1
|
Yadav S, Zaman K, Bashyal P, Bhatta R, Bhandari S, Mohanty A, Sah R. Newer emerging SARS-COV2 variant: Omicron EG.5. Ann Med Surg (Lond) 2023; 85:5845-5846. [PMID: 38098560 PMCID: PMC10718343 DOI: 10.1097/ms9.0000000000001386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/28/2023] [Indexed: 12/17/2023] Open
Affiliation(s)
- Shailendra Yadav
- Malaria Division, ICMR-Regional Medical Research Centre Dibrugarh (ICMR-RMRC Dibrugarh), Dibrugarh, Assam
| | - Kamran Zaman
- Department of Microbiology and Molecular Biology, Indian Council of Medical Research—National Institute of Traditional Medicine Belagavi (ICMR-NITM Belagavi), Karnataka
| | | | | | | | - Aroop Mohanty
- Department of Microbiology, All India Institute of Medical Sciences, Gorakhpur
| | - Ranjit Sah
- Dr. D.Y Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
- Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| |
Collapse
|
2
|
Dorji T, Dorji K, Wangchuk T, Pelki T, Gyeltshen S. Genetic diversity and evolutionary patterns of SARS-CoV-2 among the Bhutanese population during the pandemic. Osong Public Health Res Perspect 2023; 14:494-507. [PMID: 38204428 PMCID: PMC10788421 DOI: 10.24171/j.phrp.2023.0209] [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: 07/26/2023] [Revised: 10/12/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic, caused by a dynamic virus, has had a profound global impact. Despite declining global COVID-19 cases and mortality rates, the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants remains a major concern. This study provides a comprehensive analysis of the genomic sequences of SARS-CoV-2 within the Bhutanese population during the pandemic. The primary aim was to elucidate the molecular epidemiology and evolutionary patterns of SARS-CoV-2 in Bhutan, with a particular focus on genetic variations and lineage dynamics. METHODS Whole-genome sequences of SARS-CoV-2 collected from Bhutan between May 2020 and February 2023 (n=135) were retrieved from the Global Initiative on Sharing All Influenza Database. RESULTS The SARS-CoV-2 variants in Bhutan were predominantly classified within the Nextstrain clade 20A (31.1%), followed by clade 21L (20%) and clade 22D (15.6%). We identified 26 Pangolin lineages with variations in their spatial and temporal distribution. Bayesian time-scaled phylogenetic analysis estimated the time to the most recent common ancestor as February 15, 2020, with a substitution rate of 0.97×10-3 substitutions per site per year. Notably, the spike glycoprotein displayed the highest mutation frequency among major viral proteins, with 116 distinct mutations, including D614G. The Bhutanese isolates also featured mutations such as E484K, K417N, and S477N in the spike protein, which have implications for altered viral properties. CONCLUSION This is the first study to describe the genetic diversity of SARS-CoV-2 circulating in Bhutan during the pandemic, and this data can inform public health policies and strategies for preventing future outbreaks in Bhutan.
Collapse
Affiliation(s)
- Tshering Dorji
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Kunzang Dorji
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Tandin Wangchuk
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Tshering Pelki
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Sonam Gyeltshen
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| |
Collapse
|
3
|
Garg KM, Lamba V, Chattopadhyay B. Genomic Insights Into the Evolution and Demographic History of the SARS-CoV-2 Omicron Variant: Population Genomics Approach. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2023; 4:e40673. [PMID: 37456139 PMCID: PMC10331448 DOI: 10.2196/40673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 03/07/2023] [Accepted: 05/05/2023] [Indexed: 07/18/2023]
Abstract
Background A thorough understanding of the patterns of genetic subdivision in a pathogen can provide crucial information that is necessary to prevent disease spread. For SARS-CoV-2, the availability of millions of genomes makes this task analytically challenging, and traditional methods for understanding genetic subdivision often fail. Objective The aim of our study was to use population genomics methods to identify the subtle subdivisions and demographic history of the Omicron variant, in addition to those captured by the Pango lineage. Methods We used a combination of an evolutionary network approach and multivariate statistical protocols to understand the subdivision and spread of the Omicron variant. We identified subdivisions within the BA.1 and BA.2 lineages and further identified the mutations associated with each cluster. We further characterized the overall genomic diversity of the Omicron variant and assessed the selection pressure for each of the genetic clusters identified. Results We observed concordant results, using two different methods to understand genetic subdivision. The overall pattern of subdivision in the Omicron variant was in broad agreement with the Pango lineage definition. Further, 1 cluster of the BA.1 lineage and 3 clusters of the BA.2 lineage revealed statistically significant signatures of selection or demographic expansion (Tajima's D<-2), suggesting the role of microevolutionary processes in the spread of the virus. Conclusions We provide an easy framework for assessing the genetic structure and demographic history of SARS-CoV-2, which can be particularly useful for understanding the local history of the virus. We identified important mutations that are advantageous to some lineages of Omicron and aid in the transmission of the virus. This is crucial information for policy makers, as preventive measures can be designed to mitigate further spread based on a holistic understanding of the variability of the virus and the evolutionary processes aiding its spread.
Collapse
Affiliation(s)
- Kritika M Garg
- Department of Biology Ashoka University Sonipat India
- Centre for Interdisciplinary Archaeological Research Ashoka University Sonipat India
| | - Vinita Lamba
- Trivedi School of Biosciences Ashoka University Sonipat India
- J William Fulbright College of Arts and Sciences Department of Biological Sciences University of Arkansas Fayetteville, AR United States
| | - Balaji Chattopadhyay
- Department of Biology Ashoka University Sonipat India
- Trivedi School of Biosciences Ashoka University Sonipat India
| |
Collapse
|
4
|
Singh J, Anantharaj A, Panwar A, Rani C, Bhardwaj M, Kumar P, Chattopadhyay P, Devi P, Maurya R, Mishra P, Pandey AK, Pandey R, Medigeshi GR. BA.1, BA.2 and BA.2.75 variants show comparable replication kinetics, reduced impact on epithelial barrier and elicit cross-neutralizing antibodies. PLoS Pathog 2023; 19:e1011196. [PMID: 36827451 PMCID: PMC9994724 DOI: 10.1371/journal.ppat.1011196] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 03/08/2023] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
The Omicron variant of SARS-CoV-2 is capable of infecting unvaccinated, vaccinated and previously-infected individuals due to its ability to evade neutralization by antibodies. With multiple sub-lineages of Omicron emerging in the last 12 months, there is inadequate information on the quantitative antibody response generated upon natural infection with Omicron variant and whether these antibodies offer cross-protection against other sub-lineages of Omicron variant. In this study, we characterized the growth kinetics of Kappa, Delta and Omicron variants of SARS-CoV-2 in Calu-3 cells. Relatively higher amounts infectious virus titers, cytopathic effect and disruption of epithelial barrier functions was observed with Delta variant whereas infection with Omicron sub-lineages led to a more robust induction of interferon pathway, lower level of virus replication and mild effect on epithelial barrier. The replication kinetics of BA.1, BA.2 and BA.2.75 sub-lineages of the Omicron variant were comparable in cell culture and natural infection in a subset of individuals led to a significant increase in binding and neutralizing antibodies to the Delta variant and all the three sub-lineages of Omicron but the level of neutralizing antibodies were lowest against the BA.2.75 variant. Finally, we show that Cu2+, Zn2+ and Fe2+ salts inhibited in vitro RdRp activity but only Cu2+ and Fe2+ inhibited both the Delta and Omicron variants in cell culture. Thus, our results suggest that high levels of interferons induced upon infection with Omicron variant may counter virus replication and spread. Waning neutralizing antibody titers rendered subjects susceptible to infection by Omicron variants and natural Omicron infection elicits neutralizing antibodies that can cross-react with other sub-lineages of Omicron and other variants of concern.
Collapse
Affiliation(s)
- Janmejay Singh
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Anbalagan Anantharaj
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Aleksha Panwar
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Chitra Rani
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Monika Bhardwaj
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Parveen Kumar
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priti Devi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pallavi Mishra
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anil Kumar Pandey
- Employees State Insurance Corporation Medical College and Hospital, Faridabad, Haryana, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Guruprasad R. Medigeshi
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| |
Collapse
|