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LIBRIS Formathandbok  (Information om MARC21)
FältnamnIndikatorerMetadata
00007359nam a2200661 4500
001oai:DiVA.org:liu-206227
003SwePub
008240813s2023 | |||||||||||000 ||eng|
0247 a https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-2062272 URI
0247 a https://doi.org/10.2139/ssrn.46149382 DOI
040 a (SwePub)liu
041 a engb eng
042 9 SwePub
072 7a vet2 swepub-contenttype
072 7a ovr2 swepub-publicationtype
1001 a Selvavinayagam, Sivaprakasam T.u Directorate of Public Health and Preventive Medicine - State Public Health Laboratory; Directorate of Public Health and Preventive Medicine4 aut
2451 0a Evolution of the Omicron B.1.1.529 Sars-Cov-2 and its Variants in Tamil Nadu, India – a State-Wide Prospective Longitudinal Genomic Surveillance
264 1c 2023
338 a print2 rdacarrier
500 a Funding: National Health Mission (India), SIDA SARC, VINNMER (Sweden), ORIP/NIH (USA). The findings, interpretations and conclusions expressed in the paper are entirely those of the authors, and do not represent the views of the National Health Mission (India), SIDA SARC, VINNMER (Sweden), ORIP/NIH (USA), or the countries they represent.
520 a Background: The emergence of the omicron SARS-CoV-2 variant beholding many mutations, especially in the spike (S) protein severely threatens global health. With an aim to understand the mutational pattern of the variant and its genetic interrelationship in the Indian population, here we prospectively followed the viral evolution and transmission between December 2021 and March 2023 in Tamil Nadu.Methods: A total of 11526 nasopharyngeal and oropharyngeal swabs (6431 males, 5095 females including 603 children) collected from across the 38 districts of Tamil Nadu were subjected to WGS. Of the 10663 samples (92.5%) positive for omicron variants, 1688 were sequenced at the State Public Health Laboratory. We longitudinally studied the evolutionary dynamics of the different omicron variants, starting from the first detected case (B.1.1.529) to the recently reported recombinant XBB variants by sequencing the S gene and by performing phylo-geographic and molecular modeling analyses.Findings: Administration of a booster dose was associated with reduced risk of hospitalization and death. BA.1 sub-variants and BA.2.75 were associated with increased risk of severe disease, whereas BA.1 and BA.2 were associated with increased risk of death. High quality WGS data from 150 samples revealed six major omicron clusters and several other sub-clusters. Seven variants in the same BA lineages with different divergences in the S protein were noticed. Of the 5009 mutations detected, the highest was seen in the receptor-binding domain (RBD) followed by the N-terminal domain (NTD) in varying proportions among the different omicron lineages. Importantly, the mutations were observed in the sub-domain (SD1/2) furin cleavage site, fusion peptide (FP), and the heptapeptide repeat sequence (HR1) regions. Notably, unique mutations Y473I, P479F, C480F, V483T, E484C, G485T, P491G, L492K, S494M, Y495C, and G496Q were detected in BA.2.43 whereas A475Q and T478S occurred in the RBD domain of the BA.2.43 variant. The XBB variant showed 41 different mutations between the HR1 and HR2 domains of the S2 subunit. Molecular modeling using BA.2 lineage as a template for seven divergent proteins showed that BA.2.12.1, BA.4 and BA.5 exhibited strong binding affinity towards ACE2.Interpretation: The high frequency of mutations in the RBD highlights the wider distribution of vaccine escape-variants that would impact the structural and functional attributes of the omicron variant in the population. Further, our work provides key insights on the evolutionary pattern leading to the identification of seven divergent variants of omicron in Tamil Nadu, India.
650 7a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Medicinsk genetik0 (SwePub)301072 hsv//swe
650 7a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Medical Genetics0 (SwePub)301072 hsv//eng
653 a COVID-19
653 a Dynamics
653 a Evolution
653 a SARS-Cov-2
653 a Omicron
653 a Morbidity
653 a India
7001 a Suvaithenamudhan, Suvaiyarasanu Central University of Tamil Nadu - Department of Infection and Inflammation4 aut
7001 a Yong, Yean Kongu Xiamen University - Laboratory Centre4 aut
7001 a Kannan, Hemashreeu Directorate of Public Health and Preventive Medicine - State Public Health Laboratory4 aut
7001 a Rajeshkumar, Manivannanu Directorate of Public Health and Preventive Medicine - State Public Health Laboratory4 aut
7001 a Kumaresan, Anandhazhvaru Directorate of Public Health and Preventive Medicine - State Public Health Laboratory4 aut
7001 a Kannan, Meganathanu Central University of Tamil Nadu - Department of Blood and Vascular Biology4 aut
7001 a Gopalan, Natarajanu Central University of Tamil Nadu - Department of Epidemiology and Public Health4 aut
7001 a Vignesh, Ramachandranu Royal College of Medicine Perak - Preclinical Department4 aut
7001 a Murugesan, Amudhanu Government Theni Medical College - Department of Microbiology4 aut
7001 a Sivasankaran, Munusamy P.u Seattle Children's Research Institute4 aut
7001 a Cheedarla, Narayanaiahu Emory University4 aut
7001 a Anshad, Abdul R.u Central University of Tamil Nadu - Department of Infection and Inflammation4 aut
7001 a Govindaraj, Sakthivelu Emory University - Department of Pathology4 aut
7001 a Zhang, Yingu Xiamen University Malaysia Campus - Chemical Engineering4 aut
7001 a Tan, Hong Yienu Xiamen University Malaysia Campus - School of Traditional Chinese Medicine4 aut
7001 a Larsson, Marie,d 1966-u Linköpings universitet,Medicinska fakulteten,Avdelningen för molekylär medicin och virologi4 aut0 (Swepub:liu)marla67
7001 a Shanmugam, Saravananu Saveetha University - Saveetha Institute of Medical And Technical Sciences4 aut
7001 a Balakrishnan, Pachamuthuu Saveetha University - Centre for Infectious Diseases4 aut
7001 a Kulanthaivel, Langeswaranu Alagappa University4 aut
7001 a Singh, Kamalendrau University of Missouri at Columbia - Bond Life Science Center4 aut
7001 a Joseph, Narcisseu University Putra Malaysia - Department of Medical Microbiology and Parasitology4 aut
7001 a Velu, Vijayakumaru Emory University - Department of Pathology4 aut
7001 a Byrareddy, Siddappau University of Nebraska at Omaha - Department of Pharmacology and Experimental Neuroscience4 aut
7001 a Shankar, Esaki Muthuu Central University of Tamil Nadu - Department of Infection and Inflammation4 aut
7001 a Raju, Sivadossu Directorate of Public Health and Preventive Medicine - State Public Health Laboratory4 aut
7102 a Directorate of Public Health and Preventive Medicine - State Public Health Laboratory; Directorate of Public Health and Preventive Medicineb Central University of Tamil Nadu - Department of Infection and Inflammation4 org
8564 8u https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-206227
8564 8u https://doi.org/10.2139/ssrn.4614938

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