An Epidemiological Analysis of Severe Acute Repiratory Syndrome Coronavirus 2 Genome Sequencing: A Hospital-based Retrospective Study
Introduction: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a positive-sense enveloped single-stranded Ribonucleic Acid (RNA) virus. Structural proteins help the virus package its RNA, while other proteins enable viral replication by facilitating host entry. Through constant mu...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
JCDR Research and Publications Private Limited
2023-12-01
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| Series: | Journal of Clinical and Diagnostic Research |
| Subjects: | |
| Online Access: | https://www.jcdr.net/articles/PDF/18782/64648_CE[Ra1]_F(IS)_QC(SHK_RDW_IS)_PF1(AG_OM)_PFA(AG_KM)_PN(KM).pdf |
| Summary: | Introduction: Severe Acute Respiratory Syndrome Coronavirus-2
(SARS-CoV-2) is a positive-sense enveloped single-stranded
Ribonucleic Acid (RNA) virus. Structural proteins help the virus
package its RNA, while other proteins enable viral replication
by facilitating host entry. Through constant mutation, the virus
changes its emergence profile, and combinations of mutations
can lead to increased transmissibility and receptor binding
capacity, altering its surface structure. Whole genome sequencing
is an important tool for studying these changes. In this study, the
authors report on the genome sequencing of patients who tested
positive for SARS-CoV-2 using real-time Reverse TranscriptasePolymerase Chain Reaction (RT-PCR) tests.
Aim: To identify the different lineages circulating in specific
districts of West Bengal, India, and perform an epidemiological
analysis of the patients to control disease severity during the
second wave of Coronavirus Disease-2019 (COVID-19).
Materials and Methods: This retrospective hospital-based
study was conducted at the Virus Research and Diagnostic
Laboratory (VRDL) at RG Kar Medical College and Hospital,
West Bengal, India from January 2021 to October 2021. Data
collection started in January 2021 and was analysed in October
2021. Nasopharyngeal and oropharyngeal swabs were taken
from patients with SARS-CoV-2, and the samples were tested
using RT-PCR. Positive samples were sent to the Regional
Virus Research and Diagnostic Laboratory-National Institute of
Cholera and Enteric Diseases (NICED) for sequencing. Samples
were collected from patients in different districts of West Bengal
who were reported to the VRDL of RG Kar Medical College and
Hospital. A total of 172,550 samples were tested for SARSCoV-2, and out of 13,764 positive samples, 230 were sent for
genome sequencing. The primary inclusion criteria were SARSCoV-2 positive patients with CT values between 25 and 30 who
were vaccinated. Patient information, address, gene variant,
and gene mutation of the samples were analysed. Statistical
analysis was performed using t-test with Statistical Package for
Social Sciences (SPSS) software.
Results: Whole-genome sequencing helped identify new trends
and their prevalence in specific areas, aiding in prevention
efforts. The most common type of mutation observed after
double vaccination was the delta variant (B.1.617.2), followed by
the kappa variant (B.1.617.1) and the alpha variant (B.1.1.7).
Conclusion: Epidemiological genome sequencing studies help
to identify emerging and changing viral trends, contributing to
the mitigation of the spread of new variants. The delta, kappa,
and alpha variants were the three primary sequences discovered
in this study. The identification of these lineages facilitates the
design of novel vaccines and diagnostic medications. Continuous
monitoring and analysis of sequences from new cases in India
and other affected countries are crucial for understanding the
genetic evolution and substitution rates of SARS-CoV-2. |
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| ISSN: | 2249-782X 0973-709X |