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| 1 | Cold-chain food contamination as the possible origin of COVID-19 resurgence in Beijing显示文摘COVID-19,caused by SARS-CoV-2[1,2],has been contained in China through stringent non-pharmaceutical interventions.Border control and quarantine have effectively prevented the virus from being spread by infected travellers,but the risk of resurgence caused by other routes of introduction and transmission remains unclear,and current strategies to prevent resurgence could be flawed.Since July,SARS-CoV-2 RNA contaminations in frozen food imported from countries with ongoing epidemics have been reported in nine provinces in China[3,4].However,there is no robust evidence of COVID-19 outbreaks initiated by environmentto-human transmission.Here we add to evidence of such transmission by investigating the recent COVID-19 resurgence in Beijing. | Xinghuo Pang Lili Ren Shuangsheng Wu Wentai Ma Jian Yang Lin Di Jie Li Yan Xiao Lu Kang Shichang Du Jing Du Jing Wang Gang Li Shuguang Zhai Lijuan Chen Wenxiong Zhou Shengjie Lai Lei Gao Yang Pan Quanyi Wang Mingkun Li Jianbin Wang Yanyi Huang Jianwei Wang COVID-19 Field Response Group COVID-19 Laboratory Testing Group | 2020 | National Science Review2020，7，12： | 51 |
| 2 | Genomic Epidemiology of SARS-CoV-2 in Pakistan显示文摘COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this cluster.Furthermore,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control. | Shuhui Song Cuiping Li Lu Kang Dongmei Tian Nazish Badar Wentai Ma Shilei Zhao Xuan Jiang Chun Wang Yongqiao Sun Wenjie Li Meng Lei Shuangli Li Qiuhui Qi Aamer Ikram Muhammad Salman Massab Umair Huma Shireen Fatima Batool Bing Zhang Hua Chen Yun-Gui Yang Amir Ali Abbasi Mingkun Li Yongbiao Xue Yiming Bao | 2021 | Genomics, Proteomics & Bioinformatics2021，19，5： | 0 |
| 3 | Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant显示文摘A new variant of concern for SARS-CoV-2,Omicron(B.1.1.529),was designated by the World Health Organization on November 26,2021.This study analyzed the viral genome sequencing data of 108 samples collected from patients infected with Omicron.First,we found that the enrichment efficiency of viral nucleic acids was reduced due to mutations in the region where the primers anneal to.Second,the Omicron variant possesses an excessive number of mutations compared to other variants circulating at the same time(median:62 vs.45),especially in the Spike gene.Mutations in the Spike gene confer alterations in 32 amino acid residues,more than those observed in other SARS-CoV-2 variants.Moreover,a large number of nonsynonymous mutations occur in the codons for the amino acid residues located on the surface of the Spike protein,which could potentially affect the replication,infectivity,and antigenicity of SARS-CoV-2.Third,there are 53 mutations between the Omicron variant and its closest sequences available in public databases.Many of these mutations were rarely observed in public databases and had a low mutation rate.In addition,the linkage disequilibrium between these mutations was low,with a limited number of mutations concurrently observed in the same genome,suggesting that the Omicron variant would be in a different evolutionary branch from the currently prevalent variants.To improve our ability to detect and track the source of new variants rapidly,it is imperative to further strengthen genomic surveillance and data sharing globally in a timely manner. | Wentai Ma Jing Yang Haoyi Fu Chao Su Caixia Yu Qihui Wang Ana Tereza Ribeiro de Vasconcelos Georgii A.Bazykin Yiming Bao Mingkun Li | 2022 | Genomics, Proteomics & Bioinformatics2022，20，1： | 0 |
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