Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India
From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of ind...
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MDPI AG
2021-09-01
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| author | Nivedita Gupta Harmanmeet Kaur Pragya Dhruv Yadav Labanya Mukhopadhyay Rima R. Sahay Abhinendra Kumar Dimpal A. Nyayanit Anita M. Shete Savita Patil Triparna Majumdar Salaj Rana Swati Gupta Jitendra Narayan Neetu Vijay Pradip Barde Gita Nataraj Amrutha Kumari B. Manasa P. Kumari Debasis Biswas Jyoti Iravane Sharmila Raut Shanta Dutta Sulochana Devi Purnima Barua Piyali Gupta Biswa Borkakoty Deepjyoti Kalita Kanwardeep Dhingra Bashir Fomda Yash Joshi Kapil Goyal Reena John Ashok Munivenkatappa Rahul Dhodapkar Priyanka Pandit Sarada Devi Manisha Dudhmal Deepa Kinariwala Neeta Khandelwal Yogendra Kumar Tiwari Prabhat Kiran Khatri Anjli Gupta Himanshu Khatri Bharti Malhotra Mythily Nagasundaram Lalit Dar Nazira Sheikh Jayanthi Shastri Neeraj Aggarwal Priya Abraham |
| author_facet | Nivedita Gupta Harmanmeet Kaur Pragya Dhruv Yadav Labanya Mukhopadhyay Rima R. Sahay Abhinendra Kumar Dimpal A. Nyayanit Anita M. Shete Savita Patil Triparna Majumdar Salaj Rana Swati Gupta Jitendra Narayan Neetu Vijay Pradip Barde Gita Nataraj Amrutha Kumari B. Manasa P. Kumari Debasis Biswas Jyoti Iravane Sharmila Raut Shanta Dutta Sulochana Devi Purnima Barua Piyali Gupta Biswa Borkakoty Deepjyoti Kalita Kanwardeep Dhingra Bashir Fomda Yash Joshi Kapil Goyal Reena John Ashok Munivenkatappa Rahul Dhodapkar Priyanka Pandit Sarada Devi Manisha Dudhmal Deepa Kinariwala Neeta Khandelwal Yogendra Kumar Tiwari Prabhat Kiran Khatri Anjli Gupta Himanshu Khatri Bharti Malhotra Mythily Nagasundaram Lalit Dar Nazira Sheikh Jayanthi Shastri Neeraj Aggarwal Priya Abraham |
| author_sort | Nivedita Gupta |
| collection | DOAJ |
| description | From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (<i>n</i> = 592) and one dose (<i>n</i> = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (<i>n</i> = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality. |
| first_indexed | 2024-03-10T07:08:52Z |
| format | Article |
| id | doaj.art-a4b6027c39c14c17bcd673236b8f0974 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T07:08:52Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-a4b6027c39c14c17bcd673236b8f09742023-11-22T15:37:54ZengMDPI AGViruses1999-49152021-09-01139178210.3390/v13091782Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of IndiaNivedita Gupta0Harmanmeet Kaur1Pragya Dhruv Yadav2Labanya Mukhopadhyay3Rima R. Sahay4Abhinendra Kumar5Dimpal A. Nyayanit6Anita M. Shete7Savita Patil8Triparna Majumdar9Salaj Rana10Swati Gupta11Jitendra Narayan12Neetu Vijay13Pradip Barde14Gita Nataraj15Amrutha Kumari B.16Manasa P. Kumari17Debasis Biswas18Jyoti Iravane19Sharmila Raut20Shanta Dutta21Sulochana Devi22Purnima Barua23Piyali Gupta24Biswa Borkakoty25Deepjyoti Kalita26Kanwardeep Dhingra27Bashir Fomda28Yash Joshi29Kapil Goyal30Reena John31Ashok Munivenkatappa 32Rahul Dhodapkar33Priyanka Pandit34Sarada Devi35Manisha Dudhmal36Deepa Kinariwala37Neeta Khandelwal38Yogendra Kumar Tiwari39Prabhat Kiran Khatri40Anjli Gupta41Himanshu Khatri42Bharti Malhotra43Mythily Nagasundaram44Lalit Dar45Nazira Sheikh46Jayanthi Shastri47Neeraj Aggarwal48Priya Abraham49Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, IndiaIndian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaIndian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, IndiaIndian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, IndiaIndian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, IndiaIndian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, IndiaViral Research and Diagnostic Laboratory, National Institute of Research in Tribal Health (NIRTH), Jabalpur 482003, IndiaViral Research and Diagnostic Laboratory, Department of Microbiology, KEM Medical College, Mumbai 400012, IndiaViral Research and Diagnostic Laboratory, Department of Microbiology, Mysore Medical College, Mysore 570015, IndiaViral Research and Diagnostic Laboratory, Department of Microbiology, Mysore Medical College, Mysore 570015, IndiaViral Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaViral Research and Diagnostic Laboratory, Government Medical College, Aurangabad 431001, IndiaViral Research and Diagnostic Laboratory, Indira Gandhi Government Medical College, Nagpur 440012, IndiaViral Research and Diagnostic Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata 700010, IndiaViral Research and Diagnostic Laboratory, Regional Institute of Medical Sciences, Imphal 795004, IndiaViral Research and Diagnostic Laboratory, Jorhat Medical College, Jorhat 785001, IndiaViral Research and Diagnostic Laboratory, Mahatma Gandhi Memorial Medical College, Jamshedpur 831020, IndiaViral Research and Diagnostic Laboratory, ICMR-Regional Medical Research Centre, Dibrugarh 786001, IndiaViral Research and Diagnostic Laboratory, All India Institutes of Medical Sciences, Rishikesh 249203, IndiaViral Research and Diagnostic Laboratory, Government Medical College, Amritsar 143001, IndiaViral Research and Diagnostic Laboratory, Sher-i-Kashmir Institute of Medical Sciences, Srinagar 190011, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaDepartment of Virology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, IndiaViral Research and Diagnostic Laboratory, Government Medical College, Thrissur 680596, IndiaICMR-National Institute of Virology Field Unit, Bangalore 560011, IndiaViral Research and Diagnostic Laboratory, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605006, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaViral Research and Diagnostic Laboratory, Government Medical College, Thiruvanthapuram 695011, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaViral Research and Diagnostic Laboratory, B. J. Medical College, Ahmedabad 380016, IndiaViral Research and Diagnostic Laboratory, Government Medical College, Surat 395001, IndiaViral Research and Diagnostic Laboratory, Jhalawar Medical College, Jhalawar 326001, IndiaViral Research and Diagnostic Laboratory, Dr. Sampurnanand Medical College, Jodhpur 342003, IndiaViral Research and Diagnostic Laboratory, Sarder Patel Medical College, Bikaner 334001, IndiaViral Research and Diagnostic Laboratory, Department of Microbiology, GMERS Medical College, Himmatnagar 383001, IndiaViral Research and Diagnostic Laboratory, Sawai Man Singh Medical College, Jaipur 302004, IndiaViral Research and Diagnostic Laboratory, Coimbatore Medical College, Coimbatore 641018, IndiaViral Research and Diagnostic Laboratory, All India Institute of Medical Sciences, Delhi 110029, IndiaViral Research and Diagnostic Laboratory, Dr. V.M Government Medical College, Solapur 413003, IndiaViral Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai 400011, IndiaIndian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, IndiaIndian Council of Medical Research-National Institute of Virology, Pune 411021, IndiaFrom March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (<i>n</i> = 592) and one dose (<i>n</i> = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (<i>n</i> = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.https://www.mdpi.com/1999-4915/13/9/1782breakthroughCOVID-19VRDLDelta and Delta plus variantIndiavaccine |
| spellingShingle | Nivedita Gupta Harmanmeet Kaur Pragya Dhruv Yadav Labanya Mukhopadhyay Rima R. Sahay Abhinendra Kumar Dimpal A. Nyayanit Anita M. Shete Savita Patil Triparna Majumdar Salaj Rana Swati Gupta Jitendra Narayan Neetu Vijay Pradip Barde Gita Nataraj Amrutha Kumari B. Manasa P. Kumari Debasis Biswas Jyoti Iravane Sharmila Raut Shanta Dutta Sulochana Devi Purnima Barua Piyali Gupta Biswa Borkakoty Deepjyoti Kalita Kanwardeep Dhingra Bashir Fomda Yash Joshi Kapil Goyal Reena John Ashok Munivenkatappa Rahul Dhodapkar Priyanka Pandit Sarada Devi Manisha Dudhmal Deepa Kinariwala Neeta Khandelwal Yogendra Kumar Tiwari Prabhat Kiran Khatri Anjli Gupta Himanshu Khatri Bharti Malhotra Mythily Nagasundaram Lalit Dar Nazira Sheikh Jayanthi Shastri Neeraj Aggarwal Priya Abraham Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India Viruses breakthrough COVID-19 VRDL Delta and Delta plus variant India vaccine |
| title | Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India |
| title_full | Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India |
| title_fullStr | Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India |
| title_full_unstemmed | Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India |
| title_short | Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India |
| title_sort | clinical characterization and genomic analysis of samples from covid 19 breakthrough infections during the second wave among the various states of india |
| topic | breakthrough COVID-19 VRDL Delta and Delta plus variant India vaccine |
| url | https://www.mdpi.com/1999-4915/13/9/1782 |
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