COVID-19 Vaccine Hesitancy Worldwide: A Concise Systematic Review of Vaccine Acceptance Rates.

Novel SARS-CoV-2 variants: the pandemics within the pandemic.

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel.

The Spike protein is the target of both antibody-based therapeutics (convalescent plasma, polyclonal serum, monoclonal antibodies) and vaccines. Mutations in Spike could affect efficacy of those treatments. Hence, monitoring of mutations is necessary to forecast and readapt the inventory of therapeutics. Different phylogenetic nomenclatures have been used for the currently circulating SARS-CoV-2 clades. The Spike protein has different hotspots of mutation and deletion, the most dangerous for immune escape being the ones within the receptor binding domain (RBD), such as K417N/T, N439K, L452R, Y453F, S477N, E484K, and N501Y. Convergent evolution has led to different combinations of mutations among different clades. In this review we focus on the main variants of concern, that is, the so-called UK (B.1.1.7), South African (B.1.351) and Brazilian (P.1) strains.

Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines.

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil.

Phylogenetic and phylodynamic analyses of SARS-CoV-2.

Analysis of genetic sequence data from the pandemic SARS Coronavirus 2 can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed data sets with few isolates in any given location. Here we report an analysis of 20 whole SARS-CoV 2 genomes from a single relatively small and geographically constrained outbreak in Weifang, People9s Republic of China. Using Bayesian model-based phylodynamic methods, we estimate the reproduction number for the outbreak to be 1.99(95% CI:1.48-3.14). We further estimate the number of infections through time and compare these estimates to confirmed diagnoses by the Weifang Centers for Disease Control. We find that these estimates are consistent with reported cases and there is unlikely to be a large undiagnosed burden of infection over the period we studied.

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Genomic epidemiology of a densely sampled COVID19 outbreak in China

We gratefully acknowledge China National GeneBank at Shenzhen, China for the sequencing strategy and capacity support. We also gratefully acknowledge the laboratories that have contributed publicly available genomes via GISAID: The Public Health Agency of Sweden, Sweden; Public Health Ontario Laboratories, Canada; Pathogen Discovery, Respiratory Viruses Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, United States; Programme in Emerging Infectious Diseases, Duke-NUS Medical School, United State; Alaska State Virology Laboratory, United States; Respiratory Virus Unit, Microbiology Services Colindale, Public Health England, United Kingdom; Laboratory for Functional Genome Analysis, Dept. Genomics, Gene Center of the LMU Munich, Germany; Michigan Department of Health and Human Services, Bureau of Laboratories, United State; National Public Health Laboratory, National Centre for Infectious Diseases, Singapore; BGI-shenzhen & The First Affiliated Hospital of Guangzhou Medical University, China; NSW Health Pathology - Institute of Clinical Pathology and Medical Research; Westmead Hospital; University of Sydney, Australia; BCCDC Public Health Laboratory, Canada; COVID-19 Genomics UK (COG-UK) Consortium, United Kingdom; Guangdong Provincial Institution of Public Health, China; Department of Microbiology, Guangdong Provincial Center for Diseases Control and Prevention, China; Department of Health Technology and Informatics, Faculty of Health and Social Science, The Hong Kong Polytechnic University, Hong Kong; School of Public Health, The University of Hong Kong, Hong Kong; Pathogen Genomics Center, National Institute of Infectious Diseases, Japan; National Research Center for Translational Medicine (Shanghai), Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine & Shanghai Public Health Clinical Center, China; Seattle Flu Study, United States; UW Virology Lab, United States; National Institute for Viral Disease Control & Prevention, CCDC, China; Beijing Institute of Microbiology and Epidemiology, China; National Institute for Viral Disease Control and Prevention, China CDC, China; Inspection Center of Hangzhou Center for Disease Control and Prevention, China; Pathogen Genomics Lab King Abdullah University of Science and Technology (KAUST), Saudi Arabia; Chinese PLA Institute for Disease Control and Prevention, China; National Institute of Health. Department of medical Sciences, Ministry of Public Health, Thailand; Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Greece; Wellcome Sanger Institute for the COVID-19 Genomics UK Consortium, United Kingdom; State Key Laboratory of Biotherapy of Sichuan University, China; SeqCOVID-SPAIN consortium/IBV(CSIC), Spain; Oxford University Clinical Research Unit, Hanoi, Vietnam; Institute of Environmental Science and Research (ESR), New Zealand; Erasmus Medical Center, Netherlands.

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Wei Chen

Papers

Phylogenetic and phylodynamic analyses of SARS-CoV-2.

Genomic epidemiology of a densely sampled COVID19 outbreak in China

Genomic epidemiology of a densely sampled COVID-19 outbreak in China