recent studies have investigated the factors involved in viral spreading and persistence, at least at the local level. However, despite the topic's relevance, no statistically grounded evidence is currently available evaluating the variables more involved in porcine reproductive and respiratory syndrome virus (PRRSV) epidemiological success at a broader scale, such as the European scale. In the present study, an extensive phylodynamic and phylogeographic analysis was performed on more than 1000 ORF5 sequences to investigate the history, dynamics and spreading patterns of PRRSV within European borders. Moreover, several potential predictors, representative of swine population features and trade, human population, economy and geographic characteristics, were evaluated through a specifically designed generalized linear model (GLM) to assess their weight on viral migration rate between countries over time. Although pig stock density, mean PRRSV strain genetic diversity, investments in agriculture (including a likely role of vaccination) and farmer education were involved to a certain extent, the major determinant was proven to be by far the live pig trade. Providing a robust depiction of PRRSV European molecular epidemiology patterns and determinants, the present study could contribute to a more rational allocation of limited resources based on an effective prioritization of control measures.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS)University of PaduaLegnaro PDItaly
| | - Giulia Faustini
- Department of Animal Medicine, Production and Health (MAPS)University of PaduaLegnaro PDItaly
| | - Matteo Legnardi
- Department of Animal Medicine, Production and Health (MAPS)University of PaduaLegnaro PDItaly
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS)University of PaduaLegnaro PDItaly
| | - Michele Drigo
- Department of Animal Medicine, Production and Health (MAPS)University of PaduaLegnaro PDItaly
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105
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Charon J, Buchmann JP, Sadiq S, Holmes EC. RdRp-Scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data. Virus Evol 2022; 8:veac082. [PMID: 36533143 PMCID: PMC9752661 DOI: 10.1093/ve/veac082] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Despite a rapid expansion in the number of documented viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remains challenging, particularly from poorly characterized hosts and environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral “dusk matter”: viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational and resource – RdRp-scan – that contains a standardized bioinformatic toolkit to identify and annotate divergent RNA viruses in metagenomic sequence data based on the detection of RNA dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific Hidden Markov models (HMM) and structural comparisons we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10% to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and divergent virus-like sequences into the diversity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motifs, as well as pre-built RdRp multiple sequence alignments. In parallel, our analysis of the sequence diversity detected by RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, with some falling into potentially new orders of RNA viruses related to the Wolframvirales and Tolivirales. Finally, a survey of the conserved A, B and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position that might provide new insights into the structure, function and evolution of viral polymerases.
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Affiliation(s)
- Justine Charon
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney , Sydney, NSW 2006, Australia
| | - Jan P Buchmann
- Institute for Biological Data Science, Heinrich-Heine-University , Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney , Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney , Sydney, NSW 2006, Australia
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106
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Faustini G, Drigo M, Menandro ML, Pasotto D, Giovanni F. Phylodynamic analysis of current Porcine circovirus 4 sequences: Does the porcine circoviruses evolutionary history repeat itself? Transbound Emerg Dis 2022; 69:e3363-e3369. [PMID: 35735227 PMCID: PMC9796702 DOI: 10.1111/tbed.14638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/12/2022] [Accepted: 06/18/2022] [Indexed: 01/07/2023]
Abstract
Four porcine circoviruses (PCVs) have been discovered over time and seem to share a common history, particularly for PCV-2 and -3. Despite being reported as apparently new viruses, rapidly emerging as a threat for the worldwide swine industry, they were then proven to have been circulating and coexisting with domestic pigs undetected for decades, without causing relevant health issues. A similar scenario could be true for the most recently identified PCV-4. However, its detection in Asia only and the limited genetic variability could suggest a truly recent origin. To investigate which of the above-mentioned scenarios is more plausible, a phylodynamic analysis was performed on all available PCV-4 sequences for which adequate metadata were available to reconstruct the viral history and evolution. Obtained results suggest an ancient origin, at least decades ago, followed by a prolonged low-level circulation and a moderate increase in viral population size after the second half of the XX century, in parallel with a progressive rise in pig population and farming intensification. A relevant local geographical clustering was also highlighted. The reason behind such low spreading capacity and limited geographical distribution compared to other circoviruses is currently obscure and will require dedicated studies, involving a more extensive sampling and sequencing activity.
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Affiliation(s)
- Giulia Faustini
- Department of Animal MedicineProduction and Health (MAPS)University of Padua, LegnaroPaduaItaly
| | - Michele Drigo
- Department of Animal MedicineProduction and Health (MAPS)University of Padua, LegnaroPaduaItaly
| | - Maria Luisa Menandro
- Department of Animal MedicineProduction and Health (MAPS)University of Padua, LegnaroPaduaItaly
| | - Daniela Pasotto
- Department of Animal MedicineProduction and Health (MAPS)University of Padua, LegnaroPaduaItaly
| | - Franzo Giovanni
- Department of Animal MedicineProduction and Health (MAPS)University of Padua, LegnaroPaduaItaly
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107
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Franzo G, Dundon WG, De Villiers M, De Villiers L, Coetzee LM, Khaiseb S, Cattoli G, Molini U. Phylodynamic and phylogeographic reconstruction of beak and feather disease virus epidemiology and its implications for the international exotic bird trade. Transbound Emerg Dis 2022; 69:e2677-e2687. [PMID: 35695014 PMCID: PMC9795873 DOI: 10.1111/tbed.14618] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/21/2022] [Accepted: 06/05/2022] [Indexed: 12/30/2022]
Abstract
Beak and feather disease virus (BFDV) infects domestic and wild psittacine species and is able to cause progressive beak, claw and feather malformation and necrosis. In addition to having an impact on the health and welfare of domesticated birds, BFDV represents a significant threat to wild endangered species. Understanding the epidemiology, dynamics, viral migration rate, interaction between wild and domestic animals and the effect of implemented control strategies is fundamental in controlling the spread of the disease. With this in mind, a phylodynamic and phylogeographic analysis has been performed on a database of more than 400 replication-associated protein (Rep) gene (ORF1) sequences downloaded from Genbank including some recently generated sequences from fifteen samples collected in Namibia. The results allowed us to reconstruct the variation of viral population size and demonstrated the effect of enforced international bans on these dynamics. A good correlation was found between viral migration rate and the intensity of animal trade between regions over time. A dominant flux of viral strains was observed from wild to domestic populations, highlighting the directionality of viral transmission and the risk associated with the capturing and trade of wild birds. Nevertheless, the flow of viruses from domestic to wild species was not negligible and should be considered as a threat to biodiversity. Therefore, considering the strong relationship demonstrated in this study between animal trade and BFDV viral fluxes more effort should be made to prevent contact opportunities between wild and domestic populations from different countries in order to control disease spread.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal MedicineProduction and HealthUniversity of PadovaViale dell'UniversitàLegnaroItaly
| | - William G. Dundon
- Animal Production and Health LaboratoryAnimal Production and Health SectionJoint FAO/IAEA DivisionDepartment of Nuclear Sciences and ApplicationsInternational Atomic Energy AgencyViennaAustria
| | - Mari De Villiers
- School of Veterinary MedicineFaculty of Health Sciences and Veterinary MedicineUniversity of NamibiaNeudamm CampusWindhoekNamibia
| | - Lourens De Villiers
- School of Veterinary MedicineFaculty of Health Sciences and Veterinary MedicineUniversity of NamibiaNeudamm CampusWindhoekNamibia
| | | | | | - Giovanni Cattoli
- Animal Production and Health LaboratoryAnimal Production and Health SectionJoint FAO/IAEA DivisionDepartment of Nuclear Sciences and ApplicationsInternational Atomic Energy AgencyViennaAustria
| | - Umberto Molini
- School of Veterinary MedicineFaculty of Health Sciences and Veterinary MedicineUniversity of NamibiaNeudamm CampusWindhoekNamibia,Central Veterinary Laboratory (CVL)WindhoekNamibia
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108
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Chan ER, Jones LD, Linger M, Kovach JD, Torres-Teran MM, Wertz A, Donskey CJ, Zimmerman PA. COVID-19 infection and transmission includes complex sequence diversity. PLoS Genet 2022; 18:e1010200. [PMID: 36074769 PMCID: PMC9455841 DOI: 10.1371/journal.pgen.1010200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/27/2022] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 whole genome sequencing has played an important role in documenting the emergence of polymorphisms in the viral genome and its continuing evolution during the COVID-19 pandemic. Here we present data from over 360 patients to characterize the complex sequence diversity of individual infections identified during multiple variant surges (e.g., Alpha and Delta). Across our survey, we observed significantly increasing SARS-CoV-2 sequence diversity during the pandemic and frequent occurrence of multiple biallelic sequence polymorphisms in all infections. This sequence polymorphism shows that SARS-CoV-2 infections are heterogeneous mixtures. Convention for reporting microbial pathogens guides investigators to report a majority consensus sequence. In our study, we found that this approach would under-report sequence variation in all samples tested. As we find that this sequence heterogeneity is efficiently transmitted from donors to recipients, our findings illustrate that infection complexity must be monitored and reported more completely to understand SARS-CoV-2 infection and transmission dynamics. Many of the nucleotide changes that would not be reported in a majority consensus sequence have now been observed as lineage defining SNPs in Omicron BA.1 and/or BA.2 variants. This suggests that minority alleles in earlier SARS-CoV-2 infections may play an important role in the continuing evolution of new variants of concern.
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Affiliation(s)
- Ernest R. Chan
- Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Lucas D. Jones
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Marlin Linger
- The Center for Global Health & Diseases, Pathology Department, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jeffrey D. Kovach
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- The Center for Global Health & Diseases, Pathology Department, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Maria M. Torres-Teran
- Pathology Department, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Audric Wertz
- Biology Department, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Curtis J. Donskey
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Geriatric Research, Education, and Clinical Center, Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, United States of America
| | - Peter A. Zimmerman
- The Center for Global Health & Diseases, Pathology Department, Case Western Reserve University, Cleveland, Ohio, United States of America
- Master of Public Health Program, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
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109
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Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland. Viruses 2022; 14:v14091911. [PMID: 36146717 PMCID: PMC9505930 DOI: 10.3390/v14091911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/08/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.
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110
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Rychc Confers Extreme Resistance to Potato virus Y in Potato. Cells 2022; 11:cells11162577. [PMID: 36010654 PMCID: PMC9406545 DOI: 10.3390/cells11162577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
The Potato virus Y (PVY) is responsible for huge economic losses for the potato industry worldwide and is the fifth most consequential plant virus globally. The main strategies for virus control are to limit aphid vectors, produce virus-free seed potatoes, and breed virus-resistant varieties. The breeding of PVY-resistant varieties is the safest and most effective method in terms of cost and environmental protection. Rychc, a gene that confers extreme resistance to PVY, is from S. chacoense, which is a wild diploid potato species that is widely used in many PVY-resistant breeding projects. In this study, Rychc was fine mapped and successfully cloned from S. chacoense accession 40-3. We demonstrated that Rychc encodes a TIR-NLR protein by stably transforming a diploid susceptible cultivar named AC142 and a tetraploid potato variety named E3. The Rychc conferred extreme resistance to PVYO, PVYN:O and PVYNTN in both of the genotypes. To investigate the genetic events occurring during the evolution of the Rychc locus, we sequenced 160 Rychc homologs from 13 S. chacoense genotypes. Based on the pattern of sequence identities, 160 Rychc homologs were divided into 11 families. In Family 11 including Rychc, we found evidence for Type I evolutionary patterns with frequent sequence exchanges, obscured orthologous relationships and high non-synonymous to synonymous substitutions (Ka/Ks), which is consistent with rapid diversification and positive selection in response to rapid changes in the PVY genomes. Furthermore, a functional marker named MG64-17 was developed in this study that indicates the phenotype with 100% accuracy and, therefore, can be used for marker-assisted selection in breeding programs that use S. chacoense as a breeding resource.
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111
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Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lassig M, Łuksza M, Das S, Gresham D, Ghedin E. Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.05.05.442873. [PMID: 36656775 PMCID: PMC9836620 DOI: 10.1101/2021.05.05.442873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller, and use of replicate sequencing have the most significant impact on single nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false negative rates. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intrahost viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intrahost variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus, nor strongly beneficial, can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in inclusion of false positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant calling tools. We used simulated and synthetic data to test their performance against a true set of variants, and then used these studies to inform variant identification in data from clinical SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.
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112
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Jia X, Han Q, Lu Z. Constructing the boundary between potent and ineffective siRNAs by MG-algorithm with C-features. BMC Bioinformatics 2022; 23:337. [PMID: 35963993 PMCID: PMC9375269 DOI: 10.1186/s12859-022-04867-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In siRNA based antiviral therapeutics, selection of potent siRNAs is an indispensable step, but these commonly used features are unable to construct the boundary between potent and ineffective siRNAs. RESULTS Here, we select potent siRNAs by removing ineffective ones, where these conditions for removals are constructed by C-features of siRNAs, C-features are generated by MG-algorithm, Icc-cluster and the different combinations of some commonly used features, MG-algorithm and Icc-cluster are two different algorithms to search the nearest siRNA neighbors. For the ineffective siRNAs in test data, they are removed from test data by I-iteration, where I-iteration continually updates training data by adding these successively removed siRNAs. Furthermore, the efficacy of siRNAs of test data is predicted by their nearest neighbors of training data. CONCLUSIONS By siRNAs of Hencken dataset, results show that our algorithm removes almost ineffective siRNAs from test data, gives the clear boundary between potent and ineffective siRNAs, and accurately predicts the efficacy of siRNAs also. We suggest that our algorithm can provide new insights for selecting the potent siRNAs.
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Affiliation(s)
- Xingang Jia
- School of Mathematics, Southeast University, Nanjing, 210096, People's Republic of China.
| | - Qiuhong Han
- Department of Mathematics, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, People's Republic of China
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113
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Aranguren Caro LF, Gomez-Sanchez MM, Piedrahita Y, Mai HN, Cruz-Flores R, Alenton RRR, Dhar AK. Current status of infection with infectious hypodermal and hematopoietic necrosis virus (IHHNV) in the Peruvian and Ecuadorian shrimp industry. PLoS One 2022; 17:e0272456. [PMID: 35947538 PMCID: PMC9365166 DOI: 10.1371/journal.pone.0272456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Infection with infectious hypodermal and hematopoietic necrosis virus (IHHNV) is a crustacean disease that caused large-scale mortality in Penaeus stylirostris, deformity and growth retardation in Penaeus vannamei and Penaeus monodon. We surveyed the presence of IHHNV in three major shrimp-producing regions in Ecuador, namely Guayas, El Oro, and Esmeralda. The data show that IHHNV is endemic (3.3–100% prevalence) to shrimp farms in these regions. The whole genome sequences of representative circulating IHHNV genotypes in Ecuador and Peru showed that these genotypes formed a separate cluster within the Type II genotypes and were divergent from other geographical isolates of IHHNV originating in Asia, Africa, Australia, and Brazil. In experimental bioassays using specific pathogen-free (SPF) P. vannamei, P. monodon, and P. stylirostris and representative IHHNV isolates from Ecuador and Peru, the virus did not cause any mortality or induce clinical signs in any of the three penaeid species. Although IHHNV-specific Cowdry type A inclusion bodies were histologically detected in experimentally challenged P. vannamei and P. monodon and confirmed by in situ hybridization, no such inclusions were observed in P. stylirostris. Moreover, P. vannamei had the highest viral load, followed by P. monodon and P. stylirostris. Based on IHHNV surveillance data, we conclude that the currently farmed P. vannamei lines in Ecuador are tolerant to circulating IHHNV genotypes. The genome sequence and experimental bioassay data showed that, although the currently circulating genotypes are infectious, they do not induce clinical lesions in the three commercially important penaeid species. These findings suggest a potentially evolving virus-host relationship where circulating genotypes of IHHNV co-exist in equilibrium with P. vannamei raised in Peru and Ecuador.
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Affiliation(s)
- Luis Fernando Aranguren Caro
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
| | - Muriel Maria Gomez-Sanchez
- Subdireccion de Sanidad, Dirección de Sanidad e inocuidad, National Fisheries Health Agency in Peru (SANIPES), San Isidro, Lima, Perú
| | - Yahira Piedrahita
- Camara Nacional de Acuacultura, CNA, Avenida Francisco de Orellana y Miguel H Alcivar, Guayaquil, Ecuador
| | - Hung Nam Mai
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Roberto Cruz-Flores
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
- Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, Baja California, México
| | - Rod Russel R. Alenton
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Arun K. Dhar
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
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114
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Tan CY, Thanawongnuwech R, Arshad SS, Hassan L, Fong MWC, Ooi PT. Genotype Shift of Malaysian Porcine Circovirus 2 (PCV2) from PCV2b to PCV2d within a Decade. Animals (Basel) 2022; 12:1849. [PMID: 35883396 PMCID: PMC9311952 DOI: 10.3390/ani12141849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 12/18/2022] Open
Abstract
This paper aims to update the molecular status of porcine circovirus 2 (PCV2) in Malaysia. Firstly, the molecular detection rate of PCV2 in farm and sampled pig population were reported to be 83.78% (31/37 farms) and 83.54% (66/79 pigs) positive for PCV2, respectively. PCV2 was detected across all age groups, from fetuses, porkers to sows. Co-detection of PCV2 and PCV3 antigens was also reported at a rate of 28.77% (21/73). Secondly, PCV2 antigen was also detected in Malaysian abattoir lung samples: 18 out of 19 (94.74%) samples originating from clinically healthy finishers were tested positive. Further, this is the first study to confirm the circulation of PCV2 in the wild boar population roaming Peninsular Malaysia, where 28 out of 28 (100%) wild boar lung samples were found positive. One decade earlier, only genotype PCV2b was reported in Malaysia. This most recent update revealed that genotypes PCV2a, PCV2b and PCV2d were present, with PCV2d being the predominant circulating genotype. PCV2 cap gene nucleotide sequences in this study were found to be under negative selection pressure, with an estimated substitution rate of 1.102 × 10-3 substitutions/site/year (ssy).
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Affiliation(s)
- Chew Yee Tan
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (C.Y.T.); (S.S.A.); (L.H.); (M.W.C.F.)
| | - Roongroje Thanawongnuwech
- Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, 39 Henri Dunant Road, Pathumwan, Bangkok 10330, Thailand;
| | - Siti Suri Arshad
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (C.Y.T.); (S.S.A.); (L.H.); (M.W.C.F.)
| | - Latiffah Hassan
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (C.Y.T.); (S.S.A.); (L.H.); (M.W.C.F.)
| | - Michelle Wai Cheng Fong
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (C.Y.T.); (S.S.A.); (L.H.); (M.W.C.F.)
| | - Peck Toung Ooi
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM Serdang, Selangor 43400, Malaysia; (C.Y.T.); (S.S.A.); (L.H.); (M.W.C.F.)
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115
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Jung JS, Lee R, Yoon SI, Lee GS, Sung HW, Kwon HM, Park J. Genetic and immunological characterization of commercial infectious bronchitis virus vaccines used in Korea. Arch Virol 2022; 167:2123-2132. [PMID: 35816229 PMCID: PMC9272870 DOI: 10.1007/s00705-022-05519-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/17/2022] [Indexed: 11/26/2022]
Abstract
The aim of the study was to investigate the genetic and immunogenic features of commercial vaccines against infectious bronchitis virus (IBV), which is a major contagious pathogen of poultry. Although numerous vaccines have been developed based on the genetic characteristics of field strains, the continual emergence of variants decreases vaccine efficacy and cross-protection. To address this issue, we compared the S1 gene sequences of three IBV vaccines commercially available in Korea with those of various field isolates. Phylogenetic analysis showed that the vaccine strains clustered into two different lineages. Comparison of commercial vaccines with their parental viruses showed that most of the genetic variability occurred around hypervariable regions (HVRs). Conversely, antigenic stimulation with commercial vaccines and regional IBV variants was not sufficient to alter major immune cell phenotypes. Our study suggests that vaccines should be selected carefully based on their genetic background because genetic variability can affect the antigenicity of vaccines and host immune responses.
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Affiliation(s)
- Ji Seung Jung
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Rangyeon Lee
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Sung-Il Yoon
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Geun-Shik Lee
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Haan Woo Sung
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Hyuk Moo Kwon
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Jeongho Park
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea.
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116
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Roy V, Agrofoglio LA. Nucleosides and emerging viruses: A new story. Drug Discov Today 2022; 27:1945-1953. [PMID: 35189369 PMCID: PMC8856764 DOI: 10.1016/j.drudis.2022.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/13/2022] [Accepted: 02/16/2022] [Indexed: 12/24/2022]
Abstract
With several US Food and Drug Administration (FDA)-approved drugs and high barriers to resistance, nucleoside and nucleotide analogs remain the cornerstone of antiviral therapies for not only herpesviruses, but also HIV and hepatitis viruses (B and C); however, with the exception of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which vaccines have been developed at unprecedented speed, there are no vaccines or small antivirals yet available for (re)emerging viruses, which are primarily RNA viruses. Thus, herein, we present an overview of ribonucleoside analogs recently developed and acting as inhibitors of the viral RNA-dependent RNA polymerase (RdRp). They are new lead structures that will be exploited for the discovery of new antiviral nucleosides.
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Affiliation(s)
- Vincent Roy
- ICOA, University of Orléans, CNRS UMR 7311, Rue de Chartres, 45067 Orléans, France
| | - Luigi A Agrofoglio
- ICOA, University of Orléans, CNRS UMR 7311, Rue de Chartres, 45067 Orléans, France.
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Mekhail K, Lee M, Sugiyama M, Astori A, St-Germain J, Latreille E, Khosraviani N, Wei K, Li Z, Rini J, Lee WL, Antonescu C, Raught B, Fairn GD. Fatty Acid Synthase inhibitor TVB-3166 prevents S-acylation of the Spike protein of human coronaviruses. J Lipid Res 2022; 63:100256. [PMID: 35921881 PMCID: PMC9339154 DOI: 10.1016/j.jlr.2022.100256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/24/2022] Open
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other coronaviruses mediates host cell entry and is S-acylated on multiple phylogenetically conserved cysteine residues. Multiple protein acyltransferase enzymes have been reported to post-translationally modify spike proteins; however, strategies to exploit this modification are lacking. Using resin-assisted capture MS, we demonstrate that the spike protein is S-acylated in SARS-CoV-2-infected human and monkey epithelial cells. We further show that increased abundance of the acyltransferase ZDHHC5 associates with increased S-acylation of the spike protein, whereas ZDHHC5 knockout cells had a 40% reduction in the incorporation of an alkynyl-palmitate using click chemistry detection. We also found that the S-acylation of the spike protein is not limited to palmitate, as clickable versions of myristate and stearate were also labelled the protein. Yet, we observed that ZDHHC5 was only modified when incubated with alkyne-palmitate, suggesting it has specificity for this acyl-CoA, and that other ZDHHC enzymes may use additional fatty acids to modify the spike protein. Since multiple ZDHHC isoforms may modify the spike protein, we also examined the ability of the FASN inhibitor TVB-3166 to prevent S-acylation of the spike proteins of SARS-CoV-2 and human CoV-229E. We show that treating cells with TVB-3166 inhibited S-acylation of expressed spike proteins and attenuated the ability of SARS-CoV-2 and human CoV-229E to spread in vitro. Our findings further substantiate the necessity of CoV spike protein S-acylation and demonstrate that de novo fatty acid synthesis is critical for the proper S-acylation of the spike protein.
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Affiliation(s)
- Katrina Mekhail
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Minhyoung Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Michael Sugiyama
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Audrey Astori
- Princess Margaret Cancer Centre, University Health Network, Ontario, Canada
| | | | - Elyse Latreille
- Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Negar Khosraviani
- Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Kuiru Wei
- Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Zhijie Li
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - James Rini
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Warren L Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Costin Antonescu
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Gregory D Fairn
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Keenan Research Centre, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Department of Surgery, University of Toronto, Toronto, Ontario, Canada; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.
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118
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Chakrabartty I, Khan M, Mahanta S, Chopra H, Dhawan M, Choudhary OP, Bibi S, Mohanta YK, Emran TB. Comparative overview of emerging RNA viruses: Epidemiology, pathogenesis, diagnosis and current treatment. Ann Med Surg (Lond) 2022; 79:103985. [PMID: 35721786 PMCID: PMC9188442 DOI: 10.1016/j.amsu.2022.103985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
From many decades, emerging infections have threatened humanity. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. The SARS, Ebola, MERS epidemics and the most recent emergence of COVID-19 pandemic have threatened populations across borders. Since a highly pathogenic CoV has been evolved into the human population in the twenty-first century known as SARS, scientific advancements and innovative methods to tackle these viruses have increased in order to improve response preparedness towards the unpredictable threat posed by these rapidly emerging pathogens. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. However, in this review, we have done a systematic comparison of all three CoVs i.e., SARS, MERS and SARS-CoV-2 along with Ebola and Zika in terms of their epidemiology, virology, clinical features and current treatment strategies. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Each of these viruses has been elaborated on the basis of their epidemiology, virulence, transmission and treatment. However, special attention has been given to SARS-CoV-2 and the disease caused by it i.e., COVID-19 due to current havoc caused worldwide. At the end, insights into the current understanding of the lessons learned from previous epidemics to combat emerging CoVs have been described. The travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates associated with these highly transmissible and pathogenic viruses highlight the need for new prophylactic and therapeutic actions which include but are not limited to clinical indicators, contact tracing, and laboratory investigations as important factors that need to be taken into account in order to arrive at the final conclusion. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Globally, numerous studies and researchers have recently started fighting this virus.
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Affiliation(s)
- Ishani Chakrabartty
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Maryam Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology (NIELIT), Guwahati Centre Guwahati, 781008, Assam, India
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.,Trafford College, Altrincham, Manchester, WA14 5PQ, UK
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, India
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan.,Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Yugal Kishore Mohanta
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
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119
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Rodrigues JR, Roy SW, Sehgal RNM. Novel RNA viruses associated with avian haemosporidian parasites. PLoS One 2022; 17:e0269881. [PMID: 35771829 PMCID: PMC9246168 DOI: 10.1371/journal.pone.0269881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
Avian haemosporidian parasites can cause malaria-like symptoms in their hosts and have been implicated in the demise of some bird species. The newly described Matryoshka RNA viruses (MaRNAV1 and MaRNAV2) infect haemosporidian parasites that in turn infect their vertebrate hosts. MaRNAV2 was the first RNA virus discovered associated with parasites of the genus Leucocytozoon. By analyzing metatranscriptomes from the NCBI SRA database with local sequence alignment tools, we detected two novel RNA viruses; we describe them as MaRNAV3 associated with Leucocytozoon and MaRNAV4 associated with Parahaemoproteus. MaRNAV3 had ~59% amino acid identity to the RNA-dependent RNA-polymerase (RdRp) of MaRNAV1 and ~63% amino acid identity to MaRNAV2. MaRNAV4 had ~44% amino acid identity to MaRNAV1 and ~47% amino acid identity to MaRNAV2. These findings lead us to hypothesize that MaRNAV_like viruses are widespread and tightly associated with the order Haemosporida since they have been described in human Plasmodium vivax, and now two genera of avian haemosporidians.
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Affiliation(s)
- Jose Roberto Rodrigues
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
| | - Scott W. Roy
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
- * E-mail: (RNMS); (SWR)
| | - Ravinder N. M. Sehgal
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
- * E-mail: (RNMS); (SWR)
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120
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Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
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121
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Chen Y, Liu Q, Zhou L, Zhou Y, Yan H, Lan K. Emerging SARS-CoV-2 variants: Why, how, and what's next? CELL INSIGHT 2022; 1:100029. [PMID: 37193049 PMCID: PMC9057926 DOI: 10.1016/j.cellin.2022.100029] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 01/18/2023]
Abstract
The emergence of the SARS-CoV-2 Omicron variant poses a striking threat to human society. More than 30 mutations in the Spike protein of the Omicron variant severely compromised the protective immunity elicited by either vaccination or prior infection. The persistent viral evolutionary trajectory generates Omicron-associated lineages, such as BA.1 and BA.2. Moreover, the virus recombination upon Delta and Omicron co-infections has been reported lately, although the impact remains to be assessed. This minireview summarizes the characteristics, evolution and mutation control, and immune evasion mechanisms of SARS-CoV-2 variants, which will be helpful for the in-depth understanding of the SARS-CoV-2 variants and policy-making related to COVID-19 pandemic control.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qianyun Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Li Zhou
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - You Zhou
- Systems Immunity University Research Institute and Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Huan Yan
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ke Lan
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
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122
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Dang S, Ren L, Wang J. Functional mutations of SARS-CoV-2: implications to viral transmission, pathogenicity and immune escape. Chin Med J (Engl) 2022; 135:1213-1222. [PMID: 35788093 PMCID: PMC9337262 DOI: 10.1097/cm9.0000000000002158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Indexed: 11/27/2022] Open
Abstract
ABSTRACT The pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to major public health challenges globally. The increasing viral lineages identified indicate that the SARS-CoV-2 genome is evolving at a rapid rate. Viral genomic mutations may cause antigenic drift or shift, which are important ways by which SARS-CoV-2 escapes the human immune system and changes its transmissibility and virulence. Herein, we summarize the functional mutations in SARS-CoV-2 genomes to characterize its adaptive evolution to inform the development of vaccination, treatment as well as control and intervention measures.
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Affiliation(s)
- Shengyuan Dang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lili Ren
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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123
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Chou JM, Tsai JL, Hung JN, Chen IH, Chen ST, Tsai MH. The ORF8 Protein of SARS-CoV-2 Modulates the Spike Protein and Its Implications in Viral Transmission. Front Microbiol 2022; 13:883597. [PMID: 35663899 PMCID: PMC9161165 DOI: 10.3389/fmicb.2022.883597] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/01/2022] [Indexed: 01/09/2023] Open
Abstract
COVID-19 is currently global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Accompanying the rapid spread of the error-prone RNA-based genome, several dominant SARS-CoV-2 variants have been genetically identified. The mutations in the spike protein, which are essential for receptor binding and fusion, have been intensively investigated for their contributions to viral transmission. Nevertheless, the importance of other viral proteins and their mutations in SARS-CoV-2 lifecycle and transmission remains fairly understood. Here, we report the strong potency of an accessory protein ORF8 in modulating the level and processing of the spike protein. The expression of ORF8 protein does not affect propagation but expression of spike protein, which may lead to pseudovirions with less spike protein on the surface, therefore less infection potential. At the protein level, ORF8 expression led to downregulation and insufficient S1/S2 cleavage of the spike protein in a dose-dependent manner. ORF8 exhibits a strong interaction with the spike protein mainly at S1 domains and mediates its degradation through multiple pathways. The dominant clinical isolated ORF8 variants with the reduced protein stability exhibited the increased capacity of viral transmission without compromising their inhibitory effects on HLA-A2. Although the increase in spike protein level and Spike pseudovirus production observed by using highly transmissible clinical spike variants, there was no significant compromise in ORF8-mediated downregulation. Because ORF8 is important for immune surveillance and might be required for viral fitness in vivo, the alteration of the spike protein might be an optional strategy used by SARS-CoV-2 to promote viral transmission by escaping the inhibitory effects of ORF8. Therefore, our report emphasized the importance of ORF8 in SARS-CoV-2 spike protein production, maturation, and possible evolution.
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Affiliation(s)
- Jen-Mei Chou
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Jo-Ling Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Jo-Ning Hung
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - I-Hua Chen
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Szu-Ting Chen
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ming-Han Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- *Correspondence: Ming-Han Tsai,
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124
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Isaeva OI, Ketelaars SLC, Kvistborg P. In Silico Analysis Predicts a Limited Impact of SARS-CoV-2 Variants on CD8 T Cell Recognition. Front Immunol 2022; 13:891524. [PMID: 35572563 PMCID: PMC9094405 DOI: 10.3389/fimmu.2022.891524] [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: 03/07/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Since the start of the COVID-19 pandemic, mutations have led to the emergence of new SARS-CoV-2 variants, and some of these have become prominent or dominant variants of concern. This natural course of development can have an impact on how protective the previously naturally or vaccine induced immunity is. Therefore, it is crucial to understand whether and how variant specific mutations influence host immunity. To address this, we have investigated how mutations in the recent SARS-CoV-2 variants of interest and concern influence epitope sequence similarity, predicted binding affinity to HLA, and immunogenicity of previously reported SARS-CoV-2 CD8 T cell epitopes. Our data suggests that the vast majority of SARS-CoV-2 CD8 T cell recognized epitopes are not altered by variant specific mutations. Interestingly, for the CD8 T cell epitopes that are altered due to variant specific mutations, our analyses show there is a high degree of sequence similarity between mutated and reference SARS-CoV-2 CD8 T cell epitopes. However, mutated epitopes, primarily derived from the spike protein, in SARS-CoV-2 variants Delta, AY.4.2 and Mu display reduced predicted binding affinity to their restriction element. These findings indicate that the recent SARS-CoV-2 variants of interest and concern have limited ability to escape memory CD8 T cell responses raised by vaccination or prior infection with SARS-CoV-2 early in the pandemic. The overall low impact of the mutations on CD8 T cell cross-recognition is in accordance with the notion that mutations in SARS-CoV-2 are primarily the result of receptor binding affinity and antibody selection pressures exerted on the spike protein, unrelated to T cell immunity.
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Affiliation(s)
- Olga I Isaeva
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Steven L C Ketelaars
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Pia Kvistborg
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
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125
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Wang H, Cui X, Cai X, An T. Recombination in Positive-Strand RNA Viruses. Front Microbiol 2022; 13:870759. [PMID: 35663855 PMCID: PMC9158499 DOI: 10.3389/fmicb.2022.870759] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/21/2022] [Indexed: 12/28/2022] Open
Abstract
RNA recombination is a major driver of genetic shifts tightly linked to the evolution of RNA viruses. Genomic recombination contributes substantially to the emergence of new viral lineages, expansion in host tropism, adaptations to new environments, and virulence and pathogenesis. Here, we review some of the recent progress that has advanced our understanding of recombination in positive-strand RNA viruses, including recombination triggers and the mechanisms behind them. The study of RNA recombination aids in predicting the probability and outcome of viral recombination events, and in the design of viruses with reduced recombination frequency as candidates for the development of live attenuated vaccines. Surveillance of viral recombination should remain a priority in the detection of emergent viral strains, a goal that can only be accomplished by expanding our understanding of how these events are triggered and regulated.
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Affiliation(s)
| | | | | | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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126
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Zhang T, Li J, Jiang YZ, Xu JQ, Guan XH, Wang LQ, Chen J, Liang Y. Genotype Distribution and Evolutionary Analysis of Rotavirus Associated with Acute Diarrhea Outpatients in Hubei, China, 2013–2016. Virol Sin 2022; 37:503-512. [PMID: 35643410 PMCID: PMC9437618 DOI: 10.1016/j.virs.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2022] [Indexed: 11/23/2022] Open
Abstract
Group A human rotaviruses (RVAs) annually cause the deaths of 215,000 infants and young children. To understand the epidemiological characteristics and genetic evolution of RVAs, we performed sentinel surveillance on RVA prevalence in a rotavirus-surveillance network in Hubei, China. From 2013 to 2016, a total of 2007 fecal samples from hospital outpatients with acute gastroenteritis were collected from four cities of Hubei Province. Of the 2007 samples, 153 (7.62%) were identified positive for RVA by real-time RT-PCR. RVA infection in Hubei mainly occurred in autumn and winter. The highest detection rate of RVA infection was in 1–2 years old of outpatients (16.97%). No significant difference of RVA positive rate was observed between females and males. We performed a phylogenetic analysis of the G/P genotypes based on the partial VP7/VP4 gene sequences of RVAs. G9P[8] was the most predominant strain in all four years but the prevalence of G2P[4] genotype increased rapidly since 2014. We reconstructed the evolutionary time scale of RVAs in Hubei, and found that the evolutionary rates of the G9, G2, P[8], and P[4] genotypes of RVA were 1.069 × 10−3, 1.029 × 10−3, 1.283 × 10−3 and 1.172 × 10−3 nucleotide substitutions/site/year, respectively. Importantly, using a molecular clock model, we showed that most G9, G2, P[8], and P[4] genotype strains dated from the recent ancestor in 2005, 2005, 1993, and 2013, respectively. The finding of the distribution of RVAs in infants and young children in Hubei Province will contribute to the understanding of the epidemiological characteristics and genetic evolution of RVAs in China. A four-year study of sentinel surveillance program of RVAs was performed in Hubei, China. The key population of rotavirus infection is 1–2 years old of outpatients with acute gastroenteritis. G9P[8] was the most predominant strain between 2013 and 2016. The estimating time to the most recent common ancestor for the G9 genotype based on partial VP7 gene was 46 years. RVA distribution in Hubei Province contributes to the understanding of the epidemiological characteristics of RVAs in China.
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127
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Ruiz-Aravena M, McKee C, Gamble A, Lunn T, Morris A, Snedden CE, Yinda CK, Port JR, Buchholz DW, Yeo YY, Faust C, Jax E, Dee L, Jones DN, Kessler MK, Falvo C, Crowley D, Bharti N, Brook CE, Aguilar HC, Peel AJ, Restif O, Schountz T, Parrish CR, Gurley ES, Lloyd-Smith JO, Hudson PJ, Munster VJ, Plowright RK. Ecology, evolution and spillover of coronaviruses from bats. Nat Rev Microbiol 2022; 20:299-314. [PMID: 34799704 PMCID: PMC8603903 DOI: 10.1038/s41579-021-00652-2] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 12/24/2022]
Abstract
In the past two decades, three coronaviruses with ancestral origins in bats have emerged and caused widespread outbreaks in humans, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the first SARS epidemic in 2002-2003, the appreciation of bats as key hosts of zoonotic coronaviruses has advanced rapidly. More than 4,000 coronavirus sequences from 14 bat families have been identified, yet the true diversity of bat coronaviruses is probably much greater. Given that bats are the likely evolutionary source for several human coronaviruses, including strains that cause mild upper respiratory tract disease, their role in historic and future pandemics requires ongoing investigation. We review and integrate information on bat-coronavirus interactions at the molecular, tissue, host and population levels. We identify critical gaps in knowledge of bat coronaviruses, which relate to spillover and pandemic risk, including the pathways to zoonotic spillover, the infection dynamics within bat reservoir hosts, the role of prior adaptation in intermediate hosts for zoonotic transmission and the viral genotypes or traits that predict zoonotic capacity and pandemic potential. Filling these knowledge gaps may help prevent the next pandemic.
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Affiliation(s)
- Manuel Ruiz-Aravena
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Clifton McKee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Amandine Gamble
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tamika Lunn
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Aaron Morris
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Celine E Snedden
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Claude Kwe Yinda
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Julia R Port
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - David W Buchholz
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yao Yu Yeo
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Christina Faust
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Elinor Jax
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lauren Dee
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Devin N Jones
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Maureen K Kessler
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
- Department of Ecology, Montana State University, Bozeman, MT, USA
| | - Caylee Falvo
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Daniel Crowley
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Nita Bharti
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Cara E Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Hector C Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Alison J Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Colin R Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Emily S Gurley
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter J Hudson
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Vincent J Munster
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Raina K Plowright
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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128
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Wang H, Yang GX, Hu Y, Lam P, Sangha K, Siciliano D, Swenerton A, Miller R, Tilley P, Von Dadelszen P, Kalyan S, Tang P, Patel MS. Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis. Sci Rep 2022; 12:6875. [PMID: 35477737 PMCID: PMC9046152 DOI: 10.1038/s41598-022-10869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/04/2022] [Indexed: 11/17/2022] Open
Abstract
As metagenomic approaches for detecting infectious agents have improved, each tissue that was once thought to be sterile has been found to harbor a variety of microorganisms. Controversy still exists over the status of amniotic fluid, which is part of an immunologically privileged zone that is required to prevent maternal immune system rejection of the fetus. Due to this privilege, the exclusion of microbes has been proposed to be mandatory, leading to the sterile womb hypothesis. Since nucleic acid yields from amniotic fluid are very low, contaminating nucleic acid found in water, reagents and the laboratory environment frequently confound attempts to address this hypothesis. Here we present metagenomic criteria for microorganism detection and a metagenomic method able to be performed with small volumes of starting material, while controlling for exogenous contamination, to circumvent these and other pitfalls. We use this method to show that human mid-gestational amniotic fluid has no detectable virome or microbiome, supporting the sterile womb hypothesis.
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Affiliation(s)
- HanChen Wang
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Physiology, McGill University, Montreal, QC, Canada
| | - Gui Xiang Yang
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Yuxiang Hu
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,CureImmune Therapeutics Inc., Vancouver, BC, Canada
| | - Patricia Lam
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Karan Sangha
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Dawn Siciliano
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Anne Swenerton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ruth Miller
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada.,Contextual Genomics Inc., Vancouver, BC, Canada
| | - Peter Tilley
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Peter Von Dadelszen
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada.,Department of Women and Children's Health, School of Life Course Sciences, King's College London, London, UK
| | - Shirin Kalyan
- Division of Endocrinology and Metabolism, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Patrick Tang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control, Vancouver, BC, Canada.,Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Millan S Patel
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada. .,Department of Medical Genetics, University of British Columbia, 4500 Oak St., Rm. C234, Vancouver, BC, V6H 3N1, Canada.
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129
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Lu H, Li J, Yang P, Jiang F, Liu H, Cui F. Mutation in the RNA-Dependent RNA Polymerase of a Symbiotic Virus Is Associated With the Adaptability of the Viral Host. Front Microbiol 2022; 13:883436. [PMID: 35432275 PMCID: PMC9005967 DOI: 10.3389/fmicb.2022.883436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Host adaptation has the potential to cause rapid genetic variation in symbiotic microorganisms in insects. How mutations in symbiotic viruses favor viral fitness in hosts and even influence host adaptability to new environments remains elusive. Here, we explored the role of genetic divergence at one site of a symbiotic virus, Acyrthosiphon pisum virus (APV), in the host aphid's adaptation to unfavorable plants. Based on the transcriptomes of the pea aphid Vicia faba colony and Vicia villosa colony, 46 single nucleotide polymorphism (SNP) sites were found in the APV genomes from the two aphid colonies. One SNP at site 5,990, G5990A, located at the RNA-dependent RNA polymerase (RdRp) domain, demonstrated a predominance from G to A when the host aphids were shifted from V. faba to the low-fitness plants V. villosa or Medicago sativa. This SNP resulted in a substitution from serine (S) to asparagine (N) at site 196 in RdRp. Although S196N was predicted to be located at a random coil far away from conserved functional motifs, the polymerase activity of the N196 type of RdRp was increased by 44.5% compared to that of the S196 type. The promoted enzymatic activity of RdRp was associated with a higher replication level of APV, which was beneficial for aphids as APV suppressed plant's resistance reactions toward aphids. The findings showed a novel case in which mutations selected in a symbiotic virus may confer a favor on the host as the host adapts to new environmental conditions.
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Affiliation(s)
- Hong Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Pengcheng Yang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fei Jiang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongran Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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130
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Tohma K, Ford-Siltz LA, Kendra JA, Parra GI. Dynamic immunodominance hierarchy of neutralizing antibody responses to evolving GII.4 noroviruses. Cell Rep 2022; 39:110689. [PMID: 35417705 DOI: 10.1016/j.celrep.2022.110689] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/20/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
A paradigm of RNA viruses is their ability to mutate and escape from herd immunity. Because antibody responses are a major effector for viral immunity, antigenic sites are usually under strong diversifying pressure. Here, we use norovirus as a model to study mechanisms of antigenic diversification of non-enveloped, fast-evolving RNA viruses. We comprehensively characterize all variable antigenic sites involved in virus neutralization and find that single neutralizing monoclonal antibodies (mAbs) map to multiple antigenic sites of GII.4 norovirus. Interactions of multiple epitopes on the viral capsid surface provide a broad mAb-binding repertoire with a remarkable difference in the mAb-binding profiles and immunodominance hierarchy for two distantly related GII.4 variants. Time-ordered mutant viruses confirm a progressive change of antibody immunodominance along with point mutations during the process of norovirus evolution. Thus, in addition to point mutations, switches in immunodominance that redirect immune responses could facilitate immune escape in RNA viruses.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1309, Silver Spring, MD 20993, USA
| | - Lauren A Ford-Siltz
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1309, Silver Spring, MD 20993, USA
| | - Joseph A Kendra
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1309, Silver Spring, MD 20993, USA
| | - Gabriel I Parra
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1309, Silver Spring, MD 20993, USA.
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131
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Abstract
A simple, pervasive biological entity in the ocean sheds light on evolution.
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Affiliation(s)
- Jessica M Labonté
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, USA
| | - Kathryn L Campbell
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, USA
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132
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Huang YW, Lee CW, Lin NS, Cuong HV, Hu CC, Hsu YH. First Report of Distinct Bamboo mosaic virus (BaMV) Isolates Infecting Bambusa funghomii in Vietnam and the Identification of a Highly Variable Region in the BaMV Genome. Viruses 2022; 14:698. [PMID: 35458428 PMCID: PMC9032891 DOI: 10.3390/v14040698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
New isolates of the Bamboo mosaic virus (BaMV) were identified in Bambusa funghomii bamboo in Vietnam. Sequence analyses revealed that the Vietnam isolates are distinct from all known BaMV strains, sharing the highest sequence identities (about 77%) with the Yoshi isolates reported in California, USA. Unique satellite RNAs were also found to be associated with the BaMV Vietnam isolates. A possible recombination event was detected in the genome of BaMV-VN2. A highly variable region was identified in the ORF1 gene, in between the methyl transferase domain and helicase domain. These results revealed the presence of unique BaMV isolates in an additional bamboo species in one more country, Vietnam, and provided evidence in support of the possible involvement of environmental or host factors in the diversification and evolution of BaMV.
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Affiliation(s)
- Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Rd, Taichung 40227, Taiwan; (Y.-W.H.); (C.-W.L.)
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chin-Wei Lee
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Rd, Taichung 40227, Taiwan; (Y.-W.H.); (C.-W.L.)
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Ha Viet Cuong
- Department of Plant Pathology, Research Center for Tropic Plant Diseases, Vietnam National University of Agriculture, Hanoi 100915, Vietnam;
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Rd, Taichung 40227, Taiwan; (Y.-W.H.); (C.-W.L.)
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Rd, Taichung 40227, Taiwan; (Y.-W.H.); (C.-W.L.)
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
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133
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Wen L, Yin L, Zhu J, Li H, Zhang F, Hu Q, Xiao Q, Xie J, He K. Nearly 20 Years of Genetic Diversity and Evolution of Porcine Circovirus-like Virus P1 from China. Viruses 2022; 14:v14040696. [PMID: 35458426 PMCID: PMC9030576 DOI: 10.3390/v14040696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Porcine circovirus-like virus P1 can infect many kinds of animals and mainly causes postweaning multisystemic wasting syndrome. In China, the genetic diversity, variation, and evolutionary processes of this virus have not been described yet. To improve our knowledge of its genetic diversity, evolution, and gene flow, we performed a bioinformatics analysis using the available nucleotide sequences of the P1 virus; among them, 12 nucleotide sequences were from ten pig farms in Jiangsu Province in this epidemiological survey, and 84 sequences were downloaded from GenBank. The P1 sequences showed a rich composition of AT nucleotides. Analyses of the complete genomic sequences were polymorphic and revealed high haplotype (gene) diversity and nucleotide diversity. A phylogenetic analysis based on the NJ method showed that all P1 virus sequences formed two distinct groups: A and B. High genetic differentiation was observed between strains from groups A and B. The codon usage pattern of P1 was affected by dinucleotide compositions. Dinucleotide UU/CC was overrepresented, and dinucleotide CG was underrepresented. The mean evolutionary rate of the P1 virus was estimated to be 3.64 × 10−4 nucleotide substitutions per site per year (subs/site/year). The neutrality tests showed negative values. The purifying selection and recombination events may play a major driving role in generating the genetic diversity of the P1 population. The information from this research may be helpful to obtain new insights into the evolution of P1.
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Affiliation(s)
- Libin Wen
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (L.Y.); (J.Z.); (H.L.); (F.Z.); (Q.H.); (Q.X.); (J.X.)
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infections Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Correspondence: (L.W.); (K.H.)
| | - Lihong Yin
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (L.Y.); (J.Z.); (H.L.); (F.Z.); (Q.H.); (Q.X.); (J.X.)
| | - Jiaping Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (L.Y.); (J.Z.); (H.L.); (F.Z.); (Q.H.); (Q.X.); (J.X.)
| | - Heran Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (L.Y.); (J.Z.); (H.L.); (F.Z.); (Q.H.); (Q.X.); (J.X.)
| | - Fengxi Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (L.Y.); (J.Z.); (H.L.); (F.Z.); (Q.H.); (Q.X.); (J.X.)
| | - Qun Hu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (L.Y.); (J.Z.); (H.L.); (F.Z.); (Q.H.); (Q.X.); (J.X.)
| | - Qi Xiao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (L.Y.); (J.Z.); (H.L.); (F.Z.); (Q.H.); (Q.X.); (J.X.)
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infections Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Jianping Xie
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (L.Y.); (J.Z.); (H.L.); (F.Z.); (Q.H.); (Q.X.); (J.X.)
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infections Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Kongwang He
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (L.Y.); (J.Z.); (H.L.); (F.Z.); (Q.H.); (Q.X.); (J.X.)
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infections Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- Correspondence: (L.W.); (K.H.)
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134
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Host diversification is concurrent with linear motif evolution in a Mastadenovirus hub protein. J Mol Biol 2022; 434:167563. [PMID: 35351519 DOI: 10.1016/j.jmb.2022.167563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 02/28/2022] [Accepted: 03/22/2022] [Indexed: 12/23/2022]
Abstract
Over one hundred Mastadenovirus types infect seven orders of mammals. Virus-host coevolution may involve cospeciation, duplication, host switch and partial extinction events. We reconstruct Mastadenovirus diversification, finding that while cospeciation is dominant, the other three events are also common in Mastadenovirus evolution. Linear motifs are fast-evolving protein functional elements and key mediators of virus-host interactions, thus likely to partake in adaptive viral evolution. We study the evolution of eleven linear motifs in the Mastadenovirus E1A protein, a hub of virus-host protein-protein interactions, in the context of host diversification. The reconstruction of linear motif gain and loss events shows fast linear motif turnover, corresponding a virus-host protein-protein interaction turnover orders of magnitude faster than in model host proteomes. Evolution of E1A linear motifs is coupled, indicating functional coordination at the protein scale, yet presents motif-specific patterns suggestive of convergent evolution. We report a pervasive association between Mastadenovirus host diversification events and the evolution of E1A linear motifs. Eight of 17 host switches associate with the gain of one linear motif and the loss of four different linear motifs, while five of nine partial extinctions associate with the loss of one linear motif. The specific changes in E1A linear motifs during a host switch or a partial extinction suggest that changes in the host molecular environment lead to modulation of the interactions with the retinoblastoma protein and host transcriptional regulators. Altogether, changes in the linear motif repertoire of a viral hub protein are associated with adaptive evolution events during Mastadenovirus evolution.
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135
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Geographical prevalence of SARS-CoV-2 variants, August 2020 to July 2021. Sci Rep 2022; 12:4704. [PMID: 35304553 PMCID: PMC8931783 DOI: 10.1038/s41598-022-08684-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
We extracted one-year genomic data (August 2020–July 2021) from GISAID EpiCoV™ database and estimated monthly proportions of 11 SARS-CoV-2 variants in various geographical regions. From continental perspective, Delta VOC predominated in Africa, Asia, Europe, North America and Oceania, with proportions of 67.58–98.31% in July 2021. In South America, proportion of Delta VOC (23.24%) has been approaching the predominant yet diminishing Gamma VOC (56.86%). We further analyzed monthly data on new COVID-19 cases, new deaths, vaccination status and variant proportions of 6 countries. Delta VOC predominated in all countries except Brazil (Gamma VOC) in July 2021. In most occasions, rise and predominance of Alpha, Beta, Gamma, Delta and Zeta variants were accompanied with surges of new cases, especially after the time point of major lineage interchange. The ascending phases of new cases lasted for 1–5 months with 1.69- to 40.63-fold peak growth, whereas new death tolls varied with regional vaccination status. Our data suggested surges of COVID-19 cases might be predicted from variant surveillance data. Despite vaccine breakthroughs by Delta VOC, death tolls were more stable in countries with better immunization coverage. Another takeaway is the urgent need to improve vaccine efficacy against Delta and emerging variants.
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136
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Lee K, Pusterla N, Barnum SM, Lee DH, Martínez-López B. Investigation of cross-regional spread and evolution of equine influenza H3N8 at US and global scales using Bayesian phylogeography based on balanced subsampling. Transbound Emerg Dis 2022; 69:e1734-e1748. [PMID: 35263501 DOI: 10.1111/tbed.14509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
Equine influenza virus (EIV) is a highly contagious pathogen of equids, and a well-known burden in global equine health. EIV H3N8 variants seasonally emerged and resulted in EIV outbreaks in the United States (US) and worldwide. The present study evaluated the pattern of cross-regional EIV H3N8 spread and evolutionary characteristics at US and global scales using Bayesian phylogeography with balanced subsampling based on regional horse population size. A total of 297 Haemagglutinin (HA) sequences of global EIV H3N8 were collected from 1963 to 2019 and subsampled to global subset (n = 67), raw US sequences (n = 100) and US subset (n = 44) datasets. Discrete trait phylogeography analysis was used to estimate the transmission history of EIV using four global and US genome datasets. The North American lineage was the major source of globally dominant EIV variants and spread to other global regions. The US EIV strains generally spread from the southern and midwestern regions to other regions. The EIV H3N8 accumulated approximately three nucleotide substitutions per year in the HA gene under heterogenous local positive selection. Our findings will guide better decision making of target intervention strategies of EIV H3N8 infection and provide the better scheme of genomic surveillance in the US and global equine health. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kyuyoung Lee
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Samantha M Barnum
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
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137
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Ao D, Lan T, He X, Liu J, Chen L, Baptista‐Hon DT, Zhang K, Wei X. SARS-CoV-2 Omicron variant: Immune escape and vaccine development. MedComm (Beijing) 2022; 3:e126. [PMID: 35317190 PMCID: PMC8925644 DOI: 10.1002/mco2.126] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 02/05/2023] Open
Abstract
New genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) constantly emerge through unmitigated spread of the virus in the ongoing Coronavirus disease 2019 pandemic. Omicron (B.1.1.529), the latest variant of concern (VOC), has so far shown exceptional spread and infectivity and has established itself as the dominant variant in recent months. The SARS-CoV-2 spike glycoprotein is a key component for the recognition and binding to host cell angiotensin-converting enzyme 2 receptors. The Omicron variant harbors a cluster of substitutions/deletions/insertions, and more than 30 mutations are located in spike. Some noticeable mutations, including K417N, T478K, N501Y, and P681H, are shared with the previous VOCs Alpha, Beta, Gamma, or Delta variants and have been proven to be associated with higher transmissibility, viral infectivity, and immune evasion potential. Studies have revealed that the Omicron variant is partially resistant to the neutralizing activity of therapeutic antibodies and convalescent sera, which poses significant challenges for the clinical effectiveness of the current vaccines and therapeutic antibodies. We provide a comprehensive analysis and summary of the epidemiology and immune escape mechanisms of the Omicron variant. We also suggest some therapeutic strategies against the Omicron variant. This review, therefore, aims to provide information for further research efforts to prevent and contain the impact of new VOCs during the ongoing pandemic.
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Affiliation(s)
- Danyi Ao
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Tianxia Lan
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Xuemei He
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jian Liu
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Li Chen
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
| | - Daniel T. Baptista‐Hon
- Center for Biomedicine and InnovationsFaculty of MedicineMacau University of Science and TechnologyMacauChina
| | - Kang Zhang
- Center for Biomedicine and InnovationsFaculty of MedicineMacau University of Science and TechnologyMacauChina
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanChina
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138
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Targeted inhibition of the endonuclease activity of influenza polymerase acidic proteins. Future Med Chem 2022; 14:571-586. [PMID: 35213253 DOI: 10.4155/fmc-2021-0264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Influenza is a type of acute respiratory virus infection caused by the influenza virus that occurs in epidemics worldwide every year. Due to the increasing incidence of influenza virus resistance to existing drugs, researchers are looking for novel antiviral drugs with new mechanisms. The endonuclease activity of polymerase acidic protein is essential in the process of influenza virus reproduction, and inhibiting it could prevent the virus from replicating. There are relatively few drugs that act on this protein, and only baloxavir marboxil has been approved for clinical use. In this article, the structure and function of influenza virus polymerase acidic protein endonuclease, mechanism of action of polymerase acidic endonuclease inhibitors and the research progress of inhibitors are reviewed.
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139
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Adhikari P, Jawad B, Rao P, Podgornik R, Ching WY. Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. Viruses 2022; 14:465. [PMID: 35336872 PMCID: PMC8955942 DOI: 10.3390/v14030465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 12/21/2022] Open
Abstract
The SARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing for the virus to invade human cells much faster and with an increased efficiency. In particular, an especially dangerous mutation P681R close to the furin cleavage site has been identified as responsible for increasing the infection rate. Together with the earlier reported mutation D614G in the same domain, it offers an excellent instance to investigate the nature of mutations and how they affect the interatomic interactions in the spike protein. Here, using ultra large-scale ab initio computational modeling, we study the P681R and D614G mutations in the SD2-FP domain, including the effect of double mutation, and compare the results with the wild type. We have recently developed a method of calculating the amino-acid-amino-acid bond pairs (AABP) to quantitatively characterize the details of the interatomic interactions, enabling us to explain the nature of mutation at the atomic resolution. Our most significant finding is that the mutations reduce the AABP value, implying a reduced bonding cohesion between interacting residues and increasing the flexibility of these amino acids to cause the damage. The possibility of using this unique mutation quantifiers in a machine learning protocol could lead to the prediction of emerging mutations.
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Affiliation(s)
- Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (P.A.); (B.J.)
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (P.A.); (B.J.)
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Praveen Rao
- Department of Health Management and Informatics, Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO 65212, USA;
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China;
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou 325000, China
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (P.A.); (B.J.)
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140
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Kim G, Shin HM, Kim HR, Kim Y. Effects of Host and Pathogenicity on Mutation Rates in Avian Influenza A Viruses. Virus Evol 2022; 8:veac013. [PMID: 35295747 PMCID: PMC8922178 DOI: 10.1093/ve/veac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/11/2022] [Accepted: 02/20/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Mutation is the primary determinant of genetic diversity in influenza viruses. The rate of mutation, measured in an absolute time-scale, is likely to be dependent on the rate of errors in copying RNA sequences per replication and the number of replications per unit time. Conditions for viral replication are probably different among host taxa, potentially generating the host-specificity of the viral mutation rate, and possibly between highly and low pathogenic viruses. This study investigated whether mutation rates per year in avian influenza A viruses depend on host taxa and pathogenicity. We inferred mutation rates from the rates of synonymous substitutions, which are assumed to be neutral and thus equal to mutation rates, at four segments that code internal viral proteins (PB2, PB1, PA, NP). On the phylogeny of all avian viral sequences for each segment, multiple distinct subtrees (clades) were identified that represent viral subpopulations, which are likely to have evolved within particular host taxa. Using simple regression analysis, we found that mutation rates were significantly higher in viruses infecting chickens than domestic ducks, and in those infecting wild shorebirds than wild ducks. Host-dependency of the substitution rate was also confirmed by Bayesian phylogenetic analysis. However, we did not find evidence that the mutation rate is higher in highly pathogenic than in low pathogenic viruses. We discuss these results considering viral replication rate as the major determinant of mutation rate per unit time.
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Affiliation(s)
- Gwanghun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hyun Mu Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon 25159, Republic of Korea
| | - Hang-Rae Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon 25159, Republic of Korea
| | - Yuseob Kim
- Division of EcoScience and Department of Life Science, Ewha Womans University, Seoul 03760, Republic of Korea
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141
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Bandrick M, Balasch M, Heinz A, Taylor L, King V, Toepfer J, Foss D. A bivalent porcine circovirus type 2 (PCV2), PCV2a-PCV2b, vaccine offers biologically superior protection compared to monovalent PCV2 vaccines. Vet Res 2022; 53:12. [PMID: 35180885 PMCID: PMC8857852 DOI: 10.1186/s13567-022-01029-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/21/2022] [Indexed: 11/10/2022] Open
Abstract
Recent publications suggest PCV2 vaccine-induced protection is superior when the vaccine and challenge are closely matched. PCV2's evolutionary rate, propensity for recombination, and genotype shifting, all provide rationale for modernizing PCV2 vaccines. One mechanism to increase a vaccine's epitope breadth is by designing a bivalent vaccine. The objective of these studies was to evaluate efficacy of a monovalent (PCV1-2 chimera, cPCV2a or cPCV2b) and bivalent (cPCV2a-cPCV2b) vaccine in terms of homologous and heterologous efficacy. In Study A, pigs were vaccinated with cPCV2a or saline and challenged with PCV2a or PCV2b. In Study B, pigs were vaccinated with cPCV2a, cPCV2a-cPCV2b bivalent, or saline, and challenged with PCV2a. In Study C, pigs were vaccinated with cPCV2b, cPCV2a-cPCV2b bivalent, or saline, and challenged with PCV2b. In all studies vaccines and saline were administered intramuscularly to pigs at three to four weeks of age. Virulent PCV2b or PCV2a was administered to all animals approximately three weeks post-vaccination. Both mono and bivalent vaccinated groups demonstrated significantly lower viremia, percent of animals ever viremic, percent of animals with lymphoid depletion and/or histiocytic replacement, and percent of animals with PCV2 colonization of lymphoid tissues compared to saline controls. In Study A, a biologically relevant, though not significantly different, improvement in homologous versus heterologous protection was observed. In Studies B and C, biologically superior efficacy of the bivalent cPCV2a-cPCV2b vaccine compared to either monovalent vaccine was demonstrated. Taken together, cross-protection among mismatched PCV2 vaccine and challenge genotypes is not 100%; a bivalent PCV2 vaccine may provide the best opportunity to broaden coverage to circulating strains of PCV2.
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Affiliation(s)
- Meggan Bandrick
- Zoetis Inc, Veterinary Medicine Research and Development, 333 Portage Street, Kalamazoo, MI, 49007, USA.
| | - Monica Balasch
- Zoetis Manufacturing and Research Spain S.L. , Ctra. Camprodon s/n, Finca La Riba, 17813, Vall de Bianya, Spain
| | - Andrea Heinz
- Zoetis Inc, Veterinary Medicine Research and Development, 333 Portage Street, Kalamazoo, MI, 49007, USA
| | - Lucas Taylor
- Zoetis Inc, Veterinary Medicine Research and Development, 333 Portage Street, Kalamazoo, MI, 49007, USA
| | - Vickie King
- Zoetis Inc, Veterinary Medicine Research and Development, 333 Portage Street, Kalamazoo, MI, 49007, USA
| | - Jeri Toepfer
- Zoetis Inc, Veterinary Medicine Research and Development, 333 Portage Street, Kalamazoo, MI, 49007, USA
| | - Dennis Foss
- Zoetis Inc, Veterinary Medicine Research and Development, 333 Portage Street, Kalamazoo, MI, 49007, USA
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142
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Gene Overlapping as a Modulator of Begomovirus Evolution. Microorganisms 2022; 10:microorganisms10020366. [PMID: 35208820 PMCID: PMC8875319 DOI: 10.3390/microorganisms10020366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
In RNA viruses, which have high mutation—and fast evolutionary— rates, gene overlapping (i.e., genomic regions that encode more than one protein) is a major factor controlling mutational load and therefore the virus evolvability. Although DNA viruses use host high-fidelity polymerases for their replication, and therefore should have lower mutation rates, it has been shown that some of them have evolutionary rates comparable to those of RNA viruses. Notably, these viruses have large proportions of their genes with at least one overlapping instance. Hence, gene overlapping could be a modulator of virus evolution beyond the RNA world. To test this hypothesis, we use the genus Begomovirus of plant viruses as a model. Through comparative genomic approaches, we show that terminal gene overlapping decreases the rate of virus evolution, which is associated with lower frequency of both synonymous and nonsynonymous mutations. In contrast, terminal overlapping has little effect on the pace of virus evolution. Overall, our analyses support a role for gene overlapping in the evolution of begomoviruses and provide novel information on the factors that shape their genetic diversity.
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143
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Bianco A, Capozzi L, Del Sambro L, Simone D, Pace L, Rondinone V, Difato LM, Miccolupo A, Manzari C, Fedele A, Parisi A. Persistent SARS-CoV-2 Infection in a Patient With Non-hodgkin Lymphoma: Intra-Host Genomic Diversity Analysis. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.758191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic, threatening global public health. Several cases of persistent infection have been described, but there are few reports that compared the genetic variability among samples collected from the patient during infection. In the current study, we reported a viral genetic analysis of a diabetic male patient with Non-Hodgkin Lymphoma affected by persistent SARS-CoV-2 infection. We sequenced the patient-derived viral isolated both from oro/nasopharyngeal swab and VeroE6 cell line, collected from the same patient at different points of the infection. Due to the insufficient material of the second swab received, in order to obtain a complete coverage of the viral genome, it was convenient to perform a virus isolation after cell culture. Both genomes belonged to Pangolin Lineage B.1, Nextstrain clade 20A and GISAID clade G. The mutation spectrum predicted for the two viral genomes reveal three additionally mutations in the sequence of second sample when compared with mutations set identified in the first sample. Our findings show the evolution of the intra-host variability during the course of a long-lasting infection.
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144
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Kumar A, Goyal N, Saranathan N, Dhamija S, Saraswat S, Menon MB, Vivekanandan P. The slowing rate of CpG depletion in SARS-CoV-2 genomes is consistent with adaptations to the human host. Mol Biol Evol 2022; 39:6521032. [PMID: 35134218 PMCID: PMC8892944 DOI: 10.1093/molbev/msac029] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Depletion of CpG dinucleotides in SARS-CoV-2 genomes has been linked to virus evolution, host-switching, virus replication, and innate immune responses. Temporal variations, if any, in the rate of CpG depletion during virus evolution in the host remain poorly understood. Here, we analysed the CpG content of over 1.4 million full-length SARS-CoV-2 genomes representing over 170 million documented infections during the first 17 months of the pandemic. Our findings suggest that the extent of CpG depletion in SARS-CoV-2 genomes is modest. Interestingly, the rate of CpG depletion is highest during early evolution in humans and it gradually tapers off almost reaching an equilibrium; this is consistent with adaptations to the human host. Furthermore, within the coding regions, CpG depletion occurs predominantly at codon positions 2-3 and 3-1. Loss of ZAP-binding motifs in SARS-CoV-2 genomes is primarily driven by the loss of the terminal CpG in the motifs. Nonetheless, majority of the CpG depletion in SARS-CoV-2 genomes occurs outside ZAP-binding motifs. SARS-CoV-2 genomes selectively lose CpGs-motifs from a U-rich context; this may help avoid immune recognition by TLR7. SARS-CoV-2 alpha-, beta- and delta-variants of concern have reduced CpG content compared to sequences from the beginning of the pandemic. In sum, we provide evidence that the rate of CpG depletion in virus genomes is not uniform and it greatly varies over time and during adaptations to the host. This work highlights how temporal variations in selection pressures during virus adaption may impact the rate and the extent of CpG depletion in virus genomes.
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Affiliation(s)
- Akhil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Nishank Goyal
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Sonam Dhamija
- CSIR-Institute of Genomics and Integrative Biology, New Delhi-110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Saurabh Saraswat
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Manoj B Menon
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
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145
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Human SUMOylation Pathway Is Critical for Influenza B Virus. Viruses 2022; 14:v14020314. [PMID: 35215907 PMCID: PMC8876058 DOI: 10.3390/v14020314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
The identification and elucidation of host pathways for viral infection are critical for understanding the viral infection processes and novel therapeutics development. Here, for the first time, we discover that the human SUMOylation pathway is essential for the IBV viral life cycle. First, IBV viruses were completely inhibited by a novel SUMOylation specific inhibitor, STE025, discovered from our FRET-based high-throughput screening, and the inhibition was very potent, with IC50~ 0.1 µM in an IBV-induced cell death rescue assay; Second, we determined that the IBV M1 protein was SUMOylated, which was mediated by the SUMOylation E2 conjugation enzyme and the E3 ligase enzyme at very high affinities, of 0.20 µM and 0.22 µM, respectively; Third, the mutation of the IBV M1 SUMOylation site, K21R, completely abolished the viral particle generation, strongly suggesting the requirement of SUMOylation for the IBV life cycle. These results suggest that the blockage of the host human SUMOylation pathway is very effective for IBV inhibition. We therefore propose that the host SUMOylation pathway is a critical host factor for the IBV virus life cycle. The identification and inhibition of critical host factor(s) provide a novel strategy for future anti-viral therapeutics development, such as IBV and other viruses.
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146
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Pourkarim F, Pourtaghi‐Anvarian S, Rezaee H. Molnupiravir: A new candidate for COVID-19 treatment. Pharmacol Res Perspect 2022; 10:e00909. [PMID: 34968008 PMCID: PMC8929331 DOI: 10.1002/prp2.909] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/05/2021] [Accepted: 12/15/2021] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) emerged in late December 2019 in china and has rapidly spread to many countries around the world. The effective pharmacotherapy can reduce the mortality of COVID-19. Antiviral medications are the candidate therapies for the management of COVID-19. Molnupiravir is an antiviral drug with anti-RNA polymerase activity and currently is under investigation for the treatment of patients with COVID-19. This review focuses on summarizing published literature for the mechanism of action, safety, efficacy, and clinical trials of molnupiravir in the treatment of COVID-19 patients.
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Affiliation(s)
- Fariba Pourkarim
- Student Research CommitteeFaculty of PharmacyTabriz University of Medical SciencesTabrizIran
- Department of Clinical PharmacyFaculty of PharmacyTabriz University of Medical SciencesTabrizIran
| | - Samira Pourtaghi‐Anvarian
- Student Research CommitteeFaculty of PharmacyTabriz University of Medical SciencesTabrizIran
- Department of Clinical PharmacyFaculty of PharmacyTabriz University of Medical SciencesTabrizIran
| | - Haleh Rezaee
- Department of Clinical PharmacyFaculty of PharmacyTabriz University of Medical SciencesTabrizIran
- Infectious Diseases and Tropical Medicine Research CenterTabriz University of Medical SciencesTabrizIran
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147
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Qian Z, Li P, Tang X, Lu J. Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes. MEDICAL REVIEW (BERLIN, GERMANY) 2022; 2:3-22. [PMID: 35658106 PMCID: PMC9047652 DOI: 10.1515/mr-2021-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/23/2022] [Indexed: 12/27/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has caused immense losses in human lives and the global economy and posed significant challenges for global public health. As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has evolved, thousands of single nucleotide variants (SNVs) have been identified across the viral genome. The roles of individual SNVs in the zoonotic origin, evolution, and transmission of SARS-CoV-2 have become the focus of many studies. This review summarizes recent comparative genomic analyses of SARS-CoV-2 and related coronaviruses (SC2r-CoVs) found in non-human animals, including delineation of SARS-CoV-2 lineages based on characteristic SNVs. We also discuss the current understanding of receptor-binding domain (RBD) evolution and characteristic mutations in variants of concern (VOCs) of SARS-CoV-2, as well as possible co-evolution between RBD and its receptor, angiotensin-converting enzyme 2 (ACE2). We propose that the interplay between SARS-CoV-2 and host RNA editing mechanisms might have partially resulted in the bias in nucleotide changes during SARS-CoV-2 evolution. Finally, we outline some current challenges, including difficulty in deciphering the complicated relationship between viral pathogenicity and infectivity of different variants, and monitoring transmission of SARS-CoV-2 between humans and animals as the pandemic progresses.
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Affiliation(s)
- Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China
| | - Pei Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100176, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100176, China
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148
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Retel C, Kowallik V, Becks L, Feulner PGD. Strong Selection and High Mutation Supply Characterize Experimental Chlorovirus Evolution. Virus Evol 2022; 8:veac003. [PMID: 35169490 PMCID: PMC8838748 DOI: 10.1093/ve/veac003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
Characterizing how viruses evolve expands our understanding of the underlying fundamental processes, such as mutation, selection and drift. One group of viruses whose evolution has not yet been extensively studied is the Phycodnaviridae, a globally abundant family of aquatic large double-stranded (ds) DNA viruses. Here we studied the evolutionary change of Paramecium bursaria chlorella virus 1 during experimental coevolution with its algal host. We used pooled genome sequencing of six independently evolved populations to characterize genomic change over five time points. Across six experimental replicates involving either strong or weak demographic fluctuations, we found single nucleotide polymorphisms (SNPs) at sixty-seven sites. The occurrence of genetic variants was highly repeatable, with just two of the SNPs found in only a single experimental replicate. Three genes A122/123R, A140/145R and A540L showed an excess of variable sites, providing new information about potential targets of selection during Chlorella–Chlorovirus coevolution. Our data indicated that the studied populations were not mutation-limited and experienced strong positive selection. Our investigation highlighted relevant processes governing the evolution of aquatic large dsDNA viruses, which ultimately contributes to a better understanding of the functioning of natural aquatic ecosystems.
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Affiliation(s)
- Cas Retel
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Bio-geochemistry, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, Kastanienbaum 6047, Switzerland
- Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
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149
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Mazur FG, Morinisi LM, Martins JO, Guerra PPB, Freire CCM. Exploring Virome Diversity in Public Data in South America as an Approach for Detecting Viral Sources From Potentially Emerging Viruses. Front Genet 2022; 12:722857. [PMID: 35126446 PMCID: PMC8814814 DOI: 10.3389/fgene.2021.722857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
The South American continent presents a great diversity of biomes, whose ecosystems are constantly threatened by the expansion of human activity. The emergence and re-emergence of viral populations with impact on the human population and ecosystem have shown increases in the last decades. In deference to the growing accumulation of genomic data, we explore the potential of South American-related public databases to detect signals that contribute to virosphere research. Therefore, our study aims to investigate public databases with emphasis on the surveillance of viruses with medical and ecological relevance. Herein, we profiled 120 "sequence read archives" metagenomes from 19 independent projects from the last decade. In a coarse view, our analyses identified only 0.38% of the total number of sequences from viruses, showing a higher proportion of RNA viruses. The metagenomes with the most important viral sequences in the analyzed environmental models were 1) aquatic samples from the Amazon River, 2) sewage from Brasilia, and 3) soil from the state of São Paulo, while the models of animal transmission were detected in mosquitoes from Rio Janeiro and Bats from Amazonia. Also, the classification of viral signals into operational taxonomic units (OTUs) (family) allowed us to infer from metadata a probable host range in the virome detected in each sample analyzed. Further, several motifs and viral sequences are related to specific viruses with emergence potential from Togaviridae, Arenaviridae, and Flaviviridae families. In this context, the exploration of public databases allowed us to evaluate the scope and informative capacity of sequences from third-party public databases and to detect signals related to viruses of clinical or environmental importance, which allowed us to infer traits associated with probable transmission routes or signals of ecological disequilibrium. The evaluation of our results showed that in most cases the size and type of the reference database, the percentage of guanine-cytosine (GC), and the length of the query sequences greatly influence the taxonomic classification of the sequences. In sum, our findings describe how the exploration of public genomic data can be exploited as an approach for epidemiological surveillance and the understanding of the virosphere.
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Affiliation(s)
| | | | | | | | - Caio C. M. Freire
- Department Genetics and Evolution, UFSCar—Federal University of São Carlos, São Carlos, Brazil
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150
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Zhu F, Duong V, Lim XF, Hul V, Chawla T, Keatts L, Goldstein T, Hassanin A, Tu VT, Buchy P, Sessions OM, Wang LF, Dussart P, Anderson DE. Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats. Viruses 2022; 14:v14020176. [PMID: 35215769 PMCID: PMC8877364 DOI: 10.3390/v14020176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 12/04/2022] Open
Abstract
Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.
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Affiliation(s)
- Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Vibol Hul
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
- Unité des Virus Émergents, (UVÉ: Aix-Marseille Univ-IRD 190-INSERM 1207), 13005 Marseille, France
| | - Tanu Chawla
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Lucy Keatts
- Wildlife Conservation Society, Health Program, Bronx, NY 10460, USA;
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité, Sorbonne Université, MNHN, CNRS, EPHE, UA, 75005 Paris, France;
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet Road, Cau Giay District, Hanoi 10072, Vietnam;
| | - Philippe Buchy
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
| | - October M. Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
| | - Danielle E. Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
- Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne 3000, Australia
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
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