RT Journal Article
SR Electronic
T1 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.01.06.425497
DO 10.1101/2021.01.06.425497
A1 Maison, David P.
A1 Ching, Lauren L.
A1 Shikuma, Cecilia M.
A1 Nerurkar, Vivek R.
YR 2021
UL http://biorxiv.org/content/early/2021/01/07/2021.01.06.425497.abstract
AB 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 StatementThe authors have declared no competing interest.ASGPBAdvanced Studies in Genomics, Proteomics, and BioinformaticsA1708DAlanine to Aspartic Acid at Amino Acid 1708A570DAlanine to Aspartic Acid at Amino Acid 570A522SAlanine to Serine at Amino Acid 522A771SAlanine to Serine at Amino Acid 771ACE2Angiotensin-Converting Enzyme 2R577CArginine to Cysteine at Amino Acid 577R52IArginine to Isoleucine at Amino Acid 52N501YAsparagine to Tyrosine at Amino Acid 501D614GAspartic Acid to Glycine at Amino Acid 614D1118HAspartic Acid to Histidine at Amino Acid 1118D3LAspartic Acid to Leucine at Amino Acid 3cDNAcomplementary deoxyribonucleic acidCOVID-19Coronavirus Disease 2019ΔG2676deletion of Glycine Amino Acid 2676ΔH69deletion of Histidine Amino Acid 69ΔF3677deletion of Phenylalanine Amino Acid 3677ΔS3675deletion of Serine Amino Acid 3675ΔY145deletion of Tyrosine Amino Acid 145ΔV70deletion of Valine Amino Acid 70DNAdeoxyribonucleic acidEUAEmergency Use AuthorizationGISAIDGlobal Initiative of Sharing All Influenza DataE780QGlutamic Acid to Glutamine at Amino Acid 780Q27stopGlutamine to stop codon at Amino Acid 27IBCInstitutional Biosafety CommitteeIRBInstitutional Review BoardI726FIsoleucine to Phenylalanine at Amino Acid 726I2230TIsoleucine to Threonine at Amino Acid 2230I584VIsoleucine to Valine at Amino Acid 584MUSCLEMultiple Sequence Comparison by Log-ExpectationNCBINational Center for Biotechnology InformationNERVTAGNew and Emerging Respiratory Virus Threats Advisory GroupnCoVnovel coronavirusPIDPatient IdentificationF797CPhenylalanine to Cysteine at Amino Acid 797F543LPhenylalanine to Leucine at Amino Acid 543PCRPolymerase Chain ReactionP681HProline to Histidine at Amino Acid 681RBDReceptor Binding DomainRT-PCRreverse transcriptase Polymerase Chain ReactionRNAribonucleic acidS982ASerine to Alanine at Amino Acid 982S680CSerine to Cysteine at Amino Acid 680S235FSerine to Phenylalanine at Amino Acid 235SARS-CoV-2Severe Acute Respiratory Syndrome Coronavirus 2SNPSingle Nucleotide PolymorphismT1001IThreonine to Isoleucine at Amino Acid 1001T716IThreonine to Isoleucine at Amino Acid 716TBETris/Borate/Ethylenediaminetetraacetic acidY73CTyrosine to Cysteine at Amino Acid 73FDAUnited State Food and Drug AdministrationVOCVariant of ConcernVTMViral Transport Media