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

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

Research output: Contribution to journalArticle

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Abstract

Background: The SARS coronavirus is the etiologic agent for the epidemic of the Severe Acute Respiratory Syndrome. The recent emergence of this new pathogen, the careful tracing of its transmission patterns, and the ability to propagate in culture allows the exploration of the mutational dynamics of the SARS-CoV in human populations. Methods: We sequenced complete SARS-CoV genomes taken from primary human tissues (SIN3408, SIN3725V, SIN3765V), cultured isolates (SIN848, SIN846, SIN842, SIN845, SIN847, SIN849, SIN850, SIN852, SIN3408L), and five consecutive Vero cell passages (SIN2774_P1, SIN2774_P2, SIN2774_P3, SIN2774_P4, SIN2774_P5) arising from SIN2774 isolate. These represented individual patient samples, serial in vitro passages in cell culture, and paired human and cell culture isolates. Employing a refined mutation filtering scheme and constant mutation rate model, the mutation rates were estimated and the possible date of emergence was calculated. Phylogenetic analysis was used to uncover molecular relationships between the isolates. Results: Close examination of whole genome sequence of 54 SARS-CoV isolates identified before 14th October 2003, including 22 from patients in Singapore, revealed the mutations engendered during human-to-Vero and Vero-to-human transmission as well as in multiple Vero cell passages in order to refine our analysis of human-to-human transmission. Though co-infection by different quasipecies in individual tissue samples is observed, the in vitro mutation rate of the SARS-CoV in Vero cell passage is negligible. The in vivo mutation rate, however, is consistent with estimates of other RNA viruses at approximately 5.7 × 10-6 nucleotide substitutions per site per day (0.17 mutations per genome per day), or two mutations per human passage (adjusted R-square = 0.4014). Using the immediate Hotel M contact isolates as roots, we observed that the SARS epidemic has generated four major genetic groups that are geographically associated: two Singapore isolates, one Taiwan isolate, and one North China isolate which appears most closely related to the putative SARS-CoV isolated from a palm civet. Non-synonymous mutations are centered in non-essential ORFs especially in structural and antigenic genes such as the S and M proteins, but these mutations did not distinguish the geographical groupings. However, no nonsynonymous mutations were found in the 3CLpro and the polymerase genes. Conclusions: Our results show that the SARS-CoV is well adapted to growth in culture and did not appear to undergo specific selection in human populations. We further assessed that the putative origin of the SARS epidemic was in late October 2002 which is consistent with a recent estimate using cases from China. The greater sequence divergence in the structural and antigenic proteins and consistent deletions in the 3′ - most portion of the viral genome suggest that certain selection pressures are interacting with the functional nature of these validated and putative ORFs.

Original languageEnglish
Article number32
JournalBMC Infectious Diseases
Volume4
DOIs
Publication statusPublished - 6 Sep 2004
Externally publishedYes

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SARS Virus
Cell Culture Techniques
Mutation
Mutation Rate
Population
Vero Cells
Singapore
Genome
Open Reading Frames
China
Viverridae
Severe Acute Respiratory Syndrome
Viral Genome
RNA Viruses
Protein S
Coinfection
Taiwan
Genes
Nucleotides
Pressure

ASJC Scopus subject areas

  • Infectious Diseases

Cite this

Vega, V. B., Ruan, Y., Liu, J., Lee, W. H., Wei, C. L., Se-Thoe, S. Y., ... Liu, E. T. (2004). Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003. BMC Infectious Diseases, 4, [32]. https://doi.org/10.1186/1471-2334-4-32

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; Ooi, Eng Eong; Ling, Ai Ee; Stanton, Lawrence W.; Long, Philip M.; Liu, Edison T.

In: BMC Infectious Diseases, Vol. 4, 32, 06.09.2004.

Research output: Contribution to journalArticle

Vega, VB, Ruan, Y, Liu, J, Lee, WH, Wei, CL, Se-Thoe, SY, Tang, KF, Zhang, T, Kolatkar, P, Ooi, EE, Ling, AE, Stanton, LW, Long, PM & Liu, ET 2004, 'Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003', BMC Infectious Diseases, vol. 4, 32. https://doi.org/10.1186/1471-2334-4-32
Vega, Vinsensius B. ; Ruan, Yijun ; Liu, Jianjun ; Lee, Wah Heng ; Wei, Chia Lin ; Se-Thoe, Su Yun ; Tang, Kin Fai ; Zhang, Tao ; Kolatkar, Prasanna ; Ooi, Eng Eong ; Ling, Ai Ee ; Stanton, Lawrence W. ; Long, Philip M. ; Liu, Edison T. / Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003. In: BMC Infectious Diseases. 2004 ; Vol. 4.
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T1 - Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003

AU - Vega, Vinsensius B.

AU - Ruan, Yijun

AU - Liu, Jianjun

AU - Lee, Wah Heng

AU - Wei, Chia Lin

AU - Se-Thoe, Su Yun

AU - Tang, Kin Fai

AU - Zhang, Tao

AU - Kolatkar, Prasanna

AU - Ooi, Eng Eong

AU - Ling, Ai Ee

AU - Stanton, Lawrence W.

AU - Long, Philip M.

AU - Liu, Edison T.

PY - 2004/9/6

Y1 - 2004/9/6

N2 - Background: The SARS coronavirus is the etiologic agent for the epidemic of the Severe Acute Respiratory Syndrome. The recent emergence of this new pathogen, the careful tracing of its transmission patterns, and the ability to propagate in culture allows the exploration of the mutational dynamics of the SARS-CoV in human populations. Methods: We sequenced complete SARS-CoV genomes taken from primary human tissues (SIN3408, SIN3725V, SIN3765V), cultured isolates (SIN848, SIN846, SIN842, SIN845, SIN847, SIN849, SIN850, SIN852, SIN3408L), and five consecutive Vero cell passages (SIN2774_P1, SIN2774_P2, SIN2774_P3, SIN2774_P4, SIN2774_P5) arising from SIN2774 isolate. These represented individual patient samples, serial in vitro passages in cell culture, and paired human and cell culture isolates. Employing a refined mutation filtering scheme and constant mutation rate model, the mutation rates were estimated and the possible date of emergence was calculated. Phylogenetic analysis was used to uncover molecular relationships between the isolates. Results: Close examination of whole genome sequence of 54 SARS-CoV isolates identified before 14th October 2003, including 22 from patients in Singapore, revealed the mutations engendered during human-to-Vero and Vero-to-human transmission as well as in multiple Vero cell passages in order to refine our analysis of human-to-human transmission. Though co-infection by different quasipecies in individual tissue samples is observed, the in vitro mutation rate of the SARS-CoV in Vero cell passage is negligible. The in vivo mutation rate, however, is consistent with estimates of other RNA viruses at approximately 5.7 × 10-6 nucleotide substitutions per site per day (0.17 mutations per genome per day), or two mutations per human passage (adjusted R-square = 0.4014). Using the immediate Hotel M contact isolates as roots, we observed that the SARS epidemic has generated four major genetic groups that are geographically associated: two Singapore isolates, one Taiwan isolate, and one North China isolate which appears most closely related to the putative SARS-CoV isolated from a palm civet. Non-synonymous mutations are centered in non-essential ORFs especially in structural and antigenic genes such as the S and M proteins, but these mutations did not distinguish the geographical groupings. However, no nonsynonymous mutations were found in the 3CLpro and the polymerase genes. Conclusions: Our results show that the SARS-CoV is well adapted to growth in culture and did not appear to undergo specific selection in human populations. We further assessed that the putative origin of the SARS epidemic was in late October 2002 which is consistent with a recent estimate using cases from China. The greater sequence divergence in the structural and antigenic proteins and consistent deletions in the 3′ - most portion of the viral genome suggest that certain selection pressures are interacting with the functional nature of these validated and putative ORFs.

AB - Background: The SARS coronavirus is the etiologic agent for the epidemic of the Severe Acute Respiratory Syndrome. The recent emergence of this new pathogen, the careful tracing of its transmission patterns, and the ability to propagate in culture allows the exploration of the mutational dynamics of the SARS-CoV in human populations. Methods: We sequenced complete SARS-CoV genomes taken from primary human tissues (SIN3408, SIN3725V, SIN3765V), cultured isolates (SIN848, SIN846, SIN842, SIN845, SIN847, SIN849, SIN850, SIN852, SIN3408L), and five consecutive Vero cell passages (SIN2774_P1, SIN2774_P2, SIN2774_P3, SIN2774_P4, SIN2774_P5) arising from SIN2774 isolate. These represented individual patient samples, serial in vitro passages in cell culture, and paired human and cell culture isolates. Employing a refined mutation filtering scheme and constant mutation rate model, the mutation rates were estimated and the possible date of emergence was calculated. Phylogenetic analysis was used to uncover molecular relationships between the isolates. Results: Close examination of whole genome sequence of 54 SARS-CoV isolates identified before 14th October 2003, including 22 from patients in Singapore, revealed the mutations engendered during human-to-Vero and Vero-to-human transmission as well as in multiple Vero cell passages in order to refine our analysis of human-to-human transmission. Though co-infection by different quasipecies in individual tissue samples is observed, the in vitro mutation rate of the SARS-CoV in Vero cell passage is negligible. The in vivo mutation rate, however, is consistent with estimates of other RNA viruses at approximately 5.7 × 10-6 nucleotide substitutions per site per day (0.17 mutations per genome per day), or two mutations per human passage (adjusted R-square = 0.4014). Using the immediate Hotel M contact isolates as roots, we observed that the SARS epidemic has generated four major genetic groups that are geographically associated: two Singapore isolates, one Taiwan isolate, and one North China isolate which appears most closely related to the putative SARS-CoV isolated from a palm civet. Non-synonymous mutations are centered in non-essential ORFs especially in structural and antigenic genes such as the S and M proteins, but these mutations did not distinguish the geographical groupings. However, no nonsynonymous mutations were found in the 3CLpro and the polymerase genes. Conclusions: Our results show that the SARS-CoV is well adapted to growth in culture and did not appear to undergo specific selection in human populations. We further assessed that the putative origin of the SARS epidemic was in late October 2002 which is consistent with a recent estimate using cases from China. The greater sequence divergence in the structural and antigenic proteins and consistent deletions in the 3′ - most portion of the viral genome suggest that certain selection pressures are interacting with the functional nature of these validated and putative ORFs.

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