Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003.
Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003.
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DOI：
10.1186/1471-2334-4-32
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发表时间：
2004-09-06
影响因子：
3.7
通讯作者：
Liu ET
中科院分区：
文献类型：
--
作者：
Vega VB;Ruan Y;Liu J;Lee WH;Wei CL;Se-Thoe SY;Tang KF;Zhang T;Kolatkar PR;Ooi EE;Ling AE;Stanton LW;Long PM;Liu ET
SARS冠状病毒是引起SARS流行的病原体。最近出现的这种新的病原体，仔细跟踪其传播模式，并在文化中传播的能力，允许探索SARS冠状病毒在人群中的突变动力学。我们对取自原始人体组织的SARS-CoV全基因组进行了测序（SIN 3408、SIN 3725 V、SIN 3765 V），培养分离株（SIN 848、SIN 846、SIN 842、SIN 845、SIN 847、SIN 849、SIN 850、SIN 852、SIN 3408 L）和五个连续的Vero细胞传代（SIN2774_P1、SIN2774_P2、SIN2774_P3、SIN2774_P4、SIN2774_P5）源自SIN 2774分离株。这些代表个体患者样本、细胞培养物中的系列体外传代以及配对的人和细胞培养分离株。采用改进的突变过滤方案和恒定突变率模型，估计突变率，并计算可能出现的日期。系统发育分析用于揭示分离物之间的分子关系。对2003年10月14日之前鉴定的54株SARS-CoV分离株（包括22株来自新加坡患者的分离株）的全基因组序列进行仔细检查，发现在人与人之间和Vero与人之间传播以及多次Vero细胞传代期间产生的突变，以完善我们对人与人之间传播的分析。虽然在单个组织样本中观察到不同准种的共感染，但SARS-CoV在Vero细胞传代中的体外突变率可以忽略不计。然而，体内突变率与其他RNA病毒的估计值一致，约为每天每个位点5.7 × 10-6个核苷酸取代（每天每个基因组0.17个突变），或每次人类传代2个突变（校正R方= 0.4014）。使用直接M酒店接触分离株作为根，我们观察到SARS流行产生了四个主要的遗传群体，这些群体在地理上是相关的：两个新加坡分离株，一个台湾分离株，和一个华北分离株，该分离株似乎与从棕榈果子狸分离的假定SARS冠状病毒最密切相关。非同义突变集中在非必需的ORF中，特别是在结构和抗原基因如S和M蛋白中，但这些突变并不能区分地理分组。然而，在3CLpro和聚合酶基因中未发现非同义突变。我们的研究结果表明，SARS-CoV很好地适应了在文化中的增长，并没有出现在人群中进行特定的选择。我们进一步评估，SARS流行的假定起源是在2002年10月底，这与最近使用中国病例的估计一致。结构蛋白和抗原蛋白的较大序列差异以及病毒基因组3'端部分的一致缺失表明，某些选择压力与这些经验证和推定的ORF的功能性质相互作用。
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. 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. 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 non-synonymous mutations were found in the 3CLpro and the polymerase genes. 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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DOI：
10.1073/pnas.96.24.13910
发表时间：
1999-11-23
影响因子：
11.1
作者：
Drake, JW;Holland, JJ
通讯作者：
Holland, JJ
DOI：
10.1016/s0140-6736(03)13414-9
发表时间：
2003-05-24
期刊：
Lancet (London, England)
影响因子：
--
作者：
Ruan YJ;Wei CL;Ee AL;Vega VB;Thoreau H;Su ST;Chia JM;Ng P;Chiu KP;Lim L;Zhang T;Peng CK;Lin EO;Lee NM;Yee SL;Ng LF;Chee RE;Stanton LW;Long PM;Liu ET
通讯作者：
Liu ET
影响因子：
56.9
作者：
Guan, Y;Zheng, BJ;Poon, LLM
通讯作者：
Poon, LLM
影响因子：
14.9
作者：
THOMPSON, JD;HIGGINS, DG;GIBSON, TJ
通讯作者：
GIBSON, TJ
影响因子：
158.5
作者：
Ksiazek, TG;Erdman, D;Anderson, LJ
通讯作者：
Anderson, LJ