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Selvavinayagam ST, Karishma SJ, Hemashree K, Yong YK, Suvaithenamudhan S, Rajeshkumar M, Aswathy B, Kalaivani V, Priyanka J, Kumaresan A, Kannan M, Gopalan N, Chandramathi S, Vignesh R, Murugesan A, Anshad AR, Ganesh B, Joseph N, Babu H, Govindaraj S, Larsson M, Kandasamy SL, Palani S, Singh K, Byrareddy SN, Velu V, Shankar EM, Raju S. Clinical characteristics and novel mutations of omicron subvariant XBB in Tamil Nadu, India - a cohort study. Lancet Reg Health Southeast Asia 2023; 19:100272. [PMID: 38076717 PMCID: PMC10709680 DOI: 10.1016/j.lansea.2023.100272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/13/2023] [Accepted: 08/20/2023] [Indexed: 04/14/2024]
Abstract
BACKGROUND Despite the continued vaccination efforts, there had been a surge in breakthrough infections, and the emergence of the B.1.1.529 omicron variant of SARS-CoV-2 in India. There is a paucity of information globally on the role of newer XBB variants in community transmission. Here, we investigated the mutational patterns among hospitalised patients infected with the XBB omicron sub-variant, and checked if there was any association between the rise in the number of COVID-19 cases and the observed novel mutations in Tamil Nadu, India. METHODS Nasopharyngeal and oropharyngeal swabs, collected from symptomatic and asymptomatic COVID-19 patients were subjected to real-time PCR followed by Next Generation Sequencing (NGS) to rule out the ambiguity of mutations in viruses isolated from the patients (n = 98). Using the phylogenetic association, the mutational patterns were used to corroborate clinico-demographic characteristics and disease severity among the patients. FINDINGS Overall, we identified 43 mutations in the S gene across 98 sequences, of which two were novel mutations (A27S and T747I) that have not been reported previously with XBB sub-variants in the available literature. Additionally, the XBB sequences from our cohort had more mutations than omicron B.1.1.529. The phylogenetic analysis comprising six major branches clearly showed convergent evolution of XBB. Our data suggests that age, and underlying conditions (e.g., diabetes, hypertension, and cardiovascular disease) or secondary complications confers increased susceptibility to infection rather than vaccination status or prior exposure. Many vaccinated individuals showed evidence of a breakthrough infection, with XBB.3 being the predominant variant identified in the study population. INTERPRETATION Our study indicates that the XBB variant is highly evasive from available vaccines and may be more transmissible, and potentially could emerge as the 'next' predominant variant, which likely could overwhelm the existing variants of SARS-CoV-2 omicron variants. FUNDING National Health Mission (India), SIDASARC, VINNMER (Sweden), ORIP/NIH (USA).
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Affiliation(s)
- Sivaprakasam T. Selvavinayagam
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Sree J. Karishma
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Kannan Hemashree
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Yean K. Yong
- Laboratory Centre, Xiamen University Malaysia, Sepang, Selangor 43 900, Malaysia
| | - Suvaiyarasan Suvaithenamudhan
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
- Department of Bioinformatics, Bishop Heber College, Tiruchirappalli, Tamil Nadu 620 017, India
| | - Manivannan Rajeshkumar
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Bijulal Aswathy
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Vasudevan Kalaivani
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Jayapal Priyanka
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Anandhazhvar Kumaresan
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Meganathan Kannan
- Blood and Vascular Biology, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Natarajan Gopalan
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Samudi Chandramathi
- Department of Medical Microbiology, University of Malaya, Lembah Pantai, Kuala Lumpur 50603, Malaysia
| | - Ramachandran Vignesh
- Faculty of Medicine, Preclinical Department, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh, Perak 30450, Malaysia
| | - Amudhan Murugesan
- Department of Microbiology, The Government Theni Medical College and Hospital, Theni, India
| | - Abdul R. Anshad
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Balasubramanian Ganesh
- National Institute of Epidemiology, Indian Council of Medical Research, Ayappakkam, Chennai 600 077, India
| | - Narcisse Joseph
- Department of Medical Microbiology, Universiti Putra Malaysia, Kuala Lumpur, Malaysia
| | - Hemalatha Babu
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329, USA
| | - Sakthivel Govindaraj
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329, USA
| | - Marie Larsson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Shree L. Kandasamy
- Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Sampath Palani
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Kamalendra Singh
- Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Vijayakumar Velu
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329, USA
| | - Esaki M. Shankar
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Sivadoss Raju
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
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Spratt AN, Kannan SR, Sharma K, Sachdev S, Kandasamy SL, Sönnerborg A, Lorson CL, Singh K. Continued Complexity of Mutations in Omicron Sublineages. Biomedicines 2022; 10:biomedicines10102593. [PMID: 36289855 PMCID: PMC9599772 DOI: 10.3390/biomedicines10102593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/03/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
The latest SARS-CoV-2 variant of concern (VOC), Omicron (B.1.1.529), has diversified into more than 300 sublineages. With an expanding number of newly emerging sublineages, the mutation profile is also becoming complicated. There exist mutually exclusive and revertant mutations in different sublineages. Omicron sublineages share some common mutations with previous VOCs (Alpha, Beta, Gamma, and Delta), indicating an evolutionary relationship between these VOCs. A diverse mutation profile at the spike–antibody interface, flexibility of the regions harboring mutations, mutation types, and coexisting mutations suggest that SARS-CoV-2’s evolution is far from over.
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Affiliation(s)
- Austin N. Spratt
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Saathvik R. Kannan
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Kalicharan Sharma
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
| | - Shrikesh Sachdev
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Shree L. Kandasamy
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Anders Sönnerborg
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Christian L. Lorson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, 17177 Stockholm, Sweden
- Correspondence: or
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