Advanced Search

Notes from the Field: Whole-genome Sequences Analysis Revealed Relationship Between Four Local Cases and Imported Passengers of SARS-CoV-2 Delta Variant (B.1.617.2) on the Same Flight from South Africa — Shenzhen City, Guangdong Province, China, June 2021

View author affiliations
  • loading...
  • Funding: Shenzhen Science and Technology Innovation Commission Key project (no. JSGG20200225152648408), the Shenzhen Science and Technology Innovation Commission COVID-19 Special Fund (no. JSGG20200207161926465), and Sanming Project of Medicine in Shenzhen (No.SZSM202011008)
  • [1] Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018;35(6):1547 − 9. http://dx.doi.org/10.1093/molbev/msy096CrossRef
    [2] Li ZC, Nie K, Li KB, Hu Y, Song Y, Kang M, et al. Genome characterization of the first outbreak of COVID-19 delta variant B. 1. 617. 2 — Guangzhou City, Guangdong Province, China, May. China CDC Wkly 2021(27):587 − 9. http://dx.doi.org/10.46234/ccdcw2021.151CrossRef
    [3] European Centre for Disease Prevention and Control. Implications for the EU/EEA on the spread of the SARSCoV-2 delta (B. 1.617. 2) variant of concern - 23 June 2021. ECDC: Stockholm. 2021. https://www.ecdc.europa.eu/sites/default/files/documents/Implications-for-the-EU-EEA-on-the-spread-of-SARS-CoV-2-Delta-VOC-23-June-2021_2.pdf.[2021-08-14].https://www.ecdc.europa.eu/sites/default/files/documents/Implications-for-the-EU-EEA-on-the-spread-of-SARS-CoV-2-Delta-VOC-23-June-2021_2.pdf
    [4] Campbell F, Archer B, Laurenson-Schafer H, Jinnai Y, Konings F, Batra N, et al. Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021. Euro Surveill 2021;26(24):2100509. http://dx.doi.org/10.2807/1560-7917.ES.2021.26.24.2100509CrossRef
    [5] Scientific Advisory Group for Emergencies. SPI-M-O: consensus statement on COVID-19, 3 June 2021. GOV. UK. 2021. https://www.gov.uk/government/publications/spi-m-o-consensus-statement-on-covid-19-3-june-2021.[2021-08-14].https://www.gov.uk/government/publications/spi-m-o-consensus-statement-on-covid-19-3-june-2021
    [6] Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature 2021;596(7871):276 − 280. http://dx.doi.org/10.1038/s41586-021-03777-9CrossRef
    [7] Liu C, Ginn HM, Dejnirattisai W, Supasa P, Wang BB, Tuekprakhon A, et al. Reduced neutralization of SARS-CoV-2 B. 1. 617 by vaccine and convalescent serum. Cell 2021;184(16):4220 − 36.e13. http://dx.doi.org/10.1016/j.cell.2021.06.020CrossRef
  • FIGURE 1.  Evolutionary relationships of 30 SARS-CoV-2 strains of lineage B.1.617.2 from this study.

    Note: Maximum likelihood phylogenetic tree was reconstructed for 30 SARS-CoV-2 strains from this study and 16 reference strains based on the whole-genome sequences. The best fit nucleotide substitution model used for phylogenetic reconstruction was TN93+G5+I. The scale bar represents a genetic distance of 0.0002 nucleotide substitutions per site. Bootstrap analysis (1,000 replicates) was used for statistical support of the tree. The 4 local strains were indicated by red dots, and 26 imported strains were indicated by black dots.

    TABLE 1.  Nucleotide differences between 30 SARS-CoV-2 strains of lineage B.1.617.2 from this study and the reference strain Wuhan-Hu-1 (NC_045512.2).

    CladeCaseNucleotide variationNucleotide deletion mutation
    Clade ACase 1G210T, C241T, C799T, C3037T, G4181T, C6402T, C7124T, C8986T, G9053T, C10029T, A11201G, A11332G, G13812T, C14408T, G15451A, C16466T, C19220T, C21618G, G21987A, T22917G, C22995A, A23403G, C23604G, G24410A, C25413T, C25469T, T26767C, T27638C, C27752T, C27874T, A28461G, G28881T, G28916T, G29402T, and G29742Tdel22029-22034, del28248-28253, del28271
    Clade BCase A, Case 2, Case 5–9, Case 11–15, Case 18, Case 19, Case 21, Case 30–32, Case 36, Case 3831 variation sites: G210T, C241T, G410T, C3037T, C5184T, A5584G, T9429C, C9891T, T11418C, C11514T, C13019T, C14408T, G15451A, C16466T, C21618G, G21987A, C22227T, T22917G, C22995A, A23403G, C23604G, G24410A, C25469T, T26767C, T27638C, A27677C, C27752T, A28461G, G28881T, G29402T, and G29742Tdel510-518, del22029-22034, del28248-28253, del28271
    Case B, Case 2031 variation sites+C21575Tdel510-518, del22029-22034, del28248-28253, del28271
    Case C31 variation sites+C18431Tdel510-518, del22029-22034, del28249, del28253, del28271
    Case D31 variation sites+C10605Adel510-518, del22029-22034, del28248-28253, del28271
    Case 431 mutations -G210T-G410T-G21987A0 -
    C22227T+G174T+C1059T+A5839G
    del28249, del28253, del28271
    Case 1031 mutations+C11665Tdel510-518, del22029-22034, del28248-28253, del28271
    Case 34, Case 3931 mutations+G3875A+G6476Tdel510-518, del22029-22034, del28248-28253, del28271
    Case 3731 mutations+A28249T+C28253Adel510-518, del22029-22034, del28271
    Download: CSV

    TABLE S1.  Demographic characteristics of 4 local cases and 39 imported cases, and specimen testing information.

    CaseGenderAge (years)Date of first positive detection
    of COVID-19 virus
    Ct value (ORF1ab/N) of specimen used for sequencing
    DaanBojie
    Case AMale30June 14, 202114/1816/18
    Case BFemale21June 17, 202123/2122/22
    Case CMale35June 18, 202124/2222/24
    Case DFemale64June 20, 202130/3035/28
    Case 1Male36June 11, 202131/3130/31
    Case 2Male35June 11, 202131/3126/28
    Case 3Female42June 11, 202133/3434/34
    Case 4Female58June 11, 202130/2727/28
    Case 5Male53June 13, 202117/1616/17
    Case 6Male32June 14, 202124/2324/23
    Case 7Male52June 14, 202117/1716/17
    Case 8Male33June 15, 202117/1515/17
    Case 9Male47June 15, 202116/1615/16
    Case 10Male64June 15, 202121/2020/21
    Case 11Male40June 15, 202115/1414/15
    Case 12Male50June 15, 202118/1716/18
    Case 13Male33June 15, 202128/2627/28
    Case 14Female31June 15, 202119/1718/17
    Case 15Male61June 15, 202114/1415/15
    Case 16Female38June 15, 202135/3436/33
    Case 17Male39June 15, 202137/40Undet/35
    Case 18Female50June 15,202114/1514/14
    Case 19Male35June 15, 202117/1616/17
    Case 20Male58June 15, 202116/1515/16
    Case 21Female47June 15, 202129/2526/26
    Case 22Male29June 15, 202135/3538/Undet
    Case 23Male32June 15, 202138/36Undet/35
    Case 24Male63June 15, 202135/3435/32
    Case 25Female63June 15, 202135/3333/33
    Case 26Male45June 15, 202138/35Undet/Undet
    Case 27Male44June 15, 2021Undet/38Undet/35
    Case 28Male61June 15, 2021Undet/3737/Undet
    Case 29Male58June 15, 202137/UndetUndet/36
    Case 30Male 9June 15, 202121/2122/22
    Case 31Female45June 15, 202128/2827/28
    Case 32Male42June 15, 202115/1514/15
    Case 33Male35June 16, 202126/2423/26
    Case 34Male 1June 16, 202130/2727/29
    Case 35Female24June 17, 202134/3032/30
    Case 36Male25June 17, 202119/1819/18
    Case 37Female32June 19, 202122/1919/20
    Case 38Male38June 19, 202131/2928/30
    Case 39Female28June 25, 202118/1617/18
    Note: There were 43 subjects in total, and the male/female ratio and mean age of subjects was 2.58∶1 and 40.9 years, respectively.
    Abbreviations: Undet=Undetected; Ct=Cycle threshold; COVID-19=Coronavirus disease 2019.
    Download: CSV

    TABLE S2.  Genome sequence information for 30 SARS-CoV-2 strains of lineage B.1.617.2 from this study.

    CaseVirus nameLength in nt
    (% GC content)
    Closest strain by an audacity instant
    search in GISAID
    Case AhCoV-19/Shenzhen/IVDC-06-14/202129,813nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case BhCoV-19/Shenzhen/IVDC-06-17/202129,562nt (37.98)hCoV-19/England/MILK-155F811/2021
    Case ChCoV-19/Shenzhen/IVDC-06-18/202129,428nt (37.98)hCoV-19/England/MILK-155F811/2021
    Case DhCoV-19/Shenzhen/IVDC-06-20/202129,612nt (37.98)hCoV-19/England/MILK-155F811/2021
    Case 1hCoV-19/Shenzhen/IVDC-0610-01/202129,702nt (37.96)hCoV-19/India/GJ-NCDC-NIV-INSACOG-24095/2021
    Case 2hCoV-19/Shenzhen/IVDC-0610-02/202129,813nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 4hCoV-19/Shenzhen/IVDC-0610-04/202129,836nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 5hCoV-19/Shenzhen/IVDC-0610-05/202129,555nt (37.99)hCoV-19/England/MILK-155F811/2021
    Case 6hCoV-19/Shenzhen/IVDC-0610-06/202129,657nt (38.00)hCoV-19/England/MILK-155F811/2021
    Case 7hCoV-19/Shenzhen/IVDC-0610-07/202129,814nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 8hCoV-19/Shenzhen/IVDC-0610-08/202129,824nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 9hCoV-19/Shenzhen/IVDC-0610-09/202129,831nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 10hCoV-19/Shenzhen/IVDC-0610-10/202129,833nt (37.95)hCoV-19/England/MILK-155F811/2021
    Case 11hCoV-19/Shenzhen/IVDC-0610-11/202129,830nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 12hCoV-19/Shenzhen/IVDC-0610-12/202129,830nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 13hCoV-19/Shenzhen/IVDC-0610-13/202129,710nt (37.99)hCoV-19/England/MILK-155F811/2021
    Case 14hCoV-19/Shenzhen/IVDC-0610-14/202129,551nt (37.98)hCoV-19/England/MILK-155F811/2021
    Case 15hCoV-19/Shenzhen/IVDC-0610-15/202129,834nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 18hCoV-19/Shenzhen/IVDC-0610-18/202129,820nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 19hCoV-19/Shenzhen/IVDC-0610-19/202129,828nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 20hCoV-19/Shenzhen/IVDC-0610-20/202129,820nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 21hCoV-19/Shenzhen/IVDC-0610-21/202129,574nt (37.99)hCoV-19/England/MILK-155F811/2021
    Case 30hCoV-19/Shenzhen/IVDC-0610-30/202129,827nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 31hCoV-19/Shenzhen/IVDC-0610-31/202129,829nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 32hCoV-19/Shenzhen/IVDC-0610-32/202129,849nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 34hCoV-19/Shenzhen/IVDC-0610-34/202129,809nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 36hCoV-19/Shenzhen/IVDC-0610-36/202129,819nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 37hCoV-19/Shenzhen/IVDC-0610-37/202129,827nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 38hCoV-19/Shenzhen/IVDC-0610-38/202129,553nt (37.99)hCoV-19/England/MILK-155F811/2021
    Case 39hCoV-19/Shenzhen/IVDC-0610-39/202129,797nt (37.94)hCoV-19/England/MILK-155F811/2021
    Abbreviation: nt=Nucleotide.
    Download: CSV

Citation:

通讯作者: 陈斌, bchen63@163.com
  • 1. 

    沈阳化工大学材料科学与工程学院 沈阳 110142

  1. 本站搜索
  2. 百度学术搜索
  3. 万方数据库搜索
  4. CNKI搜索
Turn off MathJax
Article Contents

Article Metrics

Article views(672) PDF downloads(0) Cited by()

Share

Related

Whole-genome Sequences Analysis Revealed Relationship Between Four Local Cases and Imported Passengers of SARS-CoV-2 Delta Variant (B.1.617.2) on the Same Flight from South Africa — Shenzhen City, Guangdong Province, China, June 2021

View author affiliations
  • 1. Institute of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
  • 2. Shenzhen Center for Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen, Guangdong, China
  • 3. Department of Communicable Diseases Control and Prevention, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
  • 4. Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
  • 5. Laboratory of Molecular Epidemiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
  • Corresponding authors:

    Long Chen, chen_l_2011@163.com

    Tiejian Feng, fengtiej@126.com

    Xuan Zou, 914494557@qq.com

  • Funding: Shenzhen Science and Technology Innovation Commission Key project (no. JSGG20200225152648408), the Shenzhen Science and Technology Innovation Commission COVID-19 Special Fund (no. JSGG20200207161926465), and Sanming Project of Medicine in Shenzhen (No.SZSM202011008)
  • Online Date: October 12 2021
    doi: 10.46234/ccdcw2021.215
  • On June 14, 2021, a customs officer (Case A) went to the infirmary at Baoan International Airport in Shenzhen due to runny nose and fever. He was admitted to the Central Hospital of Baoan immediately. This patient preliminarily tested positive for coronavirus disease 2019 (COVID-19) infection, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using a quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) method in this hospital. Then, a mixed specimen of nasopharyngeal swab, oropharyngeal swab, and anal swab was sent to the virology laboratory of Shenzhen Center for Disease Control and Prevention (Shenzhen CDC) and was confirmed positive for SARS-CoV-2 by a qRT-PCR method simultaneously implemented in two commercial kits (Daan, Guangzhou, China and Bojie, Shanghai, China) (Supplementary Table S1). This patient tested negative for SARS-CoV-2 on June 8, 2021 and participated in an epidemiological investigation and sampling in a flight from South Africa that arrived at Baoan International Airport on June 10, 2021. Between June 10, 2021 and June 25, 2021, a total of 39 passengers (Case 1 to 39) from this flight were confirmed to be infected with SARS-CoV-2 in the virology laboratory of Shenzhen CDC.

    On June 17, 2021, a third-party laboratory detected SARS-CoV-2 in a mixed specimen of 10 swabs from ten individuals by qRT-PCR method, and the preliminary result was positive. This mixed specimen and one (Case B) of ten nasopharyngeal swabs from ten individuals were confirmed positive for SARS-CoV-2 in the virology laboratory of Shenzhen CDC. Case B was a 22-year-old female who worked in a restaurant at Baoan International Airport. The third case (Case C) lived in Dongguan City and worked in Nanshan District in Shenzhen City. He presented symptoms of chills, dry cough, diarrhea, and fever on June 12, 2021 and was confirmed to be infected with SARS-CoV-2 on June 18, 2021. The fourth case (Case D) lived and worked in Baoan District, Shenzhen. She was confirmed to be infected with SARS-CoV-2 during screening of key populations on June 20, 2021.

    High-throughput sequencing was performed for 4 local SARS-CoV-2 strains and 39 imported SARS-CoV-2 strains by Illumina Sequencing Technology. First, viral RNA was extracted directly from 200-μL swab samples using a High Pure Viral RNA Kit (Roche, Germany). Second, viral RNA was reverse-transcribed and amplified using ULSEN® 2019-nCoV Whole Genome Capture Kit (Beijing MicroFuture, V-090418). Third, the sequencing libraries were prepared using the Illumina Nextera® XT Library Prep Kit. The final viral-enriched libraries were sequenced using the Illumina MiSeq platform. The viral genome was assembled by MicronCoV® Analyzer (Beijing MicroFuture, M-881027). Genome sequences of the 4 local SARS-CoV-2 strains and 28 of 39 imported SARS-CoV-2 strains were successfully determined. Virus strains from this study were genotyped using the online Pangolin COVID-19 Lineage Assigner (www.pangolin.cog-uk.io/). The evolutionary relationship of local SARS-CoV-2 strains and imported SARS-CoV-2 strains was inferred with the program MEGA version Ⅹ (www.megasoftware.net) (1). Nucleotide difference between viral genome sequences from this study and the reference sequence Wuhan-Hu-1 (GenBank no. NC_045512.2) was analyzed using the programs BioEdit 7.1.9 (www.bioedit.software.informer.com) and MEGA versionⅩ.

    The 4 local SARS-CoV-2 strains and 26 of 28 imported SARS-CoV-2 strains from this study were assigned to lineage B.1.617.2 (Supplementary Table S2), which was the fourth variant of concern (VOC) (Delta variant). The other two imported SARS-CoV-2 strains were assigned to lineage B.1.351 and lineage C.1.2. Molecular phylogeny indicated that 30 SARS-CoV-2 Delta variants (lineage B.1.617.2) from this study formed 2 distinct clades (Figure 1). The imported strain hCoV-19/Shenzhen/IVDC-0610-01/2021 (Case1) clustered in clade A and showed the closest relationship to the Indian strain hCoV-19/India/GJ-NCDC-NIV-INSACOG-24095/2021 by an Audacity Instant search in Global initiative on sharing all influenza data (GISAID). The 4 local SARS-CoV-2 strains of lineage B.1.617.2 and 25 imported SARS-CoV-2 strains of lineage B.1.617.2 clustered in clade B and showed the closest relationship or showed only one nucleotide difference to the British strain hCoV-19/England/MILK-155F811/2021. These 29 SARS-CoV-2 strains of lineage B.1.617.2 showed at least 23 nucleotide differences to the strain hCoV-19/ Shenzhen/IVDC-0610-01/2021 (Case 1). In clade B, the imported strain hCoV-19/Shenzhen/IVDC-0610-04/2021 (Case 4) showed a certain degree of genetic distance to the other 28 virus strains from this study, which was also indicated by comparative analysis of genome sequences in the Table 1. The local B.1.617.2 strain hCoV-19/Shenzhen/IVDC-06-14/2021 (Case A) showed 100% sequence identity to 19 imported B.1.617.2 strains (Table 1). These 20 SARS-CoV-2 strains of lineage B.1.617.2 shared 31 nucleotide variation sites and 22 deletion mutations compared with the reference strain Wuhan-Hu-1. Except for the variation sites above, an additional variation site was observed in genomes of the 3 local strains hCoV-19/Shenzhen/IVDC-06-17/2021 (Case B), hCoV-19/Shenzhen/IVDC-06-18/2021 (Case C), and hCoV-19/Shenzhen/IVDC-06-20/2021 (Case D). The local strain hCoV-19/Shenzhen/IVDC-06-17/2021 (Case B) showed 100% sequence identity to the strain hCoV-19/Shenzhen/IVDC-0610-20/2021 from imported Case 20.

    Figure 1.  Evolutionary relationships of 30 SARS-CoV-2 strains of lineage B.1.617.2 from this study.

    Note: Maximum likelihood phylogenetic tree was reconstructed for 30 SARS-CoV-2 strains from this study and 16 reference strains based on the whole-genome sequences. The best fit nucleotide substitution model used for phylogenetic reconstruction was TN93+G5+I. The scale bar represents a genetic distance of 0.0002 nucleotide substitutions per site. Bootstrap analysis (1,000 replicates) was used for statistical support of the tree. The 4 local strains were indicated by red dots, and 26 imported strains were indicated by black dots.

    CladeCaseNucleotide variationNucleotide deletion mutation
    Clade ACase 1G210T, C241T, C799T, C3037T, G4181T, C6402T, C7124T, C8986T, G9053T, C10029T, A11201G, A11332G, G13812T, C14408T, G15451A, C16466T, C19220T, C21618G, G21987A, T22917G, C22995A, A23403G, C23604G, G24410A, C25413T, C25469T, T26767C, T27638C, C27752T, C27874T, A28461G, G28881T, G28916T, G29402T, and G29742Tdel22029-22034, del28248-28253, del28271
    Clade BCase A, Case 2, Case 5–9, Case 11–15, Case 18, Case 19, Case 21, Case 30–32, Case 36, Case 3831 variation sites: G210T, C241T, G410T, C3037T, C5184T, A5584G, T9429C, C9891T, T11418C, C11514T, C13019T, C14408T, G15451A, C16466T, C21618G, G21987A, C22227T, T22917G, C22995A, A23403G, C23604G, G24410A, C25469T, T26767C, T27638C, A27677C, C27752T, A28461G, G28881T, G29402T, and G29742Tdel510-518, del22029-22034, del28248-28253, del28271
    Case B, Case 2031 variation sites+C21575Tdel510-518, del22029-22034, del28248-28253, del28271
    Case C31 variation sites+C18431Tdel510-518, del22029-22034, del28249, del28253, del28271
    Case D31 variation sites+C10605Adel510-518, del22029-22034, del28248-28253, del28271
    Case 431 mutations -G210T-G410T-G21987A0 -
    C22227T+G174T+C1059T+A5839G
    del28249, del28253, del28271
    Case 1031 mutations+C11665Tdel510-518, del22029-22034, del28248-28253, del28271
    Case 34, Case 3931 mutations+G3875A+G6476Tdel510-518, del22029-22034, del28248-28253, del28271
    Case 3731 mutations+A28249T+C28253Adel510-518, del22029-22034, del28271

    Table 1.  Nucleotide differences between 30 SARS-CoV-2 strains of lineage B.1.617.2 from this study and the reference strain Wuhan-Hu-1 (NC_045512.2).

    Among imported SARS-CoV-2 strains, genome sequences of 19 SARS-CoV-2 strains from imported passengers showed 100% sequence identity to each other, and these 19 passengers had no common exposure history before boarding. It suggested that at least one virus transmission occurred between the 19 passengers after boarding. The only strain from Case 1 belonged to clade A within lineage B.1.617.2, which indicated that Case 1 was not related to the infection in the cabin. Based on phylogenetic relationship and comparative analysis of genome sequences, we deduced that 3 virus strains from local cases (Cases B to D) and 5 virus strains from imported passengers (Cases 10, 20, 34, 37, and 39) were progeny viruses.

    According to the report by Li et al (2), SARS-CoV-2 Delta variant strains from this study showed 18 to 28 nucleotide differences to those from the first outbreak of COVID-19 in Guangzhou, May 2021, which suggested that SARS-CoV-2 Delta variant that caused local outbreaks of COVID-19 in Guangzhou and Shenzhen came from different sources. At present, the SARS-CoV-2 Delta variant is becoming the dominant variant worldwide and has been detected in at least 142 countries as of August 10, 2021. The SARS-CoV-2 Delta variant is posing new challenges on the control and prevention of COVID-19 due to its increased transmissibility compared with Alpha variant (lineage B.1.1.7) and capacity of immune escape (3-7).

    In conclusion, whole-genome sequencing (WGS) confirmed that 4 local SARS-CoV-2 strains and 26 of 28 imported SARS-CoV-2 strains from this study were Delta variants, and phylogenetic and comparative genome analyses showed close relationship between the four local SARS-CoV-2 strains of Delta variant and imported SARS-CoV-2 strains of Delta variant introduced from South Africa.

  • Baoan CDC, Nanshan CDC, and Shenzhen Third People’s Hospital.

  • No conflicts of interest.

    CaseGenderAge (years)Date of first positive detection
    of COVID-19 virus
    Ct value (ORF1ab/N) of specimen used for sequencing
    DaanBojie
    Case AMale30June 14, 202114/1816/18
    Case BFemale21June 17, 202123/2122/22
    Case CMale35June 18, 202124/2222/24
    Case DFemale64June 20, 202130/3035/28
    Case 1Male36June 11, 202131/3130/31
    Case 2Male35June 11, 202131/3126/28
    Case 3Female42June 11, 202133/3434/34
    Case 4Female58June 11, 202130/2727/28
    Case 5Male53June 13, 202117/1616/17
    Case 6Male32June 14, 202124/2324/23
    Case 7Male52June 14, 202117/1716/17
    Case 8Male33June 15, 202117/1515/17
    Case 9Male47June 15, 202116/1615/16
    Case 10Male64June 15, 202121/2020/21
    Case 11Male40June 15, 202115/1414/15
    Case 12Male50June 15, 202118/1716/18
    Case 13Male33June 15, 202128/2627/28
    Case 14Female31June 15, 202119/1718/17
    Case 15Male61June 15, 202114/1415/15
    Case 16Female38June 15, 202135/3436/33
    Case 17Male39June 15, 202137/40Undet/35
    Case 18Female50June 15,202114/1514/14
    Case 19Male35June 15, 202117/1616/17
    Case 20Male58June 15, 202116/1515/16
    Case 21Female47June 15, 202129/2526/26
    Case 22Male29June 15, 202135/3538/Undet
    Case 23Male32June 15, 202138/36Undet/35
    Case 24Male63June 15, 202135/3435/32
    Case 25Female63June 15, 202135/3333/33
    Case 26Male45June 15, 202138/35Undet/Undet
    Case 27Male44June 15, 2021Undet/38Undet/35
    Case 28Male61June 15, 2021Undet/3737/Undet
    Case 29Male58June 15, 202137/UndetUndet/36
    Case 30Male 9June 15, 202121/2122/22
    Case 31Female45June 15, 202128/2827/28
    Case 32Male42June 15, 202115/1514/15
    Case 33Male35June 16, 202126/2423/26
    Case 34Male 1June 16, 202130/2727/29
    Case 35Female24June 17, 202134/3032/30
    Case 36Male25June 17, 202119/1819/18
    Case 37Female32June 19, 202122/1919/20
    Case 38Male38June 19, 202131/2928/30
    Case 39Female28June 25, 202118/1617/18
    Note: There were 43 subjects in total, and the male/female ratio and mean age of subjects was 2.58∶1 and 40.9 years, respectively.
    Abbreviations: Undet=Undetected; Ct=Cycle threshold; COVID-19=Coronavirus disease 2019.

    Table S1.  Demographic characteristics of 4 local cases and 39 imported cases, and specimen testing information.

    CaseVirus nameLength in nt
    (% GC content)
    Closest strain by an audacity instant
    search in GISAID
    Case AhCoV-19/Shenzhen/IVDC-06-14/202129,813nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case BhCoV-19/Shenzhen/IVDC-06-17/202129,562nt (37.98)hCoV-19/England/MILK-155F811/2021
    Case ChCoV-19/Shenzhen/IVDC-06-18/202129,428nt (37.98)hCoV-19/England/MILK-155F811/2021
    Case DhCoV-19/Shenzhen/IVDC-06-20/202129,612nt (37.98)hCoV-19/England/MILK-155F811/2021
    Case 1hCoV-19/Shenzhen/IVDC-0610-01/202129,702nt (37.96)hCoV-19/India/GJ-NCDC-NIV-INSACOG-24095/2021
    Case 2hCoV-19/Shenzhen/IVDC-0610-02/202129,813nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 4hCoV-19/Shenzhen/IVDC-0610-04/202129,836nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 5hCoV-19/Shenzhen/IVDC-0610-05/202129,555nt (37.99)hCoV-19/England/MILK-155F811/2021
    Case 6hCoV-19/Shenzhen/IVDC-0610-06/202129,657nt (38.00)hCoV-19/England/MILK-155F811/2021
    Case 7hCoV-19/Shenzhen/IVDC-0610-07/202129,814nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 8hCoV-19/Shenzhen/IVDC-0610-08/202129,824nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 9hCoV-19/Shenzhen/IVDC-0610-09/202129,831nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 10hCoV-19/Shenzhen/IVDC-0610-10/202129,833nt (37.95)hCoV-19/England/MILK-155F811/2021
    Case 11hCoV-19/Shenzhen/IVDC-0610-11/202129,830nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 12hCoV-19/Shenzhen/IVDC-0610-12/202129,830nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 13hCoV-19/Shenzhen/IVDC-0610-13/202129,710nt (37.99)hCoV-19/England/MILK-155F811/2021
    Case 14hCoV-19/Shenzhen/IVDC-0610-14/202129,551nt (37.98)hCoV-19/England/MILK-155F811/2021
    Case 15hCoV-19/Shenzhen/IVDC-0610-15/202129,834nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 18hCoV-19/Shenzhen/IVDC-0610-18/202129,820nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 19hCoV-19/Shenzhen/IVDC-0610-19/202129,828nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 20hCoV-19/Shenzhen/IVDC-0610-20/202129,820nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 21hCoV-19/Shenzhen/IVDC-0610-21/202129,574nt (37.99)hCoV-19/England/MILK-155F811/2021
    Case 30hCoV-19/Shenzhen/IVDC-0610-30/202129,827nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 31hCoV-19/Shenzhen/IVDC-0610-31/202129,829nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 32hCoV-19/Shenzhen/IVDC-0610-32/202129,849nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 34hCoV-19/Shenzhen/IVDC-0610-34/202129,809nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 36hCoV-19/Shenzhen/IVDC-0610-36/202129,819nt (37.96)hCoV-19/England/MILK-155F811/2021
    Case 37hCoV-19/Shenzhen/IVDC-0610-37/202129,827nt (37.97)hCoV-19/England/MILK-155F811/2021
    Case 38hCoV-19/Shenzhen/IVDC-0610-38/202129,553nt (37.99)hCoV-19/England/MILK-155F811/2021
    Case 39hCoV-19/Shenzhen/IVDC-0610-39/202129,797nt (37.94)hCoV-19/England/MILK-155F811/2021
    Abbreviation: nt=Nucleotide.

    Table S2.  Genome sequence information for 30 SARS-CoV-2 strains of lineage B.1.617.2 from this study.

Reference (7)

Citation:

Catalog

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return