Genomic survey of SARS-CoV-2 vaccine breakthrough infections in healthcare workers from Kerala, India

J, Beena Philomina; Jolly, Bani; John, Neethu; Bhoyar, Rahul C.; Majeed, Nisha; Senthivel, Vigneshwar; Cp, Fairoz; Rophina, Mercy; Vasudevan, Bindhu; Imran, Mohamed; Viswanathan, Prasanth; VR, Arvinden; Joseph, Anoop; Divakar, Mohit Kumar; Nair, Priyanka Raveendranadhan; Shamnath, Afra; Kumar, Pradeep; Jain, Abhinav; Geetha, P.; Bajaj, Anjali; Mathew, Samatha; Gupta, Vishu; Agrawal, Srashti Jyoti; Sivasubbu, Sridhar; Radhakrishnan, Chandni

doi:10.1016/j.jinf.2021.05.018

Cited by 46 publications

(38 citation statements)

References 11 publications

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“…Overall breakthrough infections were seen in smaller percentage of total vaccinated population [17]. A recent study has also reported mild symptomatic breakthrough infections from Kerala and Delhi, India [19,20].…”

Section: Next-generation Sequencing Analysis Of the Breakthrough Specimensmentioning

confidence: 88%

“…Breakthrough infections in healthcare workers vaccinated with the BNT162b2 vaccine were reported from Italy in the month of May, 2021 during an outbreak of SARS-CoV-2 lineage B.1.1.7 [18]. In India, few studies reported breakthrough infections in small parts of the country like Kerala [19] and Delhi [20]. Taking cognizance of such reports, in April-May, 2021, a nationwide study was undertaken to understand the clinico-demographic profile of patients and SARS-CoV-2 strains responsible for post vaccination breakthrough COVID-19 infections across the country.…”

Section: Introductionmentioning

confidence: 99%

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Clinical characterization and Genomic analysis of COVID-19 breakthrough infections during second wave in different states of India

Gupta

Kaur

Yadav

et al. 2021

Preprint

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During March to June 2021 India has experienced a deadly second wave of COVID19 with an increased number of post vaccination breakthrough infections reported across the country. To understand the possible reason of these breakthroughs we collected 677 clinical samples (throat swab/ nasal swabs) of individuals who had received two doses (n=592) and one dose (n=85) of vaccines (Covishield and Covaxin,) and tested positive for COVID19, from 17 states/Union Territories of country. These cases were telephonically interviewed and clinical data was analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both the cases. Analysis of both the cases 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 4 distinct sub-lineages. Sub-lineage I had mutations: ORF1ab, A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, A6319V and N G215C; Sub lineage II : ORF1ab P309, A3209V, V3718A, G5063S, P5401L and ORF7a L116F; Sub lineage III : ORF1ab A3209V, V3718A, T3750I, G5063S, P5401L and Spike A222V; Sub-lineage IV ORF1ab P309L, D2980N, F3138S and spike K77T. This study indicated that majority of the clinical cases in the breakthrough 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.

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Section: Next-generation Sequencing Analysis Of the Breakthrough Specimensmentioning

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Clinical characterization and Genomic analysis of COVID-19 breakthrough infections during second wave in different states of India

Gupta

Kaur

Yadav

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…In contrast, reports in which certain variants of concern were more prevalent in breakthrough infections have been published as well. 8 , 16 , 26 Our study was not designed to address this question regarding variants of concern in breakthrough infections.…”

Section: Discussionmentioning

confidence: 99%

Covid-19 Breakthrough Infections in Vaccinated Health Care Workers

et al. 2021

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Background Despite the high efficacy of the BNT162b2 messenger RNA vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rare breakthrough infections have been reported, including infections among health care workers. Data are needed to characterize these infections and define correlates of breakthrough and infectivity. Methods At the largest medical center in Israel, we identified breakthrough infections by performing extensive evaluations of health care workers who were symptomatic (including mild symptoms) or had known infection exposure. These evaluations included epidemiologic investigations, repeat reverse-transcriptase–polymerase-chain-reaction (RT-PCR) assays, antigen-detecting rapid diagnostic testing (Ag-RDT), serologic assays, and genomic sequencing. Correlates of breakthrough infection were assessed in a case–control analysis. We matched patients with breakthrough infection who had antibody titers obtained within a week before SARS-CoV-2 detection (peri-infection period) with four to five uninfected controls and used generalized estimating equations to predict the geometric mean titers among cases and controls and the ratio between the titers in the two groups. We also assessed the correlation between neutralizing antibody titers and N gene cycle threshold (Ct) values with respect to infectivity. Results Among 1497 fully vaccinated health care workers for whom RT-PCR data were available, 39 SARS-CoV-2 breakthrough infections were documented. Neutralizing antibody titers in case patients during the peri-infection period were lower than those in matched uninfected controls (case-to-control ratio, 0.361; 95% confidence interval, 0.165 to 0.787). Higher peri-infection neutralizing antibody titers were associated with lower infectivity (higher Ct values). Most breakthrough cases were mild or asymptomatic, although 19% had persistent symptoms (>6 weeks). The B.1.1.7 (alpha) variant was found in 85% of samples tested. A total of 74% of case patients had a high viral load (Ct value, <30) at some point during their infection; however, of these patients, only 17 (59%) had a positive result on concurrent Ag-RDT. No secondary infections were documented. Conclusions Among fully vaccinated health care workers, the occurrence of breakthrough infections with SARS-CoV-2 was correlated with neutralizing antibody titers during the peri-infection period. Most breakthrough infections were mild or asymptomatic, although persistent symptoms did occur.

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“…Breakthrough infections in healthcare workers vaccinated with the BNT162b2 vaccine were reported from Italy in the May 2021 during an outbreak of SARS-CoV-2 lineage B.1.1.7 [19]. In India, a few studies reported breakthrough infections in small parts of the country, such as in Kerala [20], Chennai [21], and Delhi [22]. Taking cognizance of such reports, in April-May 2021, a nationwide study was undertaken to understand the clinico-demographic profile of patients and SARS-CoV-2 strains responsible for post-vaccination breakthrough COVID-19 infections across the country.…”

Section: Introductionmentioning

confidence: 99%

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

Gupta

Kaur

Yadav

et al. 2021

Viruses

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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.

show abstract

Genomic survey of SARS-CoV-2 vaccine breakthrough infections in healthcare workers from Kerala, India

Cited by 46 publications

References 11 publications

Clinical characterization and Genomic analysis of COVID-19 breakthrough infections during second wave in different states of India

Clinical characterization and Genomic analysis of COVID-19 breakthrough infections during second wave in different states of India

Covid-19 Breakthrough Infections in Vaccinated Health Care Workers

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

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