key: cord-0961851-6phwc7s7
authors: Gong, Yu-Nong; Tsao, Kuo-Chien; Hsiao, Mei-Jen; Huang, Chung-Guei; Huang, Peng-Nien; Huang, Po-Wei; Lee, Kuo-Ming; Liu, Yi-Chun; Yang, Shu-Li; Kuo, Rei-Lin; Liu, Ming-Tsan; Yang, Ji-Rong; Chiu, Cheng-Hsun; Yang, Cheng-Ta; Shih, Shin-Ru; Chen, Guang-Wu
title: Sequence variation among SARS-CoV-2 isolates in Taiwan
date: 2020-03-31
journal: bioRxiv
DOI: 10.1101/2020.03.29.014290
sha: b8dc7e9d08905d6d58b51782edf9ee24478f2cb1
doc_id: 961851
cord_uid: 6phwc7s7

Taiwan experienced two waves of imported cases of coronavirus disease 2019 (COVID-19), first from China in January to late February, followed by those from other countries starting in early March. Additionally, several cases could not be traced to any imported cases and were suspected as sporadic local transmission. Twelve full viral genomes were determined in this study by Illumina sequencing either from virus isolates or directly from specimens, among which 5 originated from clustered infections. Phylogenetic tree analysis revealed that these sequences were in different clades, indicating that no major strain has been circulating in Taiwan. A deletion in open reading frame 8 was found in one isolate. Only a 4-nucleotide difference was observed among the 5 genomes from clustered infections.

outbreak in 2003, deletions in ORF8 were observed, which were associated with a reduced 1 8 8 ability for virus replication in human cells (11).

RNA viruses show variations in their genomes due to nucleotide substitutions generated 1 9 0 by the low fidelity of RNA-dependent RNA polymerase during replication. The genome 1 9 1 variation of these viruses is thought to facilitate successful adaption to the environment of 1 9 2 various hosts. However, previous studies showed that the mutation rates of RNA viruses vary in CoV-2 isolated from 5 patients from February 26 to March 9, 2020 in CGMH Taiwan revealed 1 9 5 only 4 mutations in their 29,903-nt genomic RNA. This suggests that the nucleotide substitution 1 9 6 rate is controlled during viral RNA replication. The nsp14 exoribonuclease encoded by several 1 9 7 coronaviruses plays a role in proofreading during genome replication (13, 14) ; further studies are 1 9 8 required to investigate the function of SARS-CoV-2 nsp14 in replication fidelity. Timely sharing full genomes of SASR-CoV-2 from different locations is important for during the early evolution of SARS-CoV-2. biorxiv. 2020. 

ORF1ab−A16576G(K5526R) S−C145T(H49Y) S−C2651T(S884F) Deletion ORF1ab−C794T(T265I)

ORF−1ab−G1132A(V378I) ORF1ab−G10818T(L3606F)

ORF1ab−C14541T(L3606F),ORF1ab−C16983T ORF3a−G752T(G251V)

ORF1ab−C2772T ORF1ab−C14144T(P4715L)