The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19

Abstract

The devastating effects of the recent global pandemic (termed COVID-19 for "coronavirus disease 2019") caused by the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) are paramount with new cases and deaths growing at an exponential rate. In order to provide a better understanding of SARS CoV-2, this article will review the proteins found in the SARS CoV-2 that caused this global pandemic.

Keywords: Proteins; SARS CoV-2; Virus.

Fig. 1

Alignment of the primary amino acid sequence of NSP1 of SARS CoV (top, NP_828860.2) and SARS CoV-2 (YP_009725297.1). Sequence identity: 84.4%. Sequence similarity: 93.9%—determined using LALIGN software (and for subsequent alignments, Figs. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, and 26, see Supporting Information for output data) [16].

Fig. 2

The primary amino acid sequence alignment of NSP2 for SARS CoV (NP_828861.2) and SARS CoV-2 (YP_009725298.1). These proteins have 68.3% sequence identity (90.0% similar)

Fig. 3

The primary amino acid sequence alignment of NSP3 for SARS CoV (NP_828862.2) and SARS CoV-2 (YP_009725299.1). Sequence identity: 76.0%, sequence similarity: 91.8%

Fig. 4

The primary amino acid sequence alignment of NSP4 for SARS CoV (NP_904322.1) and SARS CoV-2 (YP_009725300.1). Sequence identity: 80.0%, sequence similarity: 95.0%

Fig. 5

The primary amino acid sequence of NSP5 for SARS CoV (NP_828863.1) and SARS CoV-2 (YP_009725301.1). Sequence identity: 96.1%, sequence similarity: 99.7%

Fig. 6

Amino acid sequence alignment between the NSP6 proteins of SARS CoV (top: NP_828864.1) and SARS-CoV-2 (bottom: YP_009725302.1). Sequence identity: 88.2%, sequence similarity: 98.3%

Fig. 7

The primary amino acid sequence alignment of NSP7 SARS CoV (NP_828865.1) and SARS CoV-2 (YP_009725303.1). Sequence identity: 98.8%, sequence similarity: 100%

Fig. 8

The primary amino acid sequence alignment of NSP8 for SARS CoV (NP_828866.1) and SARS CoV-2 (YP_009725304.1). Sequence identity: 97.5%, sequence similarity: 100.0%

Fig. 9

The primary amino acid sequence alignment of NSP9 for SARS CoV (NP_828868.1) and SARS CoV-2 (YP_009725305.1). Sequence identity: 97.3%, sequence similarity: 99.1%

Fig. 10

The primary amino acid sequence alignment of NSP10 for SARS CoV (NP_828868.1) and SARS CoV-2 (YP_009725306.1). Sequence identity: 97.1%, sequence similarity: 99.3%

Fig. 11

The primary amino acid sequence alignment of NSP11 for SARS CoV (NP_904321.1) and SARS CoV-2 (YP_009725312.1). Sequence identity: 84.6%, sequence similarity: 100.0%

Fig. 12

The primary amino acid sequence alignment of NSP12 for SARS CoV (NP_828869.1) and SARS CoV-2 (YP_009725307.1). Sequence identity: 96.4%, sequence similarity: 99.4%

Fig. 13

The primary amino acid sequence of NSP13 SARS CoV (NP_828870.1) and SARS CoV-2 (YP_009725308.1). Sequence identity: 99.8%, sequence similarity: 100.0%

Fig. 14

The primary amino acid sequence alignment of NSP14 of SARS CoV (NP_828871.1) and SARS CoV-2(YP_009725309.1). Sequence identity: 95.1%, sequence similarity: 99.1%

Fig. 15

The primary amino acid sequence alignment of NSP15 of SARS CoV (NP_828872.1) and SARS CoV-2 (YP_009725310.1). Sequence identity: 88.7%, sequence similarity: 97.7%

Fig. 16

The primary amino acid sequence alignment of NSP16 of SARS CoV (NP_828873.2) and SARS CoV-2 (YP_009725311.1). Sequence identity: 93.3%, sequence similarity: 99.0%

Fig. 17

The primary amino acid sequence alignment of the spike proteins from SARS CoV (NP_828851.1) and SARS CoV-2 (BCA87361.1). Sequence identity: 76.0%, sequence similarity: 91.5%

Fig. 18

The primary amino acid sequence alignment of the ORF3a proteins from SARS CoV (NP_828852.2) and SARS CoV-2 (BCA87362.1). Sequence identity: 72.4%, sequence similarity: 90.2%

Fig. 19

The primary amino acid sequence of the E proteins (ORF4) from SARS CoV (NP_828854.1) and SARS CoV-2 (BCA87363.1). Sequence identity: 94.7%, sequence similarity: 97.4%

Fig. 20

The primary amino acid sequence of the M proteins (ORF5) from SARS CoV (NP_828855.1) and SARS CoV-2 (BCA87364.1). Sequence identity: 90.5%, sequence similarity: 98.2%

Fig. 21

The primary amino acid sequence alignment of the ORF6 proteins from SARS CoV (NP_828856.1) and SARS CoV-2 (BCA87365.1). Sequence identity: 68.9%, sequence similarity: 93.4%

Fig. 22

The primary amino acid sequence of the ORF7a protein from SARS CoV (NP_828857.1) and SARS CoV-2 (BCA87366.1). Sequence identity: 85.2%, sequence similarity: 95.9%

Fig. 23

The primary amino acid sequence of the ORF7b proteins from SARS CoV (NP_849175.1) and SARS CoV-2 (BCB15096.1). Sequence identity: 85.4%, sequence similarity: 97.2%

Fig. 24

Sequence alignment of ORF8a (NP_849176.1) and ORF8b (NP_849177.1) proteins from SARS CoV (top and middle) with the ORF8 protein (QJA17759.1) from SARS CoV-2 (bottom). Sequence identity and sequence similarity between ORF8a (SARS CoV) and ORF8 (SARS CoV-2): 31.7% and 70.7% in 41 amino acid overlap. Sequence identity and sequence similarity between ORF8b (SARS CoV) and ORF8 (SARS CoV-2): 40.5% and 66.7% in 42 amino acid overlap

Fig. 25

The primary amino acid sequence of the N protein from SARS CoV (ORF9a, NP_828858.1) and SARS CoV-2 (ORF9, BCA87368.1). Sequence identity: 90.5%, sequence similarity: 97.2%

Fig. 26

The primary amino acid sequence alignment of the ORF9b protein from SARS CoV and the ORF10 protein from SARS CoV-2 (Accession number: BCA87369.1). Sequence identity: 28.6%, sequence similarity: 52.4%