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. 2022 Dec;55(6 Pt 1):1060-1068.
doi: 10.1016/j.jmii.2022.06.001. Epub 2022 Jul 2.

Delta variant SARS-CoV-2 infections in pediatric cases during the second wave in India

Pragya D Yadav  1 , Gunjan Kumar  2 , Aparna Mukherjee  2 , Dimpal A Nyayanit  3 , Anita M Shete  3 , Rima R Sahay  3 , Abhinendra Kumar  3 , Triparna Majumdar  3 , Savita Patil  3 , Priyanka Pandit  3 , Yash Joshi  3 , Manisha Dudhmal  3 , Samiran Panda  2 , Lokesh Kumar Sharma  2 , Kala Yadav Ml  4 , Jayanthi Shastri  5 , Mayank Gangwar  6 , Ashok Munivenkattapa  7 , Varsha Potdar  3 , K Nagamani  8 , Kapil Goyal  9 , Ravisekhar Gadepalli  10 , Maria Thomas  11 , Suruchi Shukla  12 , P Nagraj  13 , Vivek Gupta  14 , Gaurav Dalela  15 , Nawaz Umar  16 , Sweety M Patel  17
Affiliations

Delta variant SARS-CoV-2 infections in pediatric cases during the second wave in India

Pragya D Yadav et al. J Microbiol Immunol Infect. 2022 Dec.

Abstract

Background: During October 2020, Delta variant was detected for the first time in India and rampantly spread across the globe. It also led to second wave of pandemic in India which affected millions of people. However, there is limited information pertaining to the SARS-CoV-2 strain infecting the children in India.

Methods: Here, we assessed the SARS-CoV-2 lineages circulating in the pediatric population of India during the second wave of the pandemic. Clinical and demographic details linked with the nasopharyngeal/oropharyngeal swabs (NPS/OPS) collected from SARS-CoV-2 cases (n = 583) aged 0-18 year and tested positive by real-time RT-PCR were retrieved from March to June 2021.

Results: Symptoms were reported among 37.2% of patients and 14.8% reported to be hospitalized. The E gene CT value had significant statistical difference at the point of sample collection when compared to that observed in the sequencing laboratory. Out of these 512 sequences 372 were VOCs, 51 were VOIs. Most common lineages observed were Delta, followed by Kappa, Alpha and B.1.36, seen in 65.82%, 9.96%, 6.83% and 4.68%, respectively in the study population.

Conclusion: Overall, it was observed that Delta strain was the leading cause of SARS-CoV-2 infection in Indian children during the second wave of the pandemic. We emphasize on the need of continuous genomic surveillance in SARS-CoV-2 infection even amongst children.

Keywords: COVID-19; Delta variant; India; Pediatric; SARS-CoV-2.

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Conflict of interest statement

Declaration of competing interest The authors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
Month wise distribution of the GISIAD clade: A month –wise distribution of pangolin lineages classified under (A) without D614G and (B) with D614G mutation. The x-axis depicts the different months in year 2020–2021 and the Y-axis is the Log 2 scale of SARS-CoV-2 cases reported in GISAID.
Fig. 2
Fig. 2
Month wise distribution of the Pangolin lineages: A month –wise distribution pangolin lineages classified under (A) VOC and VOI and (B) other lineages. The x-axis depicts the different months in year 2020–2021 and the Y-axis is the Log 2 scale of SARS-CoV-2 cases reported in GISAID and retrieved during this study.
Fig. 3
Fig. 3
Distribution of the SARS-CoV-2 genome prevalence among cases pediatric cases in India. The distribution in the pie chart is proportional to the numbers in each respective clade in each state. The outline of India’s map was downloaded from http://www.surveyofindia.gov.in/file/Map%20f%20India_1.jpg (accessed on 20 March 2020) and further modified to include relevant data in the SVG editor.
Fig. 4
Fig. 4
Maximum likelihood tree for the SARS-CoV-2 genomes retrieved from pediatric cases. Representative SARS-CoV-2 sequences from different lineages along with 512 sequences retrieved were used to generate the tree with a bootstrap replication of 1000 cycles. The sub-lineages I–IV of B.1.617.2 are marked in red, green, pink, and orange color on the nodes, respectively. B.1.617.1 sequence is marked in brown and B.1.617.3 in blue color. The other retrieved pangolin lineages are also marked on branches in different colors. Fig Tree v1.4.4 and Inkscape were used to visualize and edit the generated tree.
See this image and copyright information in PMC

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Supplementary concepts