Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong

Tang, Julian W.; Cheung, Jo L.K.; Chu, Ida Miu-Ting; Ip, Margaret; Hui, Mamie; Peiris, Malik; Chan, Paul K.S.

doi:10.1016/j.jcv.2006.10.001

Cited by 10 publications

(7 citation statements)

References 27 publications

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“…25 All SARS-CoV isolates from epidemic countries and regions outside mainland China could be traced to Guangdong or Hong Kong based on the S-gene SNV motif. 23,39 During the second sporadic outbreaks of 2003e2004, it was shown that the SARS-CoV sequences from index patients were almost identical to that from civets collected in the same period and all retained the 29-nt sequence in the ORF8 gene. The mild disease symptoms associated with these viruses and the lack of rapid human-to-human transmission provided further evidence that the rapid adaptation of the SARS-CoV in the first major outbreak of 2002e2003 was essential for its establishment and pathogenesis in humans.…”

Section: Rapid Adaptation Of Sars-covs In Humansmentioning

confidence: 99%

Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology

Shi

Wang

2017

Genetics and Evolution of Infectious Diseases

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Section: Rapid Adaptation Of Sars-covs In Humansmentioning

confidence: 99%

Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology

Shi

Wang

2017

Genetics and Evolution of Infectious Diseases

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“…If these CR3022 binding regions are to continue to serve as epitopes without escape mutations, one would hope to see them as not differing by non-conservative mutations in early SARS isolates. For example, we would hope that SARS isolates from Hong Kong patients have similar subsequences, and they certainly are [ 36 ] when compared with the large range of the less close variants [ 4 ] and of more distant coronaviruses [ 5 ]. Nonetheless, one sees differences within those regions that would not normally be considered as conservative substitutions: serine (S) to phenylalanine (F) (small polar to large non-polar), threonine (T) to methionine (M) (small polar to large non-polar), and histidine (H) to asparagine (N) (large partially charged to small neutral polar).…”

Section: Resultsmentioning

confidence: 99%

The use of knowledge management tools in viroinformatics. Example study of a highly conserved sequence motif in Nsp3 of SARS-CoV-2 as a therapeutic target

Robson

2020

Computers in Biology and Medicine

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Knowledge management tools that assist in systematic review and exploration of scientific knowledge generally are of obvious potential importance in evidence based medicine in general, but also to the design of therapeutics based on the protein subsequences and fold motifs of virus proteins as considered here. Rapid access to bundles (clusters) of related elements of knowledge gathered from diverse sources on the Internet and from growing knowledge repositories seem particularly helpful when exploring less obvious therapeutic targets in viruses (for which knowledge new to the researcher is important), and when using the following concept. Subsequences of amino acid residue sequences of proteins that are conserved across strains and species are (a) more likely to be important targets and (b) less likely to exhibit escape mutations that would make them resistant to vaccines and therapeutic agents. However, the terms “conserved” and even “highly conserved” used by authors are matters of degree, depending on how distant from SARS-CoV-2 they wished to go in comparing other sequences. The binding site to the human ACE2 protein as virus receptor and human antibody CR3022 binding site on the spike glycoprotein are rather variable by the criteria used in the present and preceding studies. To look for more strongly conserved targets, open reading frames of SARS-CoV-2 were examined for extremely highly conserved regions, meaning recognizable across many viruses and organisms. Most prominent is a motif found in SARS-CoV-2 non-structural protein 3 (Nsp3). It relates to a fold called type called the macro domain and has remarkably wide distribution across organisms including humans with significant homologies involving three especially conserved subsequences (a) VVVNAANVYLKHGGGVAGALNK, (b) LHVVGPNVNKG, and (c) PLLSAGIFG. Careful study of the variations of these and of the more variable sequences between and around them might provide a finer “scalpel” to ensure inhibition of a vital function of the virus without impairing the functions of related host macro domains.

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“…Phylogenies 239,241 constructed using ML 242,243 and Bayesian methods 244 consistently distinguished the late-phase strains as a monophyletic cluster, supporting the viewpoint that the local outbreaks later in Hong Kong, as well as those in other parts of the world, were largely, if not completely, derived from a common source. In fact, the SCoV spike (S) glycoprotein gene phylogeny suggested that multiple SCoV strains might have been independently introduced into Hong Kong from Guangdong before the SSE in Hotel M, although none of these strains contributed substantially to the subsequent outbreaks.…”

Section: Molecular Epidemiology Of Sars Outbreaksmentioning

confidence: 88%

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Lam

Hon

Tang

2010

Critical Reviews in Clinical Laboratory Sciences

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Since DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists.

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Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong

Cited by 10 publications

References 27 publications

Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology

Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology

The use of knowledge management tools in viroinformatics. Example study of a highly conserved sequence motif in Nsp3 of SARS-CoV-2 as a therapeutic target

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

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