Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003

Vega, Vinsensius B.; Ruan, Yijun; Liu, Jianjun; Lee, Wah Heng; Wei, Chia Lin; Se-Thoe, Su Yun; Tang, Kin Fai; Zhang, Tao; Kolatkar, Prasanna R.; Ooi, Eng Eong; Ling, Ai Ee; Stanton, Lawrence W.; Long, Philip M.; Liu, Edison T.

doi:10.1186/1471-2334-4-32

Cited by 58 publications

(64 citation statements)

References 14 publications

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“…Effective inactivation was demonstrated against two independent viral isolates. The phylogenetic analysis showed that the two strains employed in this study have a common origin being more similar to those that originated in Hong Kong than those in North China and Taiwan (Vega et al ., 2004; Vicenzi et al ., 2004). By nucleotide sequence comparison, the Urbani isolate only differs by six nucleotide changes from the HSR1 isolate (Rota et al ., 2003; Ruan et al ., 2003; Vicenzi et al ., 2004).…”

Section: Discussionmentioning

confidence: 85%

Amotosalen photochemical inactivation of severe acute respiratory syndrome coronavirus in human platelet concentrates

Pinna¹,

Sampson‐Johannes

Clementi

et al. 2005

Transfusion Medicine

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A novel human coronavirus causing severe acute respiratory syndrome (SARS) emerged in epidemic form in early 2003 in China and spread worldwide in a few months. Every newly emerging human pathogen is of concern for the safety of the blood supply during and after an epidemic crisis. For this purpose, we have evaluated the inactivation of SARS-coronavirus (CoV) in platelet concentrates using an approved pathogen inactivation device, the INTERCEPT Blood System. Apheresis platelet concentrates (APCs) were inoculated with approximately 10(6) pfu mL(-1) of either Urbani or HSR1 isolates of SARS-CoV. The inoculated units were mixed with 150 microm amotosalen and illuminated with 3 J cm(-2) UV-A light. The viral titres were determined by plaque formation in Vero E6 cells. Mixing SARS-CoV with APC in the absence of any treatment decreased viral infectivity by approximately 0.5-1 log10. Following photochemical treatment, SARS-CoV was consistently inactivated to the limit of detection in seven independent APC units. No infectious virus was detected after treatment when up to one-third of the APC unit was assayed, demonstrating a mean log10-reduction of >6.2. Potent inactivation of SARS-CoV therefore extends the capability of the INTERCEPT Blood System in inactivating a broad spectrum of human pathogens including recently emerging respiratory viruses.

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Section: Discussionmentioning

confidence: 85%

Amotosalen photochemical inactivation of severe acute respiratory syndrome coronavirus in human platelet concentrates

Pinna¹,

Sampson‐Johannes

Clementi

et al. 2005

Transfusion Medicine

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“…Zhao et al (2004) analyzed 11 genomic sequences from different parts of the world during 2003 SARS epidemic and found that the mutation rate to be in the order of 0.80-2.38 × 10 −3 nucleotide substitution per site per year (2.2-6.7 × 10 −6 nucleotide substitutions per site per day) and the most recent common ancestor of the sequences was inferred to be present as early as the spring of 2002. Analysis on the Singapore isolates from the 2003 epidemic revealed that the mutation rate to be 5.7 × 10 −6 nucleotide substitutions per site per day, with the rates for synonymous and non-synonymous mutations at 2.5 × 10 −6 and 3.2 × 10 −6 nucleotide substitutions per site per day, respectively (Vega et al, 2004). All the above studies used human samples with available clinical data from the 2003 outbreak and the substitution rates of SARS-CoV genome obtained from the various studies were in good agreement with each other.…”

Section: Evolutionary Perspectivesmentioning

confidence: 99%

A review of studies on animal reservoirs of the SARS coronavirus

2008

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In this review, we summarize the researches on animal reservoirs of the SARS coronavirus (SARS-CoV). Masked palm civets were suspected as the origin of the SARS outbreak in 2003 and was confirmed as the direct origin of SARS cases with mild symptom in 2004. Sequence analysis of the SARS-CoV-like virus in masked palm civets indicated that they were highly homologous to human SARS-CoV with nt identity over 99.6%, indicating the virus has not been circulating in the population of masked palm civets for a very long time. Alignment of 10 complete viral genome sequences from masked palm civets with those of human SARS-CoVs revealed 26 conserved single-nucleotide variations (SNVs) in the viruses from masked palm civets. These conserved SNVs were gradually lost from the genomes of viruses isolated from the early phase to late phase human patients of the 2003 SARS epidemic. In 2005, horseshoe bats were identified as the natural reservoir of a group of coronaviruses that are distantly related to SARS-CoV. The genome sequences of bat SARS-like coronavirus had about 88-92% nt identity with that of the SARS-CoV. The prevalence of antibodies and viral RNA in different bat species and the characteristics of the bat SARS-like coronavirus were elucidated. Apart from masked palm civets and bats, 29 other animal species had been tested for the SARS-CoV, and the results are summarized in this paper.

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“…However, more recent reports indicate that SARS-CoV is distinct from the civet virus and it has not been answered so far whether the SARS-CoV originated from civet, or civet was infected from other species 9., 10.. The genome is relatively stable, since its mutation rate has been determined to be between 1.83×10 −6 and 8.26×10 −6 nucleotide substitutions per site per day (11) .…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV Genome Polymorphism: A Bioinformatics Study

Pavlović-Lažetić¹,

Mitić²,

Tomović³

et al. 2005

Genomics, Proteomics &Amp; Bioinformatics

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A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a “profile”, were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.

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Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003

Cited by 58 publications

References 14 publications

Amotosalen photochemical inactivation of severe acute respiratory syndrome coronavirus in human platelet concentrates

Amotosalen photochemical inactivation of severe acute respiratory syndrome coronavirus in human platelet concentrates

A review of studies on animal reservoirs of the SARS coronavirus

SARS-CoV Genome Polymorphism: A Bioinformatics Study

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