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. 2022 Aug 25:10:974667.
doi: 10.3389/fpubh.2022.974667. eCollection 2022.

Genomic surveillance of SARS-CoV-2 by sequencing the RBD region using Sanger sequencing from North Kerala

Dhananjayan Dhanasooraj  1 , Prasanth Viswanathan  2 , Shammy Saphia  1 , Beena Philomina Jose  3 , Fairoz Cheriyalingal Parambath  3 , Saritha Sivadas  2 , N P Akash  2 , T V Vimisha  2 , Priyanka Raveendranadhan Nair  2 , Anuja Mohan  2 , Nimin Hafeez  2 , Jayesh Kumar Poovullathi  4 , Shameer Vadekkandiyil  4 , Sajeeth Kumar Keriyatt Govindan  4 , Rajan Khobragade  5 , K P Aravindan  6 , Chandni Radhakrishnan  7
Affiliations

Genomic surveillance of SARS-CoV-2 by sequencing the RBD region using Sanger sequencing from North Kerala

Dhananjayan Dhanasooraj et al. Front Public Health. .

Abstract

Next Generation Sequencing (NGS) is the gold standard for the detection of new variants of SARS-CoV-2 including those which have immune escape properties, high infectivity, and variable severity. This test is helpful in genomic surveillance, for planning appropriate and timely public health interventions. But labs with NGS facilities are not available in small or medium research settings due to the high cost of setting up such a facility. Transportation of samples from many places to few centers for NGS testing also produces delays due to transportation and sample overload leading in turn to delays in patient management and community interventions. This becomes more important for patients traveling from hotspot regions or those suspected of harboring a new variant. Another major issue is the high cost of NGS-based tests. Thus, it may not be a good option for an economically viable surveillance program requiring immediate result generation and patient follow-up. The current study used a cost-effective facility which can be set up in a common research lab and which is replicable in similar centers with expertise in Sanger nucleotide sequencing. More samples can be processed at a time and can generate the results in a maximum of 2 days (1 day for a 24 h working lab). We analyzed the nucleotide sequence of the Receptor Binding Domain (RBD) region of SARS-CoV-2 by the Sanger sequencing using in-house developed methods. The SARS-CoV-2 variant surveillance was done during the period of March 2021 to May 2022 in the Northern region of Kerala, a state in India with a population of 36.4 million, for implementing appropriate timely interventions. Our findings broadly agree with those from elsewhere in India and other countries during the period.

Keywords: Kerala; Receptor Binding Domain; SARS-CoV-2; Sanger sequencing; genomic surveillance; spike gene sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The variants detected per month during the study period (samples received from March 2021 to May 2022).
Figure 2
Figure 2
Age-wise analysis of variants observed during the study period (from March 2021 to May 2022).
See this image and copyright information in PMC

References

    1. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. (2020) 382:727–33. 10.1056/NEJMoa2001017 - DOI - PMC - PubMed
    1. Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, et al. The species Severe acute respiratory syndrome-related coronavirus : classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. (2020) 5:536–44. 10.1038/s41564-020-0695-z - DOI - PMC - PubMed
    1. Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H. The architecture of SARS-CoV-2 transcriptome. Cell. (2020) 181:914–21.e10. 10.1016/j.cell.2020.04.011 - DOI - PMC - PubMed
    1. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. (2020) 181:281–92.e6. 10.1016/j.cell.2020.11.032 - DOI - PMC - PubMed
    1. Pillay TS. Gene of the month: the 2019-nCoV/SARS-CoV-2 novel coronavirus spike protein. J Clin Pathol. (2020) 73:366–9. 10.1136/jclinpath-2020-206658 - DOI - PubMed

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Supplementary concepts