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

Author:

Gupta Nivedita,Kaur Harmanmeet,Yadav Pragya DhruvORCID,Mukhopadhyay LabanyaORCID,Sahay Rima R.ORCID,Kumar Abhinendra,Nyayanit Dimpal A.,Shete Anita M.,Patil Savita,Majumdar Triparna,Rana Salaj,Gupta Swati,Narayan JitendraORCID,Vijay Neetu,Barde PradipORCID,Nataraj Gita,B. Amrutha Kumari,Kumari Manasa P.,Biswas Debasis,Iravane Jyoti,Raut Sharmila,Dutta ShantaORCID,Devi Sulochana,Barua Purnima,Gupta Piyali,Borkakoty Biswa,Kalita DeepjyotiORCID,Dhingra Kanwardeep,Fomda Bashir,Joshi Yash,Goyal Kapil,John Reena,Munivenkatappa  AshokORCID,Dhodapkar Rahul,Pandit Priyanka,Devi Sarada,Dudhmal Manisha,Kinariwala Deepa,Khandelwal Neeta,Tiwari Yogendra Kumar,Khatri Prabhat Kiran,Gupta Anjli,Khatri Himanshu,Malhotra BhartiORCID,Nagasundaram Mythily,Dar Lalit,Sheikh Nazira,Shastri Jayanthi,Aggarwal NeerajORCID,Abraham Priya

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.

Funder

Indian Council of Medical Research

Publisher

MDPI AG

Subject

Virology,Infectious Diseases

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