key: cord-0746064-ulzzh70z authors: Wu, Bing; Zhang, Hui; Wang, Yu‐chao; Tang, An; Li, Ke‐feng; Li, Peng; Chen, Jia‐bei; Wang, Hong‐ling; Yan, Jian‐bo title: Sequencing on an imported case in China of COVID‐19 Delta variant emerging from India in a cargo ship in Zhoushan, China date: 2021-08-07 journal: J Med Virol DOI: 10.1002/jmv.27239 sha: ec42b21b1fcea4a454e26205b5ec09d0baa47db4 doc_id: 746064 cord_uid: ulzzh70z A cluster of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infections was found in a cargo ship under repair in Zhoushan, China. Twelve of 20 crew members were identified as SARS‐CoV‐2 positive. We analyzed four sequences and identified them all in the Delta branch emerging from India with 7–8 amino acid mutation sites in the spike protein. threatening global health. New variants with higher transmission rates have been spreading around the world, such as the variants of concerns (VOCs) Alpha from the UK, Beta from South Africa, and Gamma from Brazil. 1, 2 The "double mutated" variant Delta in linage B.1.617 with the spike mutations of L452R and E484Q, is becoming the most prevalent virus among all COVID-19 variants in India, and has been found in more than 21 countries throughout the world. 3 On April 23, 2021, three crew members on an under repair cargo ship at a shipyard in Zhoushan, Zhejiang Province, China, developed fever symptoms and were reported to the Customs. All the 20 crew members' throat swabs were collected for COVID-19 detection. On After consultation by the expert groups, 10 patients were diagnosed as confirmed cases of COVID-19, including nine cases of normal type and one case of mild type. In addition, one patient without symptoms was determined as asymptomatic infection. According to the expert consultant's opinion, relevant treatment plans were formulated for isolation treatment. On April 28, through clinical symptoms and expert consultation, two patients were judged to be "severe," and another two had a tendency to be severe. All close contacts were isolated and nucleic acid will be tested regularly, while prevention and control measures were determined based on the test results. After hospitalization, one turned to be "severe" (three in total), one remained asymptomatic, and the rest were of the normal type. On April 29, on the second round of detection, another case was de- Reference Zhoushan01 Zhoushan02 Zhoushan03 Zhoushan04 Amino acid Gene region 210 G T T T T Noncoding UTR 241 C T T T T Noncoding UTR 1191 C T T T T P309L ORF1ab 1267 C T T T T syn ORF1ab 2144 G T T T T V627F ORF1ab 3037 C T T T T syn ORF1ab 5184 C T T T T P1640L ORF1ab S 24745 C T T T T syn S 25469 C T T T T S26L ORF3a 26767 T C C C C I82T M 27638 T C C C C V82A ORF7a 27739 C T T T T L116F ORF7a 27752 C T T T T T120I ORF7a 28247 AGATTTC A A A A D119del, F120del ORF8 28249 A T A A T D119V ORF8 28253 C A A A A F120L ORF8 28461 A A A A G D63G N 28881 G T T T T R203M N 29402 G T T T T D377Y N 29427 G A A A A R385K N 29742 G T T T T Noncoding UTR F I G U R E 1 Phylogenetic tree of 114 published full-length genomes from GISAID and 4 Zhoushan genomes (Red box). Main severe clades are colored. GISAID, Global Initiative on Sharing All Influenza Data World Health Organization. Tracking SARS-CoV-2 variants Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. bioRxiv Parallelization of MAFFT for large-scale multiple sequence alignments IQ-TREE: a fast and effective stochastic algorithm for estimating maximumlikelihood phylogenies Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus Detection of a SARS-CoV-2 variant of concern in South Africa Emerging Variants of SARS-CoV-2 And Novel Therapeutics Against Coronavirus (COVID-19) SARS-CoV-2 spike E484K mutation reduces antibody neutralisation Covid-19: The E484K mutation and the risks it poses Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies Sequencing on an imported case in China of COVID-19 Delta variant emerging from India in a cargo ship in Zhoushan We thank all the persons involved in the response to this outbreak. Project (Grant nos. 2020C31006 and 2020C31004, and 2020C31005) and Young Talents Project of Zhoushan Medical and Health Science and Technology Plan (2020RC02). The authors declare that there are no conflicts of interest. The data that support the findings of this study are openly available in the Global Initiative on Sharing All Influenza Data (GISAID) at https://www.gisaid.org/, reference number EPI_ISL_1911195, EPI_ISL_191196, EPI_ISL_1911197, EPI_ISL_1911250. http://orcid.org/0000-0002-0442-2687