key: cord-0781490-wbomteb4
authors: Chen, Hongyou; Huang, Xiaoyan; Zhao, Xiang; Song, Yang; Hao, Peter; Jiang, Hui; Zhang, Xi; Fu, Chen
title: The First Case of New Variant COVID-19 Originating in the United Kingdom Detected in a Returning Student — Shanghai Municipality, China, December 14, 2020
date: 2021-01-01
journal: China CDC Wkly
DOI: 10.46234/ccdcw2020.270
sha: 5205875a4076ef8f85d11f1e6e5e9247e18dfd0f
doc_id: 781490
cord_uid: wbomteb4

nan

suggesting different route of transmission (1) (Figure 1 ). Compared with the Wuhan reference sequence (EPI_ISL_ 402119) (2) , this new Shanghai strain showed 32 nucleotide variation sites, containing the single nucleotide polymorphisms (SNPs) that defined L-lineage European branch I. This Shanghai strain shared all 28 variation sites (C241T, C913T,  C3037T, C3267T, C5388A, C5986T, T6954C,  C14408T,  C14676T,  C15279T,  T16176C,  A23063T, C23271A, A23403G, C23604A, C23709T,  T24506G,  G24914C,  C27972T,  G28048T,  A28111G,  G28280C,  A28281T,  T28282A , G28881A, G28882A, G28883C, and C28977T) that were first detected in the VUI202012/01 (Pangolin lineage B.1.1.7) variant from the UK (3) (4) . It also had 2 specific variation sites (C3177T, A28271del), from which site C3177T was also detected in the VUI202012/01 variants that has been circulating since late October in the UK (Figure 1 ). Just like the other VUI202012/01 variants, the Shanghai strain also had 3 amino acid deletions (H69del, V70del and Y144del) and 7 amino acid mutations (N501Y, A570D, D614G, P681H, T716I, S982A and D1118H) in the spike protein. The Shanghai strain NC20SCU2740-1 is the first imported VUI202012/01 variant in China and poses a great potential threat to the prevention and control of COVID-19 in China.

Several control measures have been implemented in the response to this case. The patient has been transferred to the designated medical institution for isolation and treatment. Due to the closed-loop management upon passenger's arrival at the airport, close contact investigation has been initiated according to national and municipal work plans: 1) close contacts currently include passengers with seats in the same row, passengers within 3 rows of seats of the patient, and flight attendants providing cabin services to that section; 2) medical personnel at the point of isolation and at the central hospital are not deemed closed contacts due to the effective personal protective hCoV-19/Italy/CAM-TIGEM-174/2020|EPI_ISL_736786|2020-12-21 NC20SCU2740-1/Shanghai hCoV-19/England/ALDP-C5842F/2020|EPI_ISL_736160|2020-12-13 hCoV-19/England/MILK-C61A8B/2020|EPI_ISL_735575|2020-12-13 hCoV-19/England/CAMC-C2628A/2020|EPI_ISL_733835|2020-12-08 hCoV-19/England/CAMC-C3FE6C/2020|EPI_ISL_719514|2020-12-10 hCoV-19/England/MILK-C2FA98/2020|EPI_ISL_733884|2020-12-07 hCoV-19/England/ALDP-C06860/2020|EPI_ISL_709330|2020-12-05 hCoV-19/Italy/CAM-TIGEM-181/2020|EPI_ISL_736787|2020-12-21 hCoV-19/England/MILK-9E05B3/2020|EPI_ISL_601443|2020-09-20 hCoV-19/England/CAMC-A58BA4/2020|EPI_ISL_596982|2020-10-08 hCoV-19/England/ALDP-C3A97F/2020|EPI_ISL_730757|2020-12-09 hCoV-19/England/MILK-A7A7A8/2020|EPI_ISL_606424|2020-10-15 hCoV-19/England/CAMC-BBC4C0/2020|EPI_ISL_724145|2020-11-21 hCoV-19/England/MILK-C619F7/2020|EPI_ISL_735610|2020-12-13 hCoV-19/England/ALDP-C58665/2020|EPI_ISL_736157|2020-12-13 EPI_ISL_416730|hCoV-19/England/SHEF-BFCB1/2020|Europe/England| EPI_ISL_420129|hCoV-19/Spain/Valencia45/2020|Europe/Spain| EPI_ISL_420877|hCoV-19/Australia/VIC-CBA3/2020|Oceania/Australia| HLJ-0418-36-Y EPI_ISL_413997|hCoV-19/Switzerland/GE3895/2020|Europe/Switzerland| HLJ-0418-32-T Shulan_02 Shulan_03 LNDL-BHQ-0722-Y_S12_L001_R1_001 LNDL-SFL-0722-Y_S9_L001_R1_001 LNDL-WY-0722-Y_S11_L001_R1_001 LNDL-XY-0722-Y_S10_L001_R1_001 nCoVBeijing_IVDC-002_06_2020 nCoVBeijing_IVDC-003_06_2020 nCoVBeijing_IVDC-001_06_2020 EPI_ISL_419656|hCoV-19/Austria/CeMM0003/2020|Europe/Austria| EPI_ISL_418366|hCoV-19/Canada/ON_PHL3350/2020|North-America/Canada| EPI_ISL_417525|hCoV-19/ Taiwan 

A case of COVID-19 detected in a cargo worker at Pudong Airport -Shanghai Municipality

A new coronavirus associated with human respiratory disease in China

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assistgenomic epidemiology

European Centre for Disease Prevention and Control, Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom-20