Notes from the Field: Whole-Genome Sequences Analysis Displays Relationship of SARS-CoV-2 Delta Variant Between Four Local Cases and Passengers of a Flight from South Africa — Shenzhen City, Guangdong Province, China, June 2021

On June 14, 2021, a customs officer (Case A) went to the infirmary at Baoan International Airport in Shenzhen due to a 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 V-090418 (Beijing MicroFuture Technology Co., Ltd, Beijing, China). Third, the sequencing libraries were prepared using the Nextera^® XT Library Prep Kit FC-131-1001(Illumina, Inc., San Diego, USA). The final viral-enriched libraries were sequenced using the MiSeq platform (Illumina, USA). The viral genome was assembled by MicronCoV^® Analyzer M-881027 (Beijing MicroFuture Technology Co., Ltd, Beijing, China). 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 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.

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 among 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 the 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.