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Maison DP, Cleveland SB, Nerurkar VR. Genomic analysis of SARS-CoV-2 variants of concern circulating in Hawai'i to facilitate public-health policies. PLoS One 2022; 17:e0278287. [PMID: 36454775 PMCID: PMC9714757 DOI: 10.1371/journal.pone.0278287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Using genomics, bioinformatics and statistics, herein we demonstrate the effect of statewide and nationwide quarantine on the introduction of SARS-CoV-2 variants of concern (VOC) in Hawai'i. To define the origins of introduced VOC, we analyzed 260 VOC sequences from Hawai'i, and 301,646 VOC sequences worldwide, deposited in the GenBank and global initiative on sharing all influenza data (GISAID), and constructed phylogenetic trees. The trees define the most recent common ancestor as the origin. Further, the multiple sequence alignment used to generate the phylogenetic trees identified the consensus single nucleotide polymorphisms in the VOC genomes. These consensus sequences allow for VOC comparison and identification of mutations of interest in relation to viral immune evasion and host immune activation. Of note is the P71L substitution within the E protein, the protein sensed by TLR2 to produce cytokines, found in the B.1.351 VOC may diminish the efficacy of some vaccines. Based on the phylogenetic trees, the B.1.1.7, B.1.351, B.1.427, and B.1.429 VOC have been introduced in Hawai'i multiple times since December 2020 from several definable geographic regions. From the first worldwide report of VOC in GenBank and GISAID, to the first arrival of VOC in Hawai'i, averages 320 days with quarantine, and 132 days without quarantine. As such, the effect of quarantine is shown to significantly affect the time to arrival of VOC in Hawai'i. Further, the collective 2020 quarantine of 43-states in the United States demonstrates a profound impact in delaying the arrival of VOC in states that did not practice quarantine, such as Utah. Our data demonstrates that at least 76% of all definable SARS-CoV-2 VOC have entered Hawai'i from California, with the B.1.351 variant in Hawai'i originating exclusively from the United Kingdom. These data provide a foundation for policy-makers and public-health officials to apply precision public health genomics to real-world policies such as mandatory screening and quarantine.
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Affiliation(s)
- David P Maison
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, University of Hawai'i-System, Honolulu, Hawai'i, United States of America
- Pacific Center for Emerging Infectious Diseases Research, University of Hawai'i-System, Honolulu, Hawai'i, United States of America
- John A. Burns School of Medicine, University of Hawai'i-System, Honolulu, Hawai'i, United States of America
| | - Sean B Cleveland
- Hawai'i Data Science Institute, University of Hawai'i-System, Honolulu, Hawai'i, United States of America
- Information Technology Services-Cyberinfrastructure, University of Hawai'i-System, Honolulu, Hawai'i, United States of America
| | - Vivek R Nerurkar
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, University of Hawai'i-System, Honolulu, Hawai'i, United States of America
- Pacific Center for Emerging Infectious Diseases Research, University of Hawai'i-System, Honolulu, Hawai'i, United States of America
- John A. Burns School of Medicine, University of Hawai'i-System, Honolulu, Hawai'i, United States of America
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Mukherjee S, Ray SK. A new wave of COVID-19 in 2021 with unique genetic characters -present global scenario and beholding onwards. Infect Disord Drug Targets 2022; 22:29-40. [PMID: 35366784 DOI: 10.2174/1871526522666220401101818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/06/2021] [Accepted: 12/02/2021] [Indexed: 11/22/2022]
Abstract
After the first report of a coronavirus-associated pneumonia outbreak in December 2019, the virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) that causes the infection/disease (COVID-19) has developed into a pandemic, with >100 million people infected in over 210 countries along with two million people have died from COVID-19 till today. Coronaviruses are positive-stranded RNA viruses having restricted RNA polymerase proofreading ability thus it is very genetically susceptible to mutation. The evolution of SARS-CoV-2 from a single-point zoonotic introduction in Wuhan in November or December 2019 was widely expected, and viral sequence surveillance was developed as a result. When the first sequence of SARS-CoV-2 was released, a race to develop vaccines started, and several vaccines are now used worldwide. Independent SARS-CoV-2 lineages have recently been identified in the UK (B.1.1.7), Brazil (P.1), South Africa (B.1.351), and India (B.1.617). The recent appearance of several SARS-CoV-2 variant strains has shattered faith in the modern generation of vaccines' ability to provide enduring defense against infection. The risk of escaping natural and induced immunity has encouraged an urgency to comprehend the implications of these improvements, as well as a drive to develop new approaches to combat SARS-CoV-2 variants.
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Affiliation(s)
- Sukhes Mukherjee
- Department of Biochemistry All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020. India
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3
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Lubinski B, Fernandes MHV, Frazier L, Tang T, Daniel S, Diel DG, Jaimes JA, Whittaker GR. Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.06.438731. [PMID: 33851153 PMCID: PMC8043443 DOI: 10.1101/2021.04.06.438731] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent causing the COVID-19 pandemic. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern (VOC) first identified in the UK in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. We performed assays using fluorogenic peptides mimicking the Wuhan-Hu-1 and B.1.1.7 S1/S2 sequence and observed no significant difference in furin cleavage. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7 or a P681H point mutant. Likewise, we observed no differences in viral growth between USA-WA1/2020 and a B.1.1.7 isolate in cell culture. Our findings suggest that while the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage this does not significantly impact viral entry or cell-cell spread.
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Affiliation(s)
- Bailey Lubinski
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Maureen H. V. Fernandes
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Laura Frazier
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Diego G. Diel
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY, 14853, USA
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4
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Yi H, Wang J, Wang J, Lu Y, Zhang Y, Peng R, Lu J, Chen Z. The Emergence and Spread of Novel SARS-CoV-2 Variants. Front Public Health 2021; 9:696664. [PMID: 34409009 PMCID: PMC8364952 DOI: 10.3389/fpubh.2021.696664] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in late 2019, laboratories around the world have widely used whole genome sequencing (WGS) to continuously monitor the changes in the viral genes and discovered multiple subtypes or branches evolved from SARS-CoV-2. Recently, several novel SARS-CoV-2 variants have been found to be more transmissible. They may affect the immune response caused by vaccines and natural infections and reduce the sensitivity to neutralizing antibodies. We analyze the distribution characteristics of prevalent SARS-CoV-2 variants and the frequency of mutant sites based on the data available from GISAID and PANGO by R 4.0.2 and ArcGIS 10.2. Our analysis suggests that B.1.1.7, B.1.351, and P.1 are more easily spreading than other variants, and the key mutations of S protein, including N501Y, E484K, and K417N/T, have high mutant frequencies, which may have become the main genotypes for the spread of SARS-CoV-2.
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Affiliation(s)
- Huaimin Yi
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jin Wang
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiong Wang
- School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuying Lu
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yali Zhang
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ruihao Peng
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiahai Lu
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zeliang Chen
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, One Health Center of Excellence for Research and Training, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shenyang, China
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Abstract
BACKGROUND SARS-CoV-2, a coronavirus (CoV), is known to cause acute respiratory distress syndrome, and a number of non-respiratory complications, particularly in older male patients with prior health conditions, such as obesity, diabetes and hypertension. These prior health conditions are associated with vascular dysfunction, and the CoV disease 2019 (COVID-19) complications include multiorgan failure and neurological problems. While the main route of entry into the body is inhalation, this virus has been found in many tissues, including the choroid plexus and meningeal vessels, and in neurons and CSF. MAIN BODY We reviewed SARS-CoV-2/COVID-19, ACE2 distribution and beneficial effects, the CNS vascular barriers, possible mechanisms by which the virus enters the brain, outlined prior health conditions (obesity, hypertension and diabetes), neurological COVID-19 manifestation and the aging cerebrovascualture. The overall aim is to provide the general reader with a breadth of information on this type of virus and the wide distribution of its main receptor so as to better understand the significance of neurological complications, uniqueness of the brain, and the pre-existing medical conditions that affect brain. The main issue is that there is no sound evidence for large flux of SARS-CoV-2 into brain, at present, compared to its invasion of the inhalation pathways. CONCLUSIONS While SARS-CoV-2 is detected in brains from severely infected patients, it is unclear on how it gets there. There is no sound evidence of SARS-CoV-2 flux into brain to significantly contribute to the overall outcomes once the respiratory system is invaded by the virus. The consensus, based on the normal route of infection and presence of SARS-CoV-2 in severely infected patients, is that the olfactory mucosa is a possible route into brain. Studies are needed to demonstrate flux of SARS-CoV-2 into brain, and its replication in the parenchyma to demonstrate neuroinvasion. It is possible that the neurological manifestations of COVID-19 are a consequence of mainly cardio-respiratory distress and multiorgan failure. Understanding potential SARS-CoV-2 neuroinvasion pathways could help to better define the non-respiratory neurological manifestation of COVID-19.
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Affiliation(s)
- Conor McQuaid
- Department of Neuroscience, University of Rochester, URMC, 601 Elmwood Avenue, Rochester, NY 14642 USA
| | - Molly Brady
- Department of Neuroscience, University of Rochester, URMC, 601 Elmwood Avenue, Rochester, NY 14642 USA
| | - Rashid Deane
- Department of Neuroscience, University of Rochester, URMC, 601 Elmwood Avenue, Rochester, NY 14642 USA
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Nagy A, Basiouni S, Parvin R, Hafez HM, Shehata AA. Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Arch Virol 2021; 166:2541-2549. [PMID: 34258664 PMCID: PMC8276844 DOI: 10.1007/s00705-021-05166-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 01/03/2023]
Abstract
The SARS-CoV-2 spike protein Q677P/H mutation and furin cleavage site (FCS) have been shown to affect cell tropism and virus transmissibility. Here, we analyzed the frequency of Q677P/H and FCS point mutations in 1,144,793 human and 1042 animal spike protein sequences and from those of the emergent variants B.1.1.7, B.1.351, P.1, B.1.429 + B.1.427, and B.1.525, which were deposited in the database of the GISAID Initiative. Different genetic polymorphisms, particularly P681H and A688V, were detected in the FCS, mainly in human isolates, and otherwise, only pangolin and bat sequences had these mutations. Multiple FCS amino acid deletions such as Δ680SPRRA684 and Δ685RSVA688 were only detected in eight and four human isolates, respectively. Surprisingly, deletion of the entire FCS motif as Δ680SPRRARSVA688 and Δ680SPRRARSVAS689 was detected only in three human isolates. On the other hand, analysis of FCS from emergent variants showed no deletions in the FCS except for spike P681del, which was detected in seven B.1.1.7 isolates from the USA. Spike Q677P was detected only once in variant, B.1.1.7, whereas Q677H was detected in all variants, i.e., B.1.1.7 (n = 1938), B.1.351 (n = 28), P.1 (n = 9), B.1.429 + B.1.427 (n = 132), and B.1.525 (n = 1584). Structural modeling predicted that mutations or deletions at or near the FCS significantly alter the cleavage loop structure and would presumably affect furin binding. Taken together, our results show that Q677H and FCS point mutations are prevalent and may have various biological effects on the circulating variants. Therefore, we recommend urgent monitoring and surveillance of the investigated mutations, as well as laboratory assessment of their pathogenicity and transmissibility.
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Affiliation(s)
- Abdou Nagy
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, 44511, Egypt.
| | - Shereen Basiouni
- Clinical Pathology Department, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Rokshana Parvin
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Hafez M Hafez
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Free University, Berlin, Germany
| | - Awad A Shehata
- Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, Sadat City University, Sadat City, Egypt. .,Research and Development Section, PerNaturam GmbH, Gödenroth, Germany.
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Lobiuc A, Dimian M, Sturdza O, Filip R, Covasa M. Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis. JMIRX MED 2021; 2:e28049. [PMID: 34424256 PMCID: PMC8363123 DOI: 10.2196/28049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 06/19/2021] [Accepted: 06/25/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The United Kingdom reported the emergence of a new and highly transmissible SARS-CoV-2 variant (B.1.1.7) that rapidly spread to other countries. The impact of this new mutation-which occurs in the S protein-on infectivity, virulence, and current vaccine effectiveness is still under evaluation. OBJECTIVE The aim of this study is to sequence SARS-CoV-2 samples of cases in Romania to detect the B.1.1.7 variant and compare these samples with sequences submitted to GISAID. METHODS SARS-CoV-2 samples were sequenced and amino acid substitution analysis was performed using the CoV-GLUE platform. RESULTS We have identified the first cases of the B.1.1.7 variant in samples collected from Romanian patients, of which one was traced to the region of the United Kingdom where the new variant was originally sequenced. Mutations in nonstructural protein 3 (Nsp3; N844S and D455N) and ORF3a (L15F) were also detected, indicating common ancestry with UK strains as well as remote connections with strains from Nagasaki, Japan. CONCLUSIONS These results indicate, for the first time, the presence and characteristics of the new variant B.1.1.7 in Romania and underscore the need for increased genomic sequencing in patients with confirmed COVID-19.
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Affiliation(s)
- Andrei Lobiuc
- Department of Human Health and Development College of Physical Exercise and Sport Stefan cel Mare University of Suceava Suceava Romania
| | - Mihai Dimian
- Department of Computers, Electronics and Automation College of Electrical Engineering and Computer Science Stefan cel Mare University of Suceava Suceava Romania
- Integrated Center for Research, Development and Innovation in Advanced Materials, Nanotechnologies, and Distributed Systems for Fabrication and Control Stefan cel Mare University of Suceava Suceava Romania
| | - Olga Sturdza
- Department of Human Health and Development College of Physical Exercise and Sport Stefan cel Mare University of Suceava Suceava Romania
- Suceava County Emergency Hospital Suceava Romania
| | - Roxana Filip
- Department of Human Health and Development College of Physical Exercise and Sport Stefan cel Mare University of Suceava Suceava Romania
- Suceava County Emergency Hospital Suceava Romania
| | - Mihai Covasa
- Department of Human Health and Development College of Physical Exercise and Sport Stefan cel Mare University of Suceava Suceava Romania
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Notable and Emerging Variants of SARS-CoV-2 Virus: A Quick Glance. Indian J Clin Biochem 2021; 36:451-458. [PMID: 34219999 PMCID: PMC8237041 DOI: 10.1007/s12291-021-00991-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent of coronavirus disease-2019 (COVID-19), is a highly contagious pathogenic coronavirus to emerge and spread in human populations. Although substantial exertions have been laid to avert spread of COVID-19 by therapeutic and preventive countermeasures, but emergence of SARS-CoV-2 variants as a result of mutations make the infection more ominous. New viral confers a higher nasopharyngeal viral load, increased viral transmissibility, higher infectiousness, immune escape, increased resistance to monoclonal/polyclonal antibodies from convalescence sera/vaccine, and an enhanced virulence. Thus, it is pertinent to monitor evolving mutations and genetic diversity of SARS-CoV-2 as it is decisive for understanding the viral variants. In this review we provide an overview of colloquial nomenclature and the genetic characteristics of different SARS-CoV-2 variants in the context of mutational changes of the circulating strains, transmissibility potential, virulence and infectivity.
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Zhao LP, Lybrand TP, Gilbert PB, Hawn TR, Schiffer JT, Stamatatos L, Payne TH, Carpp LN, Geraghty DE, Jerome KR. Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.06.15.448495. [PMID: 34159336 PMCID: PMC8219100 DOI: 10.1101/2021.06.15.448495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The emergence and establishment of SARS-CoV-2 variants of interest (VOI) and variants of concern (VOC) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking potentially relevant Spike protein mutations. We analyzed 167,893 Spike protein sequences from US COVID-19 cases (excluding 21,391 sequences from VOI/VOC strains) deposited at GISAID from January 19, 2020 to March 15, 2021. Alignment against the reference Spike protein sequence led to the identification of viral residue variants (VRVs), i.e., residues harboring a substitution compared to the reference strain. Next, generalized additive models were applied to model VRV temporal dynamics, to identify VRVs with significant and substantial dynamics (false discovery rate q-value <0.01; maximum VRV proportion > 10% on at least one day). Unsupervised learning was then applied to hierarchically organize VRVs by spatiotemporal patterns and identify VRV-haplotypes. Finally, homology modelling was performed to gain insight into potential impact of VRVs on Spike protein structure. We identified 90 VRVs, 71 of which have not previously been observed in a VOI/VOC, and 35 of which have emerged recently and are durably present. Our analysis identifies 17 VRVs ∼91 days earlier than their first corresponding VOI/VOC publication. Unsupervised learning revealed eight VRV-haplotypes of 4 VRVs or more, suggesting two emerging strains (B1.1.222 and B.1.234). Structural modeling supported potential functional impact of the D1118H and L452R mutations. The SLS approach equally monitors all Spike residues over time, independently of existing phylogenic classifications, and is complementary to existing genomic surveillance methods.
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Affiliation(s)
- Lue Ping Zhao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
| | - Terry P. Lybrand
- Quintepa Computing LLC; Nashville, TN, USA
- Department of Chemistry; Department of Pharmacology, Vanderbilt University; Nashville, TN, USA
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
| | - Thomas R. Hawn
- Department of Medicine, University of Washington School of Medicine; Seattle, WA, USA
- Department of Global Health, University of Washington; Seattle, WA, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
- Department of Medicine, University of Washington School of Medicine; Seattle, WA, USA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
- Department of Global Health, University of Washington; Seattle, WA, USA
| | - Thomas H. Payne
- Department of Medicine, University of Washington School of Medicine; Seattle, WA, USA
| | - Lindsay N. Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle; WA, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
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Huang SW, Wang SF. SARS-CoV-2 Entry Related Viral and Host Genetic Variations: Implications on COVID-19 Severity, Immune Escape, and Infectivity. Int J Mol Sci 2021; 22:3060. [PMID: 33802729 PMCID: PMC8002537 DOI: 10.3390/ijms22063060] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to display particular patterns of genetic diversity in the genome across geographical regions. These variations in the virus and genetic variation in human populations can determine virus transmissibility and coronavirus disease 2019 (COVID-19) severity. Genetic variations and immune differences in human populations could be the driving forces in viral evolution. Recently emerged SARS-CoV-2 variants show several mutations at the receptor binding domain in the spike (S) glycoprotein and contribute to immune escape and enhanced binding with angiotensin 1-converting enzyme 2 (ACE2). Since ACE2 and transmembrane protease serine 2 (TMPRSS2) play important roles in SARS-CoV-2 entry into the cell, genetic variation in these host entry-related proteins may be a driving force for positive selection in the SARS-CoV-2 S glycoprotein. Dendritic or liver/lymph cell-specific intercellular adhesion molecule (ICAM)-3-grabbing non-integrin is also known to play vital roles in several pathogens. Genetic variations of these host proteins may affect the susceptibility to SARS-CoV-2. This review summarizes the latest research to describe the impacts of genetic variation in the viral S glycoprotein and critical host proteins and aims to provide better insights for understanding transmission and pathogenesis and more broadly for developing vaccine/antiviral drugs and precision medicine strategies, especially for high risk populations with genetic risk variants.
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Affiliation(s)
- Szu-Wei Huang
- Model Development Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Clinical Microbiology Laboratory, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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