A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India
Background: Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-08-01
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| Series: | Journal of Infection and Public Health |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1876034123002113 |
| _version_ | 1797786585185386496 |
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| author | Divya Niveditha Soumen Khan Ajinkya Khilari Sanica Nadkarni Unnati Bhalerao Pradnya Kadam Ritu Yadav Jugal B. Kanekar Nikita Shah Bhagyashree Likhitkar Rutuja Sawant Shikha Thakur Manisha Tupekar Dhriti Nagar Anjani G. Rao Rutuja Jagtap Shraddha Jogi Madhuri Belekar Maitreyee Pathak Priyanki Shah Shatakshi Ranade Nikhil Phadke Rashmita Das Suvarna Joshi Rajesh Karyakarte Aurnab Ghose Narendra Kadoo LS Shashidhara Joy Merwin Monteiro Dhanasekaran Shanmugam Anu Raghunathan Krishanpal Karmodiya |
| author_facet | Divya Niveditha Soumen Khan Ajinkya Khilari Sanica Nadkarni Unnati Bhalerao Pradnya Kadam Ritu Yadav Jugal B. Kanekar Nikita Shah Bhagyashree Likhitkar Rutuja Sawant Shikha Thakur Manisha Tupekar Dhriti Nagar Anjani G. Rao Rutuja Jagtap Shraddha Jogi Madhuri Belekar Maitreyee Pathak Priyanki Shah Shatakshi Ranade Nikhil Phadke Rashmita Das Suvarna Joshi Rajesh Karyakarte Aurnab Ghose Narendra Kadoo LS Shashidhara Joy Merwin Monteiro Dhanasekaran Shanmugam Anu Raghunathan Krishanpal Karmodiya |
| author_sort | Divya Niveditha |
| collection | DOAJ |
| description | Background: Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data. Methods: A city-wide network of researchers, clinicians, and pathology diagnostic laboratories was formed for genome surveillance of COVID-19 in Pune, India. The genomic landscapes of 10,496 sequenced samples of SARS-CoV-2 driving peaks of infection in Pune between December-2020 to March-2022, were determined. As a modern response to the pandemic, a “band of five” outbreak data analytics approach was used. This integrated the genomic data (Band 1) of the virus through molecular phylogenetics with key outbreak data including sample collection dates and case numbers (Band 2), demographics like age and gender (Band 3–4), and geospatial mapping (Band 5). Results: The transmission dynamics of VOCs in 10,496 sequenced samples identified B.1.617.2 (Delta) and BA(x) (Omicron formerly known as B.1.1.529) variants as drivers of the second and third peaks of infection in Pune. Spike Protein mutational profiling during pre and post-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified a highly divergent BA.1 from Pune in addition to recombinant X lineages, XZ, XQ, and XM. Conclusions: The band of five outbreak data analytics approach, which integrates five different types of data, highlights the importance of a strong surveillance system with high-quality meta-data for understanding the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. These findings have important implications for pandemic preparedness and could be critical tools for understanding and responding to future outbreaks. |
| first_indexed | 2024-03-13T01:09:59Z |
| format | Article |
| id | doaj.art-a742dff176564f47ae3b51c4605fbcb9 |
| institution | Directory Open Access Journal |
| issn | 1876-0341 |
| language | English |
| last_indexed | 2024-03-13T01:09:59Z |
| publishDate | 2023-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Infection and Public Health |
| spelling | doaj.art-a742dff176564f47ae3b51c4605fbcb92023-07-06T04:17:35ZengElsevierJournal of Infection and Public Health1876-03412023-08-0116812901300A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, IndiaDivya Niveditha0Soumen Khan1Ajinkya Khilari2Sanica Nadkarni3Unnati Bhalerao4Pradnya Kadam5Ritu Yadav6Jugal B. Kanekar7Nikita Shah8Bhagyashree Likhitkar9Rutuja Sawant10Shikha Thakur11Manisha Tupekar12Dhriti Nagar13Anjani G. Rao14Rutuja Jagtap15Shraddha Jogi16Madhuri Belekar17Maitreyee Pathak18Priyanki Shah19Shatakshi Ranade20Nikhil Phadke21Rashmita Das22Suvarna Joshi23Rajesh Karyakarte24Aurnab Ghose25Narendra Kadoo26LS Shashidhara27Joy Merwin Monteiro28Dhanasekaran Shanmugam29Anu Raghunathan30Krishanpal Karmodiya31Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaBiochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, IndiaChemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaChemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, IndiaBiochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaBiochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaChemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaChemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, IndiaChemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, IndiaChemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaThe Pune Knowledge Cluster (PKC), Savitribai Phule Pune University, Ganeshkhind Road, 411007 Pune, IndiaGenePath Diagnostics India Private Limited, Pune 411004, IndiaGenePath Diagnostics India Private Limited, Pune 411004, IndiaByramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, IndiaByramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, IndiaByramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaBiochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University, Ganeshkhind Road, 411007 Pune, IndiaDepartment of Earth and Climate Science, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; Department of Data Science, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, IndiaBiochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, IndiaChemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India; Corresponding author at: Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, IndiaDepartment of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; Corresponding author.Background: Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data. Methods: A city-wide network of researchers, clinicians, and pathology diagnostic laboratories was formed for genome surveillance of COVID-19 in Pune, India. The genomic landscapes of 10,496 sequenced samples of SARS-CoV-2 driving peaks of infection in Pune between December-2020 to March-2022, were determined. As a modern response to the pandemic, a “band of five” outbreak data analytics approach was used. This integrated the genomic data (Band 1) of the virus through molecular phylogenetics with key outbreak data including sample collection dates and case numbers (Band 2), demographics like age and gender (Band 3–4), and geospatial mapping (Band 5). Results: The transmission dynamics of VOCs in 10,496 sequenced samples identified B.1.617.2 (Delta) and BA(x) (Omicron formerly known as B.1.1.529) variants as drivers of the second and third peaks of infection in Pune. Spike Protein mutational profiling during pre and post-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified a highly divergent BA.1 from Pune in addition to recombinant X lineages, XZ, XQ, and XM. Conclusions: The band of five outbreak data analytics approach, which integrates five different types of data, highlights the importance of a strong surveillance system with high-quality meta-data for understanding the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. These findings have important implications for pandemic preparedness and could be critical tools for understanding and responding to future outbreaks.http://www.sciencedirect.com/science/article/pii/S1876034123002113COVID-19Whole Genome Sequencing (WGS)SARS-CoV-2 genomic surveillanceVariant of concernDeltaOmicron |
| spellingShingle | Divya Niveditha Soumen Khan Ajinkya Khilari Sanica Nadkarni Unnati Bhalerao Pradnya Kadam Ritu Yadav Jugal B. Kanekar Nikita Shah Bhagyashree Likhitkar Rutuja Sawant Shikha Thakur Manisha Tupekar Dhriti Nagar Anjani G. Rao Rutuja Jagtap Shraddha Jogi Madhuri Belekar Maitreyee Pathak Priyanki Shah Shatakshi Ranade Nikhil Phadke Rashmita Das Suvarna Joshi Rajesh Karyakarte Aurnab Ghose Narendra Kadoo LS Shashidhara Joy Merwin Monteiro Dhanasekaran Shanmugam Anu Raghunathan Krishanpal Karmodiya A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India Journal of Infection and Public Health COVID-19 Whole Genome Sequencing (WGS) SARS-CoV-2 genomic surveillance Variant of concern Delta Omicron |
| title | A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India |
| title_full | A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India |
| title_fullStr | A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India |
| title_full_unstemmed | A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India |
| title_short | A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India |
| title_sort | tale of two waves delineating diverse genomic and transmission landscapes driving the covid 19 pandemic in pune india |
| topic | COVID-19 Whole Genome Sequencing (WGS) SARS-CoV-2 genomic surveillance Variant of concern Delta Omicron |
| url | http://www.sciencedirect.com/science/article/pii/S1876034123002113 |
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