Emergence of SARS-CoV-2 lineage B.1.617.2 in the local community of Hong Kong.

To the Editor,

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants had raised concerns and called variant of concern (VOC). According to the PANGO lineage nomenclature system, these VOCs belonged to B.1.1.7, B.1.351, P.1, and B.1.617.2. , , The SARS‐CoV‐2 B.1.617.2 virus has shown higher transmissibility than the other three VOCs and is becoming dominant variant worldwide. , , , Before this report, SARS‐CoV‐2 B.1.617.2 was only detected from imported cases in Hong Kong. In late June 2021, we detected two local SARS‐CoV‐2 B.1.617.2 cases in Hong Kong for the first time. Here, we report the investigations of these two cases.

In Hong Kong, all coronavirus disease 2019 (COVID‐19) confirmed cases were either diagnosed or confirmed by the Public Health Laboratory Services Branch. COVID‐19 cases investigations were performed as described. In brief, contact tracing was performed, SARS‐CoV‐2 variants were screened by partial S gene sequencing and/or different SNP real‐time reverse‐transcription polymerase chain reaction (RT‐PCR) assays. Preliminary cases of VOCs were then put to whole‐genome sequencing.

On June 24, 2021, a 27‐year‐old man was diagnosed as COVID‐19 patient and possessed 452R in the Spike (S) protein. He developed symptoms on June 21 (Patient 1). RT‐PCRs were performed for specimens collected between June 22, 2021 and June 23, 2021. All of them were positive with Ct values less than 20. Three days later, a 24‐year‐old woman was also positive for SARS‐CoV‐2 452R, she developed fever on June 26, 2021 (Patient 2). RT‐PCR results were positive (Ct 30.70) for throat saliva collected on June 26, 2021. Both Patient 1 and Patient 2 were transferred to public hospitals for further treatments, they made a complete recovery and were discharged from hospitals on July 14, 2021 and July 7, 2021 with satisfactory clinical conditions, respectively.

From January 7, 2021 to June 27, 2021, 145 cases had L452R mutation. Whole‐genome sequences were determined for 136 cases with sufficient reads for analysis. Among them, 50 (36.8%) belonged to B.1.617.1 lineage, 77 (56.6%) belonged to B.1.617.2 lineage, and nine (6.6%) belonged to non‐B.1.617 lineage. The two local SARS‐CoV‐2 452R cases belonged to B.1.617.2 lineage. To determine the relatedness of these two local SARS‐CoV‐2 B.1.617.2 cases, phylogenetic analysis was performed on all SARS‐CoV‐2 B.1.617.2 cases. It was found that the two local SARS‐CoV‐2 B.1.617.2 cases were most closely related to the other three imported cases (Table 1 and Figure 1). The two local cases had very close genetic distance (0–3 SNPs) to the three imported cases. Nucleotide with mixed calls was included for analysis, and the nucleotide between two genome sequences from patients was considered to match if there was overlap between the mixed bases. No SNP difference was observed between Patient 1 and the three imported cases. Notably, the genome sequence from Patient 1 had a mixed base A/G at position 17,527 (approximately 70% of reads were A, 30% of reads were G), while it was an “A” in the three imported cases and a “G” in Patient 2. This A‐to‐G mutation at position 17,527 encoding a T431A mutation in NSP13. In addition, two more mutations at position 22,520 (V320F in Spike) and 28,008 (I39V in ORF8) are present in Patient 2. The consensus sequences generated in the present study for SARS‐CoV‐2 B.1.617.2 have been deposited into GISAID (Table S1).

Table 1

Patients' characteristics of the local SARS‐CoV‐2 cases having 452R and their closely related sequences

Patient	HK case	Age/sex	Confirmed date	Date of onset	L452R mutation in the spike protein	Lineage
Imported case	Case 11877	32 yrs/F	June 12, 2021	Asymptomatic	Yes	B.1.617.2
Imported case	Case 11878	39 yrs/F	June 12, 2021	June 11, 2021	Yes	B.1.617.2
Imported case	Case 11881	28 yrs/F	June 15, 2021	June 14, 2021	Yes	B.1.617.2
1	Case 11902	27 yrs/M	June 24, 2021	June 21, 2021	Yes	B.1.617.2
2	Case 11918	24 yrs/F	June 27, 2021	June 26, 2021	Yes	B.1.617.2

Abbreviation: SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2.

Figure 1

Phylogenetic analysis of 77 genomes of SARS‐CoV‐2 B.1.617.2 detected in Hong Kong from January 2021 to June 2021. Cases highlighted in blue were the two local and three epidemiologically linked imported cases. The Wuhan‐Hu‐1 strain was included as a reference sequence (GenBank accession no. MN908947.3). SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2

Epidemiology information showed that Patient 1 worked in Hong Kong International Airport (HKIA) and stayed in Temporary Specimen Collection Centre (TSCC) on June 11. The three imported cases arrived in Hong Kong from Indonesia on the same day, two of them were tested positive by their specimens collected at the TSCC in HKIA. Patient 1 also worked part‐time at Uptown Plaza in Tai Po for providing customer service. Patient 1 was the colleague of Patient 2 at Uptown Plaza.

Patient 1 is more likely to acquire the virus from the three imported cases and transmitted the virus to Patient 2, considering that the genome from Patient 1 had no SNPs, and the Patient 2 genome had two SNPs and 3 SNPs when compared with Patient 1 and the imported cases, respectively. The mixed base at position 17,527 in Patient 1 was probably due to intrapatient SARS‐CoV‐2 heterogeneity. The virus evolves in‐vivo to form quasispecies in Patient 1 and subsequently transmitted the infection to Patient 2.

Successful COVID‐19 control could only be achieved by widespread testing, contact tracing and cases isolation. At the time of writing of this report (July 2021), no new COVID‐19 cases were reported from the contact cases of Patient 1 and Patient 2 since June 27, 2021. Without control measures, it is likely that silent transmission existed in the two local SARS‐CoV‐2 B.1.617.2 cases. SARS‐CoV‐2 genomic surveillance must be regularly performed.

AUTHOR CONTRIBUTIONS

Alan K. L. Tsang and Gannon C. K. Mak conceptualized the study design, led the data collection, data analysis, data interpretation, and manuscript writing. Patricia K. L. Leung, Peter K. C. Cheng, and Peter C. W. Yip coordinated and carried out the experiments. Edman T. K. Lam, Ken H. L. Ng, and Rickjason C. W. Chan supervised and oversaw all aspects of experiments. All authors participated in the drafting of the manuscript, and approval of the final version.

Supporting information.

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