Author: 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
Title: Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003 Document date: 2004_9_6
ID: 0gmtnkbh_23
Snippet: Inferring phylogenetic relationships between the known SARS-CoV isolates using existing public data has been problematic because of the potential for sequencing errors. Moreover, the rate of SARS-CoV mutation in culture was not previously known and was thought to be significant given the mutation rates in other RNA viruses. Our experiments provided information as to the potential causes and rates of sequence variations of the SARS-CoV in culture......
Document: Inferring phylogenetic relationships between the known SARS-CoV isolates using existing public data has been problematic because of the potential for sequencing errors. Moreover, the rate of SARS-CoV mutation in culture was not previously known and was thought to be significant given the mutation rates in other RNA viruses. Our experiments provided information as to the potential causes and rates of sequence variations of the SARS-CoV in culture. Based on our Vero cells passages and humanto-Vero transition data, we estimated that, at most, one sequence variation from the original tissue virus can be accounted for by in vitro culture artifacts. The average base-calling error probability (as reported by PHREP [11] ) of our sequences is about 7.5 × 10 -5 , or 2.25 errors per SARS-CoV genome. Accordingly, we suspected that sequencing errors in the reported SARS sequences would be approximately 1-2 bases per reported genome. We used this information to assess the true sequence variants reported in the public SARS sequence databases employing a "mutation filter" [5] . This mutation filter identifies a sequence variant as a probable mutation if it appeared in more than one isolate. Higher filter stringency can be applied by demanding a sequence variant to be present in two, three, or more isolates. A total of 54 isolates were analyzed, including 22 from Singapore. Our results show that the number of mutations appearing in only one isolate is high at 349 (see supplementary Table S3 ); however,
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