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10.3390/v13091782
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Article

Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India

by
Nivedita Gupta
1,
Harmanmeet Kaur
1,
Pragya Dhruv Yadav
2,*,
Labanya Mukhopadhyay
1,
Rima R. Sahay
2,
Abhinendra Kumar
2,
Dimpal A. Nyayanit
2,
Anita M. Shete
2,
Savita Patil
2,
Triparna Majumdar
2,
Salaj Rana
1,
Swati Gupta
1,
Jitendra Narayan
1,
Neetu Vijay
1,
Pradip Barde
3,
Gita Nataraj
4,
Amrutha Kumari B.
5,
Manasa P. Kumari
5,
Debasis Biswas
6,
Jyoti Iravane
7,
Sharmila Raut
8,
Shanta Dutta
9,
Sulochana Devi
10,
Purnima Barua
11,
Piyali Gupta
12,
Biswa Borkakoty
13,
Deepjyoti Kalita
14,
Kanwardeep Dhingra
15,
Bashir Fomda
16,
Yash Joshi
2,
Kapil Goyal
17,
Reena John
18,
Ashok Munivenkatappa 
19,
Rahul Dhodapkar
20,
Priyanka Pandit
2,
Sarada Devi
21,
Manisha Dudhmal
2,
Deepa Kinariwala
22,
Neeta Khandelwal
23,
Yogendra Kumar Tiwari
24,
Prabhat Kiran Khatri
25,
Anjli Gupta
26,
Himanshu Khatri
27,
Bharti Malhotra
28,
Mythily Nagasundaram
29,
Lalit Dar
30,
Nazira Sheikh
31,
Jayanthi Shastri
32,
Neeraj Aggarwal
1 and
Priya Abraham
2add Show full author list remove Hide full author list
1
Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
2
Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
3
Viral Research and Diagnostic Laboratory, National Institute of Research in Tribal Health (NIRTH), Jabalpur 482003, India
4
Viral Research and Diagnostic Laboratory, Department of Microbiology, KEM Medical College, Mumbai 400012, India
5
Viral Research and Diagnostic Laboratory, Department of Microbiology, Mysore Medical College, Mysore 570015, India
6
Viral Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India
7
Viral Research and Diagnostic Laboratory, Government Medical College, Aurangabad 431001, India
8
Viral Research and Diagnostic Laboratory, Indira Gandhi Government Medical College, Nagpur 440012, India
9
Viral Research and Diagnostic Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
10
Viral Research and Diagnostic Laboratory, Regional Institute of Medical Sciences, Imphal 795004, India
11
Viral Research and Diagnostic Laboratory, Jorhat Medical College, Jorhat 785001, India
12
Viral Research and Diagnostic Laboratory, Mahatma Gandhi Memorial Medical College, Jamshedpur 831020, India
13
Viral Research and Diagnostic Laboratory, ICMR-Regional Medical Research Centre, Dibrugarh 786001, India
14
Viral Research and Diagnostic Laboratory, All India Institutes of Medical Sciences, Rishikesh 249203, India
15
Viral Research and Diagnostic Laboratory, Government Medical College, Amritsar 143001, India
16
Viral Research and Diagnostic Laboratory, Sher-i-Kashmir Institute of Medical Sciences, Srinagar 190011, India
17
Department of Virology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
18
Viral Research and Diagnostic Laboratory, Government Medical College, Thrissur 680596, India
19
ICMR-National Institute of Virology Field Unit, Bangalore 560011, India
20
Viral Research and Diagnostic Laboratory, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605006, India
21
Viral Research and Diagnostic Laboratory, Government Medical College, Thiruvanthapuram 695011, India
22
Viral Research and Diagnostic Laboratory, B. J. Medical College, Ahmedabad 380016, India
23
Viral Research and Diagnostic Laboratory, Government Medical College, Surat 395001, India
24
Viral Research and Diagnostic Laboratory, Jhalawar Medical College, Jhalawar 326001, India
25
Viral Research and Diagnostic Laboratory, Dr. Sampurnanand Medical College, Jodhpur 342003, India
26
Viral Research and Diagnostic Laboratory, Sarder Patel Medical College, Bikaner 334001, India
27
Viral Research and Diagnostic Laboratory, Department of Microbiology, GMERS Medical College, Himmatnagar 383001, India
28
Viral Research and Diagnostic Laboratory, Sawai Man Singh Medical College, Jaipur 302004, India
29
Viral Research and Diagnostic Laboratory, Coimbatore Medical College, Coimbatore 641018, India
30
Viral Research and Diagnostic Laboratory, All India Institute of Medical Sciences, Delhi 110029, India
31
Viral Research and Diagnostic Laboratory, Dr. V.M Government Medical College, Solapur 413003, India
32
Viral Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai 400011, India
 
add Show full affiliation list
 
remove Hide full affiliation list
*
Author to whom correspondence should be addressed.
Viruses 2021, 13(9), 1782; https://doi.org/10.3390/v13091782
Submission received: 9 July 2021 / Revised: 27 August 2021 / Accepted: 29 August 2021 / Published: 7 September 2021
(This article belongs to the Special Issue Coronaviruses Research in BRICS Countries)
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Abstract

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 (n = 592) and one dose (n = 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% (n = 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.
Keywords: breakthrough; COVID-19; VRDL; Delta and Delta plus variant; India; vaccine breakthrough; COVID-19; VRDL; Delta and Delta plus variant; India; vaccine

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MDPI and ACS Style

Gupta, N.; Kaur, H.; Yadav, P.D.; Mukhopadhyay, L.; Sahay, R.R.; Kumar, A.; Nyayanit, D.A.; Shete, A.M.; Patil, S.; Majumdar, T.; et al. Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Viruses 2021, 13, 1782. https://doi.org/10.3390/v13091782

AMA Style

Gupta N, Kaur H, Yadav PD, Mukhopadhyay L, Sahay RR, Kumar A, Nyayanit DA, Shete AM, Patil S, Majumdar T, et al. Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Viruses. 2021; 13(9):1782. https://doi.org/10.3390/v13091782

Chicago/Turabian Style

Gupta, Nivedita, Harmanmeet Kaur, Pragya Dhruv Yadav, Labanya Mukhopadhyay, Rima R. Sahay, Abhinendra Kumar, Dimpal A. Nyayanit, Anita M. Shete, Savita Patil, Triparna Majumdar, and et al. 2021. "Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India" Viruses 13, no. 9: 1782. https://doi.org/10.3390/v13091782

APA Style

Gupta, N., Kaur, H., Yadav, P. D., Mukhopadhyay, L., Sahay, R. R., Kumar, A., Nyayanit, D. A., Shete, A. M., Patil, S., Majumdar, T., Rana, S., Gupta, S., Narayan, J., Vijay, N., Barde, P., Nataraj, G., B., A. K., Kumari, M. P., Biswas, D., ... Abraham, P. (2021). Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Viruses, 13(9), 1782. https://doi.org/10.3390/v13091782

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