Genomic variance of Open Reading Frames (ORFs) and Spike protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Abstract

Background: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused severe pneumonia at December 2019. Since then, it has been wildly spread from Wuhan, China, to Asia, European, and United States to become the pandemic worldwide. Now coronavirus disease 2019 were globally diagnosed over 3 084 740 cases with mortality of 212 561 toll. Current reports variants are found in SARS-CoV-2, majoring in functional ribonucleic acid (RNA) to transcribe into structural proteins as transmembrane spike (S) glycoprotein and the nucleocapsid (N) protein holds the virus RNA genome; the envelope (E) and membrane (M) alone with spike protein form viral envelope. The nonstructural RNA genome includes ORF1ab, ORF3, ORF6, 7a, 8, and ORF10 with highly conserved information for genome synthesis and replication in ORF1ab.

Methods: We apply genomic alignment analysis to observe SARS-CoV-2 sequences from GenBank (http://www.ncbi.nim.nih.gov/genebank/): MN 908947 (China, C1); MN985325 (United States: WA, UW); MN996527 (China, C2); MT007544 (Australia: Victoria, A1); MT027064 (United States: CA, UC); MT039890 (South Korea, K1); MT066175 (Taiwan, T1); MT066176 (Taiwan, T2); LC528232 (Japan, J1); and LC528233 (Japan, J2) and Global Initiative on Sharing All Influenza Data database (https://www.gisaid.org). We adopt Multiple Sequence Alignments web from Clustalw (https://www.genome.jp/tools-bin/clustalw) and Geneious web (https://www.geneious.com.

Results: We analyze database by genome alignment search for nonstructural ORFs and structural E, M, N, and S proteins. Mutations in ORF1ab, ORF3, and ORF6 are observed; specific variants in spike region are detected.

Conclusion: We perform genomic analysis and comparative multiple sequence of SARS-CoV-2. Large scaling sequence alignments trace to localize and catch different mutant strains in United possibly to transmit severe deadly threat to humans. Studies about the biological symptom of SARS-CoV-2 in clinic animal and humans will be applied and manipulated to find mechanisms and shield the light for understanding the origin of pandemic crisis.

Fig. 1

Genomic analysis of ORF1ab protein amino acid sequence. We detect eight mutations in different regions from various countries, T609I mutation in United States, G818S in Sweden and India, M902I in Korea, F3071Y in Spain, S3120L in China, L3606X in Italy and L3606F in Japan, F4321L in Sweden and India, and T6891M in Korea.

Fig. 2

Genomic analysis of ORF3a protein amino acid sequence. We find four position mutations; M128L in Korea, K136X in Spain, G196V in Spain, and G251V in Italy, Korea, and Sweden.

Fig. 3

Genomic analysis of ORF6, ORF7a, ORF8, and ORF10 protein amino acid sequence. There are not any mutations in ORF6, ORF7a, and ORF10, but we find one mutation in ORF8 located at L84S in Taiwan, United States, Spain, India, and China.

Fig. 4

Genomic analysis of E protein amino acid sequence. We found one amino acid mutation at position 37th L37H as “H” from South Korea comparing the “L” from other nine sequences. Yellow line indicates the difference in 10 sequence alignment.

Fig. 5

. Genomic analysis of M and N protein amino acid sequences. We do not observe any mutation in 10 sequences of M protein region but detect one mutation in Spain at S197L of N protein.

Fig. 6

Genomic analysis of S protein amino acid sequence. During analysis of S protein, we find four mutations from 10 countries; S221W in Korea, S247R in Australia, F737C in Sweden, and A870V in India.

Fig. 7

Spike protein reveals variants in the world. We find many variants in spike protein by alignment and phylogenetic analysis.

Fig. 8

A, Spike protein in China sequences exhibit a conserved amino acid. We found a conserved amino acid “D” at position 614 of Spike protein in most China sequences. B, Analysis indicates three variants of spike protein in the United States. We observe three variants in the analysis of United States sequences; mutant-1 found with different amino acid “G” at position 614, mutant 2-1 with same “D” at position 614 same as China but various variants at other regions. Mutant 2-2 same as 2-1 at 614 but same as China in one region as QIS60546 indicated. (I) US case. (II) Phylogenetic analysis to map three mutants in United States and China.