Search: onr:"swepub:oai:DiVA.org:liu-206227" > Evolution of the Om...
Fältnamn | Indikatorer | Metadata |
---|---|---|
000 | 07359nam a2200661 4500 | |
001 | oai:DiVA.org:liu-206227 | |
003 | SwePub | |
008 | 240813s2023 | |||||||||||000 ||eng| | |
024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-2062272 URI |
024 | 7 | a https://doi.org/10.2139/ssrn.46149382 DOI |
040 | a (SwePub)liu | |
041 | a engb eng | |
042 | 9 SwePub | |
072 | 7 | a vet2 swepub-contenttype |
072 | 7 | a ovr2 swepub-publicationtype |
100 | 1 | a Selvavinayagam, Sivaprakasam T.u Directorate of Public Health and Preventive Medicine - State Public Health Laboratory; Directorate of Public Health and Preventive Medicine4 aut |
245 | 1 0 | a 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 | 1 | c 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 | 7 | a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Medicinsk genetik0 (SwePub)301072 hsv//swe |
650 | 7 | a 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 | |
700 | 1 | a Suvaithenamudhan, Suvaiyarasanu Central University of Tamil Nadu - Department of Infection and Inflammation4 aut |
700 | 1 | a Yong, Yean Kongu Xiamen University - Laboratory Centre4 aut |
700 | 1 | a Kannan, Hemashreeu Directorate of Public Health and Preventive Medicine - State Public Health Laboratory4 aut |
700 | 1 | a Rajeshkumar, Manivannanu Directorate of Public Health and Preventive Medicine - State Public Health Laboratory4 aut |
700 | 1 | a Kumaresan, Anandhazhvaru Directorate of Public Health and Preventive Medicine - State Public Health Laboratory4 aut |
700 | 1 | a Kannan, Meganathanu Central University of Tamil Nadu - Department of Blood and Vascular Biology4 aut |
700 | 1 | a Gopalan, Natarajanu Central University of Tamil Nadu - Department of Epidemiology and Public Health4 aut |
700 | 1 | a Vignesh, Ramachandranu Royal College of Medicine Perak - Preclinical Department4 aut |
700 | 1 | a Murugesan, Amudhanu Government Theni Medical College - Department of Microbiology4 aut |
700 | 1 | a Sivasankaran, Munusamy P.u Seattle Children's Research Institute4 aut |
700 | 1 | a Cheedarla, Narayanaiahu Emory University4 aut |
700 | 1 | a Anshad, Abdul R.u Central University of Tamil Nadu - Department of Infection and Inflammation4 aut |
700 | 1 | a Govindaraj, Sakthivelu Emory University - Department of Pathology4 aut |
700 | 1 | a Zhang, Yingu Xiamen University Malaysia Campus - Chemical Engineering4 aut |
700 | 1 | a Tan, Hong Yienu Xiamen University Malaysia Campus - School of Traditional Chinese Medicine4 aut |
700 | 1 | a Larsson, Marie,d 1966-u Linköpings universitet,Medicinska fakulteten,Avdelningen för molekylär medicin och virologi4 aut0 (Swepub:liu)marla67 |
700 | 1 | a Shanmugam, Saravananu Saveetha University - Saveetha Institute of Medical And Technical Sciences4 aut |
700 | 1 | a Balakrishnan, Pachamuthuu Saveetha University - Centre for Infectious Diseases4 aut |
700 | 1 | a Kulanthaivel, Langeswaranu Alagappa University4 aut |
700 | 1 | a Singh, Kamalendrau University of Missouri at Columbia - Bond Life Science Center4 aut |
700 | 1 | a Joseph, Narcisseu University Putra Malaysia - Department of Medical Microbiology and Parasitology4 aut |
700 | 1 | a Velu, Vijayakumaru Emory University - Department of Pathology4 aut |
700 | 1 | a Byrareddy, Siddappau University of Nebraska at Omaha - Department of Pharmacology and Experimental Neuroscience4 aut |
700 | 1 | a Shankar, Esaki Muthuu Central University of Tamil Nadu - Department of Infection and Inflammation4 aut |
700 | 1 | a Raju, Sivadossu Directorate of Public Health and Preventive Medicine - State Public Health Laboratory4 aut |
710 | 2 | 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 |
856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-206227 |
856 | 4 8 | u https://doi.org/10.2139/ssrn.4614938 |
Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.
Copy and save the link in order to return to this view