Genetic diversity and evolution of SARS-CoV-2.

COVID-19 is a viral respiratory illness caused by a new coronavirus called SARS-CoV-2. The World Health Organization declared the SARS-CoV-2 outbreak a global public health emergency. We performed genetic analyses of eighty-six complete or near-complete genomes of SARS-CoV-2 and revealed many mutations and deletions on coding and non-coding regions. These observations provided evidence of the genetic diversity and rapid evolution of this novel coronavirus.

The study

A new coronavirus SARS-CoV-2 is spreading cross the world (Phan, 2020). Since the virus emerged at the seafood wholesale market at the end of last year (Zhu et al., 2019), the number of infected cases has been rising dramatically (Velavan and Meyer, 2020). Human-to-human transmission of SARS-CoV-2 has been confirmed (Nishiura et al., 2020). The virus has been detected in bronchoalveolar-lavage (Zhu et al., 2019), sputum (Lin et al., 2020), saliva (K.K. To et al., 2020), throat (Bastola et al., 2020) and nasopharyngeal swabs (To et al., 2020).

Nucleotide substitution has been proposed to be one of the most important mechanisms of viral evolution in nature (Lauring and Andino, 2010). The rapid spread of SARS-CoV-2 raises intriguing questions such as whether its evolution is driven by mutations. To assess the genetic variation, eighty-six complete or near-complete genomes of SARS-CoV-2 were collected from GISAID [https://www.gisaid.org/]. These SARS-CoV-2 strains were detected in infected patients from China (50), USA (11), Australia (5), Japan (5), France (4), Singapore (3), England (2), Taiwan (2), South Korea (1), Belgium (1), Germany (1), and Vietnam (1). The pair-wise nucleotide sequence alignment was performed by ClustalX2 (Saitou and Nei, 1987), and the sequence of the strain China/WHU01/2020/EPI_ISL_406716 was used as a reference genome.

Like other betacoronaviruses, the genome of SARS-CoV-2 has a long ORF1ab polyprotein at the 5′ end, followed by four major structural proteins, including the spike surface glycoprotein, small envelope protein, matrix protein, and nucleocapsid protein (Phan, 2020). Our genetic analysis discovered three deletions in the genomes of SARS-CoV-2 from Japan (Aichi), USA (Wisconsin), and Australia (Victoria) as shown in Fig. 1 . Two deletions (three nucleotides and twenty-four nucleotides) were in the ORF1ab polyprotein, and one deletion (ten nucleotides) was in the 3′ end of the genome.

Fig. 1

Genomic organization of SARS-CoV-2 and pairwise nucleotide sequence alignment showing deletions in the ORF1ab polyprotein and in the 3′ end of the genome.

It is interesting that our nucleotide sequence alignment also revealed ninety-three mutations over the entire genomes of SARS-CoV-2 (Table 1 ). Forty-two missense mutations were identified in all the major non-structural and structural proteins, except the envelope protein. Twenty-nine missense mutations were in the ORF1ab polyprotein, eight in the spike surface glycoprotein, one in the matrix protein, and four in the nucleocapsid protein. Of note, three mutations (D354, Y364, and F367) located in the spike surface glycoprotein receptor-binding domain. The spike surface glycoprotein plays an essential role in binding to receptors on the host cell and determines host tropism (Fung and Liu, 2019). It is also the major target of neutralizing antibodies (Yu et al., 2020). Mutations in the spike surface glycoprotein might induce its conformational changes, which probably led to the changing antigenicity. To date, a study on localization of amino acids involved in conformational changes of the SARS-CoV-2 spike surface glycoprotein structure is not available. The identification of these amino acids is of significance and should be investigated by further studies.

Table 1

Mutations found in the entire genome of SARS-CoV-2 strains. The number in the parentheses indicated the location of amino acid in its protein.

Genomic region	No. nt mutations	Missense mutation	SARV-CoV-2 strain
5′ UTR	8	N/A
ORF1ab polyprotein	48	29
		A (117) → T	USA/CA3/2020/EPI_ISL_408008USA/CA4/2020/EPI_ISL_408009
		P (309) → S	France/IDF0515/2020/EPI ISL_408430
		S (428) → N	USA/CA1/2020/EPI_ISL_406034
		T (609) → I	USA/CA5/2020/EPI_ISL_408010
		A (1176) → V	Japan/TY-WK-012/2020/EPI_ISL_408665
		L (1599) → F	Korea/KCDC03/2020/EPI_ISL_407193
		I (1607) → V	USA/CA3/2020/EPI_ISL_408008USA/CA4/2020/EPI_ISL_408009
		M (2194) → T	Shenzhen/SZTH-004/2020/EPI_ISL_406595
		L (2235) → I	Wuhan/WH01/2019/EPI_ISL_406798
		I (2244) → T	Wuhan/IPBCAMS-WH-03/2019/EPI_ISL_403930
		G (2251) → S	Wuhan/WIV05/2019/EPI_ISL_402128
		A (2345) → V	Shandong/IVDC-SD-001/2020/EPI_ISL_408482
		G (2534) → V	Wuhan/IPBCAMS-WH-05/2020/EPI_ISL_403928
		D (2579) → A	Wuhan/WIV07/2019/EPI_ISL_402130
		N (2708) → S	Wuhan/IPBCAMS-WH-01/2019/EPI_ISL_402123
		F (2908) → I	Wuhan/IPBCAMS-WH-01/2019/EPI_ISL_402123
		T (3058) → I	France/IDF0515/2020/EPI_ISL_408430
		S (3099) → L	Shenzhen/HKU-SZ-005/2020/EPI_ISL_405839
		L (3606) → F	Yunnan/IVDC-YN-003/2020/EPI_ISL_408480Shandong/IVDC-SD-001/2020/EPI_ISL_408482Chongqing/IVDC-CQ-001/2020/EPI_ISL_408481Singapore/3/2020/EPI_ISL_407988France/IDF0515/2020/EPI_ISL_408430USA/AZ1/2020/EPI_ISL_406223
		E (3764) → D	Japan/KY-V-029/2020/EPI_ISL_408669
		N (3833) → K	Wuhan/WH01/2019/EPI_ISL_406798
		W (5308) → C	Taiwan/2/2020/EPI_ISL_406031
		T (5579) → I	USA/CA2/2020/EPI_ISL_406036
		I (6075) → T	England/02/2020/EPI_ISL_407073England/01/2020/EPI_ISL_407071
		P (6083) → L	Japan/AI/I-004/2020/EPI_ISL_407084
		F (6309) → Y	Sichuan/IVDC-SC-001/2020/EPI_ISL_408484
		E (6565) → D	Shenzhen/SZTH-004/2020/EPI_ISL_406595
		K (6958) → R	Wuhan/WIV05/2019/EPI_ISL_402128
		D (7018) → N	Wuhan/WIV02/2019/EPI_ISL_402127
Spike polyprotein	14	8
		F (32) → I	Wuhan/HBCDC-HB-01/2019/EPI_ISL_402132
		H (49) → Y	Guangdong/20SF174/2020/EPI_ISL_406531Guangdong/20SF040/2020/EPI_ISL_403937Guangdong/20SF028/2020/EPI_ISL_403936
		S (247) → R	Australia/VIC01/2020/EPI_ISL_406844
		N (354) → D	Shenzhen/SZTH-004/2020/EPI_ISL_406595
		D (364) → Y	Shenzhen/SZTH-004/2020/EPI_ISL_406595
		V (367) → F	France/IDF0372/2020/EPI_ISL_406596France/IDF0373/2020/EPI_ISL_406597
		D (614) → G	Germany/BavPat1/2020/EPI_ISL_406862
		P (1143) → L	Australia/QLD02/2020/EPI_ISL_407896
Intergenic region	5	N/A
Envelope protein	0	0
Matrix protein	2	1
		D (209) → H	Singapore/2/2020/EPI_ISL_407987
Intergenic region	6	N/A
Nucleocapsid protein	7	4
		T (148) → I	Shenzhen/SZTH-004/2020/EPI_ISL_406595
		S (194) → L	Shenzhen/SZTH-003/2020/EPI_ISL_406594Foshan/20SF207/2020/EPI_ISL_406534USA/CA3/2020/EPI_ISL_408008USA/CA4/2020/EPI_ISL_408009
		S (202) → N	Australia/QLD02/2020/EPI_ISL_407896
		P (344) → S	Guangzhou/20SF206/2020/EPI_ISL_406533
3′UTR	3	N/A
Complete genome	93	42