Four COVID-19 Cases of New Variant B.1.351 First Emerging in South Africa in Chinese Passengers on Same Flight — Shenzhen, China, January 2021

Abstract

At 04∶50 on January 1, 2021, a 36-year-old Chinese project manager (Case A), a 29-year-old Chinese worker (Case B), and a 53-year-old Chinese businessman (Case C) returned from Africa (Case A and B from South Africa and Case C from Lesotho) on the same flight and tested coronavirus disease 2019 (COVID-19) RNA positive by real-time polymerase chain reaction (PCR) by Baoan District People’s Hospital Shenzhen CDC received their oral nasopharyngeal swabs packages from the hospital and retested COVID-19 RNA positive at 09∶50 Meanwhile, Case D, a close contact of Case A, was transferred to the designated hotel for centralized isolation for 14 days His oral nasopharyngeal swabs were collected and sent for the detection of COVID-19 RNA as routine surveillance testing on the 1, 4, 7, 14 days of quarantine;these were reported back as COVID-19 RNA positive at 22∶50 on January 4, 2021 and at 05∶30 on January 5, 2021 by Shenzhen CDC The four cases were transferred respectively by negative pressure ambulances to the Third People’s Hospital of Shenzhen for further treatment within five hours of COVID-19 infection confirmation by Shenzhen CDC On admission, chest CT images showed no abnormalities among all cases Epidemiological investigation revealed that the 4 cases had COVID-19 RNA negative test results before departure and self-reportedly had effective protection by wearing medical protective masks (Case A wore a disposable medical mask, while Case B, C, and D wore N95 masks) and protective suits (Case B) during the flight In addition, they reported no history of fever, fatigue, or respiratory symptoms within 14 days prior to their diagnosis However, according to the report of Case A, he was possibly exposed on his return business trip from Cape Town to Johannesburg in South Africa from December 16 to December 30, 2020, when he visited and had dinner with colleagues and had a meal in a fast food restaurant Case B had a history of performing work-related tasks, staying at the dormitory with workmates His roommate, who took the same flight from South Africa to China, was diagnosed as an asymptomatic carrier of COVID-19 on January 1, 2021 in Shenzhen Case C’s potential exposure might have been a 4-hour-trip in a vehicle from his company in Lesotho to an airport hotel with a local resident without effective protection Case D’s potential exposure was the experience that he took nucleic acid testing in South Africa and shuttle bus from workplace to the airport with Case A before boarding Using the results of the epidemiological investigation, clinical symptoms, and laboratory results, these patients were diagnosed as asymptomatic patients with COVID-19 in coordination with clinicians and experts The specimens of the 4 asymptomatic patients’ were sequenced by Illumina MiSeq Sequencing platform between January 2 to January 5, 2021 On January 4 and January 7, 3 whole genome sequences and 1 were obtained, respectively Compared with the Wuhan reference sequence (EPI_ISL_402119) (1–2), these 4 newly identified Shenzhen strains showed 29 nucleotide variation sites, which contained the single nucleotide polymorphisms (SNPs) that defined lineage B 1 351 (20H/501Y V2 branch) (3) A maximum of 29 genomic variation sites were detected in the 4 high-quality genomic sequences (for Cases A–D, number of genomic variation sites were 29, 19, 25, and 25, respectively, including G160A, G174T, C241T, C281T, C1059T, C3037T, G5230T, C8660T, C8964T, A10323G, G11230T, T13324A, C14408T, C14925T, T16062C, G19656T, A21801C, G22299T, G22813T, G23012A, A23063T, A23403G, C23664T, T25084C, G25563T, C25904T, C26456T, C28647T, C28887T;sequence coverage ranged from 91 4% to 99 2%) A major difference between the nucleotide sequences of A/D and B/C were detected in the position of 1174 (A1174C for A/D and A1174T for B/C) By online comparison of the assembled sequence with the published COVID-19 database, we obtained the phylogenetic relationship tree (Figure 1) of the virus strains The 4 COVID-19 samples of imported African cases were lineage B 1 351 (20H/501Y V2) variant strains (homology of 99 99% to 100%), which had been circulating in South Africa since October 2020 (4) The cladogram showed that the genome sequences of the 4 cases imported from Africa (Case A–D) all contained the characteristic mutation sites (the mutations of the spike protein D80A, K417N, E484K, N501Y, D614G, and A701V) of the South African variant strain B 1 351 The major differences between the A/D and B/C when comparing their amino acid sequences were as follows: L18F was detected in Case C;D215G was detected in Case B/C;R246I was detected in Case A;but data on the same position was missing in Case D These B 1 351 variants strains were imported early to China and might exert a great threat to the prevention and control of COVID-19 in China Systematically tracking higher risk international variants is therefore important as it allows monitoring of the new variants nationally and internationally