key: cord-0723254-8fprxzb0 authors: Kang, Ning; Liu, Yinpin; Bi, Fuyin; Wang, Jing; Chen, Huafeng; Wang, Jing; Liang, Zhenli; Chen, Min; Wei, Guangwu; Li, Aiming; Li, Yonghong; Lu, Bao; Jiang, Zhenling; Tan, Yi; Zhong, Ge; Lin, Mei; Ju, Yu title: Detection of Variants of B.1.617 Lineage from Five Returning Chinese Nationals at a Guangxi-Vietnam Border Port — Guangxi Zhuang Autonomous Region, China, April 2021 date: 2021-07-23 journal: China CDC Wkly DOI: 10.46234/ccdcw2021.147 sha: 6eab1fdf855b67e9a156bf93c827375d5080b6ae doc_id: 723254 cord_uid: 8fprxzb0 nan on April 26. The specimens of the confirmed patients were sent to Guangxi CDC and sequenced by Illumina MiSeq Sequencing platform using a 500-cycles MiSeq v2 Reagent Kit between April 30 to May 4. On May 3, one patient's whole genome sequence was obtained, and on May 7, the other four patients' sequences were obtained. In comparison with the COVID-19 reference strain (Gene Bank Accession: NC_045512), these isolates possessed 28-34 variation sites in nucleic acids, including 11 variations in the spike protein (T19R, G142D, A222V, L452R, T478K, D614G, P681R, D950N, E156del, F157del, and R158del) . Notably, eight variation sites of amino acid residues (T19R, L452R, T478K, D614G, P681R, D950N, F157del, and R158del), which were identical to those in Indian B.1.617.2 variants, were observed in all five isolates. Phylogenetic analysis of genome sequence indicated these isolates belonged to the PANGO lineage (1) B.1.617.2 ( Figure 1 ), an emerging variant first identified in India in October 2020 and has recently been designated as a variant of concern (VOC) which labeled as Delta by the World Health Organization (WHO) (2) (3) . The COVID-19 infection in these five patients probably occurred when they were staying in the designated isolation hotel in Vietnam and sharing space with the Indian nationals that were confirmed positive for COVID-19. Furthermore, the hotel attendant was confirmed as COVID-19 positive on April 26. The B.1.617 variant had been detected in Chongqing (4) cases in Guangxi were excluded from such doublemutant variants. Guangxi Zhuang Autonomous Region is adjacent to Association of Southeast Asian Nation (ASEAN) countries by land and sea and is an important provincial-level administrative division for China open to ASEAN. During the 13th Five-Year Plan period, the import and export trade of Guangxi to ASEAN accounted for 48.9% of the total foreign trade value. However, over the past year, cases of COVID-19 rose 40-fold to 162 million globally, while the number of deaths has increased 11-fold to more than 3.3 million. To prevent COVID-19 cases from entering, Guangxi has taken strict restrictions on all entry-exit personnel. The five patients were found among returning Chinese nationals from Vietnam at a border port for the first time, suggesting that the COVID-19 (B.1.617.2 variants) still poses a risk of transmission in some ASEAN countries. Therefore, constant surveillance of genome sequences in imported cases is required to track the transmission and evolution of the COVID-19 virus during the ongoing COVID-19 pandemic. The pathogenicity and transmissibility of these mutant variants urgently need further study (5) (6) -19/Italy/UMB-IZSGC-96118.1.35/2021|EPI ISL /Scotland/EDB11342/2020|EPI ISL 764278|2020-12-26 hCoV-19/South Africa/Tygerberg-408/2020|EPI ISL Nigeria/CV616/2021|EPI ISL Nigeria/CV625/2021|EPI ISL /India/ILSGS00308/2020|EPI ISL /Belgium/MBLG36792/2021|EPI ISL /India/ILSGS00971/2021|EPI ISL /India/ILSGS00969/2021|EPI ISL /India/DL-ICMR-PCB2301011CCM P2/2021|EPI ISL 2036301|2021 hCoV-19/Spain/IB-HUSE-00465/2021|EPI ISL /Austria/CeMM0007/2020|EPI ISL /Russia/StPetersburg-RII3992/2020|EPI ISL /Pakistan/Gilgit1/2020|EPI ISL Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1 complete genome hCoV-19/Canada A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology Weekly epidemiological update on COVID-19-1 Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra Emerging variants of B.1.617 lineage identified among returning Chinese employees working in India -Chongqing municipality, China The first case of new variant COVID-19 originating in the United Kingdom detected in a returning student-Shanghai municipality, China A case of new variant COVID-19 first emerging in South Africa detected in airplane pilot