Abstract
COVID-19 pandemic has ravaged the world, caused over 1.8 million deaths in the first year, and severely affected the global economy. Hawaii is not spared from the transmission of SARS-CoV-2 in the local population, including high infection rates in racial and ethnic minorities. Early in the pandemic, we described in this journal various technologies used for the detection of SARS-CoV-2. Herein we characterize a 969-bp SARS-CoV-2 segment of the S gene downstream of the receptor-binding domain. At the John A. Burns School of Medicine Biocontainment Facility, RNA was extracted from an oropharyngeal swab and a nasal swab from two patients from Hawaii who were infected with the SARS-CoV-2 in August 2020. Following PCR, the two viral strains were sequenced using Sanger sequencing, and phylogenetic trees were generated using MEGAX. Phylogenetic tree results indicate that the virus has been introduced to Hawaii from multiple sources. Further, we decoded 13 single nucleotide polymorphisms across 13 unique SARS-CoV-2 genomes within this region of the S gene, with one non-synonymous mutation (P681H) found in the two Hawaii strains. The P681H mutation has unique and emerging characteristics with a significant exponential increase in worldwide frequency when compared to the plateauing of the now universal D614G mutation. The P681H mutation is also characteristic of the new SARS-CoV-2 variants from the United Kingdom and Nigeria. Additionally, several mutations resulting in cysteine residues were detected, potentially resulting in disruption of the disulfide bridges in and around the receptor-binding domain. Targeted sequence characterization is warranted to determine the origin of multiple introductions of SARS-CoV-2 circulating in Hawaii.
Competing Interest Statement
The authors have declared no competing interest.
Abbreviations
- ASGPB
- Advanced Studies in Genomics, Proteomics, and Bioinformatics
- A1708D
- Alanine to Aspartic Acid at Amino Acid 1708
- A570D
- Alanine to Aspartic Acid at Amino Acid 570
- A522S
- Alanine to Serine at Amino Acid 522
- A771S
- Alanine to Serine at Amino Acid 771
- ACE2
- Angiotensin-Converting Enzyme 2
- R577C
- Arginine to Cysteine at Amino Acid 577
- R52I
- Arginine to Isoleucine at Amino Acid 52
- N501Y
- Asparagine to Tyrosine at Amino Acid 501
- D614G
- Aspartic Acid to Glycine at Amino Acid 614
- D1118H
- Aspartic Acid to Histidine at Amino Acid 1118
- D3L
- Aspartic Acid to Leucine at Amino Acid 3
- cDNA
- complementary deoxyribonucleic acid
- COVID-19
- Coronavirus Disease 2019
- ΔG2676
- deletion of Glycine Amino Acid 2676
- ΔH69
- deletion of Histidine Amino Acid 69
- ΔF3677
- deletion of Phenylalanine Amino Acid 3677
- ΔS3675
- deletion of Serine Amino Acid 3675
- ΔY145
- deletion of Tyrosine Amino Acid 145
- ΔV70
- deletion of Valine Amino Acid 70
- DNA
- deoxyribonucleic acid
- EUA
- Emergency Use Authorization
- GISAID
- Global Initiative of Sharing All Influenza Data
- E780Q
- Glutamic Acid to Glutamine at Amino Acid 780
- Q27stop
- Glutamine to stop codon at Amino Acid 27
- IBC
- Institutional Biosafety Committee
- IRB
- Institutional Review Board
- I726F
- Isoleucine to Phenylalanine at Amino Acid 726
- I2230T
- Isoleucine to Threonine at Amino Acid 2230
- I584V
- Isoleucine to Valine at Amino Acid 584
- MUSCLE
- Multiple Sequence Comparison by Log-Expectation
- NCBI
- National Center for Biotechnology Information
- NERVTAG
- New and Emerging Respiratory Virus Threats Advisory Group
- nCoV
- novel coronavirus
- PID
- Patient Identification
- F797C
- Phenylalanine to Cysteine at Amino Acid 797
- F543L
- Phenylalanine to Leucine at Amino Acid 543
- PCR
- Polymerase Chain Reaction
- P681H
- Proline to Histidine at Amino Acid 681
- RBD
- Receptor Binding Domain
- RT-PCR
- reverse transcriptase Polymerase Chain Reaction
- RNA
- ribonucleic acid
- S982A
- Serine to Alanine at Amino Acid 982
- S680C
- Serine to Cysteine at Amino Acid 680
- S235F
- Serine to Phenylalanine at Amino Acid 235
- SARS-CoV-2
- Severe Acute Respiratory Syndrome Coronavirus 2
- SNP
- Single Nucleotide Polymorphism
- T1001I
- Threonine to Isoleucine at Amino Acid 1001
- T716I
- Threonine to Isoleucine at Amino Acid 716
- TBE
- Tris/Borate/Ethylenediaminetetraacetic acid
- Y73C
- Tyrosine to Cysteine at Amino Acid 73
- FDA
- United State Food and Drug Administration
- VOC
- Variant of Concern
- VTM
- Viral Transport Media
