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Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants
The rapid spread of SARS-CoV-2 variants in the global population is indicative of the development of selective advantages in emerging virus strains. Here, we performed a case-control investigation of the clinical and demographic characteristics, clinical history, and virological markers to predict d...
Autores principales: | , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9540788/ https://www.ncbi.nlm.nih.gov/pubmed/36211690 http://dx.doi.org/10.3389/fpubh.2022.1018399 |
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author | Selvavinayagam, Sivaprakasam T. Yong, Yean Kong Joseph, Narcisse Hemashree, Kannan Tan, Hong Yien Zhang, Ying Rajeshkumar, Manivannan Kumaresan, Anandhazhvar Kalpana, Raghu Kalaivani, Vasudevan Monika, Ayyagari Venkata Devi Suvaithenamudhan, Suvaiyarasan Kannan, Meganathan Murugesan, Amudhan Narayanasamy, Krishnasamy Palani, Sampath Larsson, Marie Shankar, Esaki M. Raju, Sivadoss |
author_facet | Selvavinayagam, Sivaprakasam T. Yong, Yean Kong Joseph, Narcisse Hemashree, Kannan Tan, Hong Yien Zhang, Ying Rajeshkumar, Manivannan Kumaresan, Anandhazhvar Kalpana, Raghu Kalaivani, Vasudevan Monika, Ayyagari Venkata Devi Suvaithenamudhan, Suvaiyarasan Kannan, Meganathan Murugesan, Amudhan Narayanasamy, Krishnasamy Palani, Sampath Larsson, Marie Shankar, Esaki M. Raju, Sivadoss |
author_sort | Selvavinayagam, Sivaprakasam T. |
collection | PubMed |
description | The rapid spread of SARS-CoV-2 variants in the global population is indicative of the development of selective advantages in emerging virus strains. Here, we performed a case-control investigation of the clinical and demographic characteristics, clinical history, and virological markers to predict disease progression in hospitalized adults for COVID-19 between December 2021 and January 2022 in Chennai, India. COVID-19 diagnosis was made by a commercial TaqPath COVID-19 RT-PCR, and WGS was performed with the Ion Torrent Next Generation Sequencing System. High-quality (<5% of N) complete sequences of 73 Omicron B.1.1.529 variants were randomly selected for phylogenetic analysis. SARS-CoV-2 viral load, number of comorbidities, and severe disease presentation were independently associated with a shorter time-to-death. Strikingly, this was observed among individuals infected with Omicron BA.2 but not among those with the BA.1.1.529, BA.1.1, or the Delta B.1.617.2 variants. Phylogenetic analysis revealed severe cases predominantly clustering under the BA.2 lineage. Sequence analyses showed 30 mutation sites in BA.1.1.529 and 33 in BA.1.1. The mutations unique to BA.2 were T19I, L24S, P25del, P26del, A27S, V213G, T376A, D405N and R408S. Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and the Omicron BA.1.1.529 variant but not with Omicron BA.1.1 or BA.2 suggests that the newer strains are largely immune escape variants. The number of vaccine doses received was independently associated with increased odds of developing asymptomatic disease or recovery. We propose that the novel mutations reported herein could likely bear a significant impact on the clinical characteristics, disease progression, and epidemiological aspects of COVID-19. Surging rates of mutations and the emergence of eclectic variants of SARS-CoV-2 appear to impact disease dynamics. |
format | Online Article Text |
id | pubmed-9540788 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95407882022-10-08 Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants Selvavinayagam, Sivaprakasam T. Yong, Yean Kong Joseph, Narcisse Hemashree, Kannan Tan, Hong Yien Zhang, Ying Rajeshkumar, Manivannan Kumaresan, Anandhazhvar Kalpana, Raghu Kalaivani, Vasudevan Monika, Ayyagari Venkata Devi Suvaithenamudhan, Suvaiyarasan Kannan, Meganathan Murugesan, Amudhan Narayanasamy, Krishnasamy Palani, Sampath Larsson, Marie Shankar, Esaki M. Raju, Sivadoss Front Public Health Public Health The rapid spread of SARS-CoV-2 variants in the global population is indicative of the development of selective advantages in emerging virus strains. Here, we performed a case-control investigation of the clinical and demographic characteristics, clinical history, and virological markers to predict disease progression in hospitalized adults for COVID-19 between December 2021 and January 2022 in Chennai, India. COVID-19 diagnosis was made by a commercial TaqPath COVID-19 RT-PCR, and WGS was performed with the Ion Torrent Next Generation Sequencing System. High-quality (<5% of N) complete sequences of 73 Omicron B.1.1.529 variants were randomly selected for phylogenetic analysis. SARS-CoV-2 viral load, number of comorbidities, and severe disease presentation were independently associated with a shorter time-to-death. Strikingly, this was observed among individuals infected with Omicron BA.2 but not among those with the BA.1.1.529, BA.1.1, or the Delta B.1.617.2 variants. Phylogenetic analysis revealed severe cases predominantly clustering under the BA.2 lineage. Sequence analyses showed 30 mutation sites in BA.1.1.529 and 33 in BA.1.1. The mutations unique to BA.2 were T19I, L24S, P25del, P26del, A27S, V213G, T376A, D405N and R408S. Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and the Omicron BA.1.1.529 variant but not with Omicron BA.1.1 or BA.2 suggests that the newer strains are largely immune escape variants. The number of vaccine doses received was independently associated with increased odds of developing asymptomatic disease or recovery. We propose that the novel mutations reported herein could likely bear a significant impact on the clinical characteristics, disease progression, and epidemiological aspects of COVID-19. Surging rates of mutations and the emergence of eclectic variants of SARS-CoV-2 appear to impact disease dynamics. Frontiers Media S.A. 2022-09-20 /pmc/articles/PMC9540788/ /pubmed/36211690 http://dx.doi.org/10.3389/fpubh.2022.1018399 Text en Copyright © 2022 Selvavinayagam, Yong, Joseph, Hemashree, Tan, Zhang, Rajeshkumar, Kumaresan, Kalpana, Kalaivani, Monika, Suvaithenamudhan, Kannan, Murugesan, Narayanasamy, Palani, Larsson, Shankar and Raju. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Public Health Selvavinayagam, Sivaprakasam T. Yong, Yean Kong Joseph, Narcisse Hemashree, Kannan Tan, Hong Yien Zhang, Ying Rajeshkumar, Manivannan Kumaresan, Anandhazhvar Kalpana, Raghu Kalaivani, Vasudevan Monika, Ayyagari Venkata Devi Suvaithenamudhan, Suvaiyarasan Kannan, Meganathan Murugesan, Amudhan Narayanasamy, Krishnasamy Palani, Sampath Larsson, Marie Shankar, Esaki M. Raju, Sivadoss Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants |
title | Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants |
title_full | Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants |
title_fullStr | Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants |
title_full_unstemmed | Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants |
title_short | Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants |
title_sort | low sars-cov-2 viral load among vaccinated individuals infected with delta b.1.617.2 and omicron ba.1.1.529 but not with omicron ba.1.1 and ba.2 variants |
topic | Public Health |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9540788/ https://www.ncbi.nlm.nih.gov/pubmed/36211690 http://dx.doi.org/10.3389/fpubh.2022.1018399 |
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