PT  - JOURNAL ARTICLE
AU  - Xumin Ou
AU  - Zhishuang Yang
AU  - Dekang Zhu
AU  - Sai Mao
AU  - Mingshu Wang
AU  - Renyong Jia
AU  - Shun Chen
AU  - Mafeng Liu
AU  - Qiao Yang
AU  - Ying Wu
AU  - Xinxin Zhao
AU  - Shaqiu Zhang
AU  - Juan huang
AU  - Qun Gao
AU  - Yunya Liu
AU  - Ling Zhang
AU  - Maikel Peopplenbosch
AU  - Qiuwei Pan
AU  - Anchun Cheng
TI  - Tracing two causative SNPs reveals SARS-CoV-2 transmission in North America population
AID  - 10.1101/2020.05.12.092056
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.05.12.092056
4099  - http://biorxiv.org/content/early/2020/05/14/2020.05.12.092056.short
4100  - http://biorxiv.org/content/early/2020/05/14/2020.05.12.092056.full
AB  - During the COVID-19 pandemic, precisely tracing the route of the SARS-CoV-2 transmission in human population remains challenging. Because this RNA virus can mutate massively without a specifically tracing maker. Herein, using a geographic stratified genome-wide association study (GWAS) of 2599 full-genome sequences, we identified that two SNPs (i.e., 1059.C>T and 25563.G>T) of linkage disequilibrium were presented in approximately half of North America SARS-CoV-2 population (p = 2.44 x 10−212 and p = 2.98 x 10−261), resulting two missense mutations (i.e., Thr 265 Ile and Gln 57 His) in ORF1ab and ORF3a, respectively. Interestingly, these two SNPs exclusively occurred in the North America dominated clade 1, accumulated during mid to late March, 2020. We did not find any of these two SNPs by retrospectively tracing the two SNPs in bat and pangolin related SARS-CoV-2 and human SARS-CoV-2 from the first epicenter Wuhan or other regions of China mainland. This suggested that the SARS-CoV-2 population of Chinese mainland were different from the prevalent strains of North America. Time-dependently, we found that these two SNPs first occurred in Europe SARS-CoV-2 (26-Feb-2020) which was 3 days early than the occurring date of North America isolates and 17 days early for Asia isolates (Taiwan China dominated). Collectively, this population genetic analysis highlights a well-confidential transmission route of the North America isolates and the two SNPs we newly identified are possibly novel diagnosable or druggable targets for surveillance and treatment.Competing Interest StatementThe authors have declared no competing interest.