Unusual high number of spike protein mutations for the SARS-CoV-2 strains detected in Hong Kong

In Hong Kong, the laboratory surveillance of SARS-CoV-2 has been implemented by Public Health Laboratory Services Branch (PHLSB) since the first case of COVID-19 detected in January 2020 [1,2]. The surveillance system has been expanded to track the emergence of variants in Hong Kong in December 2020. Although rare, our system could detect variant of concern (VOC) SARS-CoV-2 cases in the local community [3, 4]. In late November 2021, we detected two SARS-CoV-2 cases with unusual features. These two strains harbored high number of spike (S) protein mutations that were present among SARS-CoV-2 cases for the first time. Here, we report the investigations of these two cases.

In Hong Kong, all COVID‐19 confirmed cases were either diagnosed or confirmed by PHLSB. COVID‐19 cases investigations were performed as described. In brief, contact tracing was performed by Communicable Disease Branch of the Centre for Health Protection, SARS-CoV-2 variants were screened by partial S gene sequencing and/or different SNP RT‐PCR assays. Whole-genome sequencing were performed for preliminary cases of variants [3,4].

On November 15, 2021, a 36-year-old man (patient 1) was diagnosed as COVID‐19 patient and his specimen possessed 501Y in the S protein by SNP RT-PCR. He returned to Hong Kong from South Africa on November 11 and was quarantined in a designated quarantine hotel. Respiratory specimens collected on November 13 and November 14 were tested positive for SARS CoV-2. Partial S gene Sanger sequencing revealed 12 mutations from protein 417 to 547 (GISAID accession number EPI_ISL_6590608) (Table 1 ) [5]. Five days later, a 62-year-old man (patient 2) was diagnosed as COVID‐19 patient and his specimen possessed 501Y in the S protein. He returned to Hong Kong from Canada on November 10. His specimens collected on November 10 and 14 were tested negative, however, specimen collected on November 18 was tested positive [6]. Partial S gene Sanger sequencing revealed the same mutations (EPI_ISL_6754457) (Table 1).

Table 1.

The non-synonymous substitutions in the Spike protein for the two SARS-CoV-2 viruses with unusual high number of spike protein mutations detected in Hong Kong in late November 2021

Position based on WIV04	WIV04	The two cases in the present study
67	A	V
69-70	HV	deletion
95	T	I
142	G	D
143-145	VYY	deletion
211	N	I
212	L	deletion
Insertion between 214-215	-	EPE
339	G	D
371	S	L
373	S	P
375	S	F
417	K	N
440	N	K
446	G	S
477	S	N
478	T	K
484	E	A
493	Q	R
496	G	S
498	Q	R
501	N	Y
505	Y	H
547	T	K
614	D	G
655	H	Y
679	N	K
681	P	H
764	N	K
796	D	Y
856	N	K
954	Q	H
969	N	K
981	L	F

Contact tracing found that patient 1 and patient 2 were quarantined in the same hotel after arriving in Hong Kong. Although they were not stayed in the same room, there rooms were located in the same floor and opposite each other [6].

Whole genome sequencing were performed for these two SARS-CoV-2 cases and found that they had identical genomic sequences. The sequences of these two cases were unusual (EPI_ISL_6590782 and EPI_ISL_6698790). There were 34 differences of the S protein when comparing with the Wuhan reference strain WIV04 (GenBank accession number MN996528) (Table 1). At the time of sequence submission to GISAID on November 22, 2021, no similar sequences could be found in the database. It was not until other similar sequences were submitted to the database, the variant was classified as B.1.1.529 according to the PANGO nomenclature system on November 24. The differences of the S protein for the four circulating VOCs as defined by the World Health Organization (WHO) when comparing with WIV04 only ranged from 4 to 12 [7].

The clinical significance of the B.1.1.529 remains unknown. Recently, WHO named this variant as Omicron and classified as VOC [8]. At the time of revising this report on December 31, 2021, the Omicron variant divided into three sub-lineages, BA.1, BA.2 and BA.3. Majority sequences available in GISAID were BA.1 which accounted for >99% [9]. The two cases analyzed in the present study belonged to BA.1. The differences of S protein for these three sub-lineages were summarized in the Appendix file. Further studies on Omicron are warranted for the colleagues in the field. SARS-CoV-2 surveillance is ongoing to monitor the emergence of variants.

Declaration of Competing Interest

None.