SARS-CoV-2 Lineage Tracking, and Evolving Trends Seen during Three Consecutive Peaks of Infection in Delhi, India: a Clinico-Genomic Study

Gautam, Pramod; Paul, Diptanu; Suroliya, Varun; Garg, Rahul; Agarwal, Reshu; Das, Santanu; Kaur, Urvinder S.; Pandey, Amit; Bhugra, Arjun; Tarai, Bansidhar; Bihari, Chhagan; Sarin, Shiv Kumar; Gupta, Ekta

doi:10.1128/spectrum.02729-21

Cited by 5 publications

(4 citation statements)

References 27 publications

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“…In the first two peaks median CT values were found to be more than 20. This is in contrast to what has been reported by Gautam et al 2022, where the median CT in the first two peaks were found to be 15 (Gautam et al, 2022).…”

Section: Discussioncontrasting

confidence: 99%

“…During the first peak B.1.560 lineage was found to be more common which was replaced by B.1.617.2 lineage during second peak. This was similar to a study in Delhi (Gautam et al, 2022). The beginning of third peak had B.1.617.2 lineage which slowly less detected with an increase in BA.2 and BA.1.1.7 lineage.…”

Section: Discussionsupporting

confidence: 92%

“…This is followed by a report from Delhi, the capital state of India, in which 612 samples were sequenced spanning first three peaks of pandemic. The study reported 26 lineages with novel mutations detected across the 3 peaks (Gautam et al, 2022). Like ours this is also a single center study, in addition to their findings we have also included samples from Jan 2022 to Mar 2022, where Omicron type dominated with a total of 25.…”

Section: Discussionmentioning

confidence: 99%

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Genomic Profiling of Sars-Cov-2 Strains Circulating in South Eastern Region of India During Three Waves of Pandemic

Kandhasamy,

Balakrishna Pillai,

Mariappan

et al. 2024

Preprint

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Continuous bio-surveillance of SARS-CoV-2 is an ongoing task at local, national and global levels since the pandemic onset for understanding genetic evolution and vaccine efficacy. Present study was designed to track the emergence of new variants along the duration of three peaks of infection in the city of Puducherry, India. A total of 128 samples were subjected to Illumina deep RNA sequencing. The results showed predominance of uncommon, delta and omicron variants in first, second and third waves respectively. The most common pangolin lineage was B.1.560 and B.1.617.2. The study observed a total of 3133 common and 11 new mutations. The most common is in the Spike_D614G. A new set of mutations was observed in key viral factors such as NS16 that are implicated to be involved in immune evasion. This may have impact on enhanced disease virulence, vaccine efficiency and possible tolerance to current antivirals. This warrants further in vitro studies to understand the significance of the mutations. While the results presented would also augment the ongoing research on evolutionary and the genetic epidemiology of SARS-CoV-2, it also emphasizes the need for continuous genetic monitoring to predict the forthcoming threats due to the emergence of new or existing variants.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

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Genomic Profiling of Sars-Cov-2 Strains Circulating in South Eastern Region of India During Three Waves of Pandemic

Kandhasamy,

Balakrishna Pillai,

Mariappan

et al. 2024

Preprint

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“…The propagated outbreak of COVID-19 and global vaccination drive have exerted an immense immunological selection pressure on SARS CoV-2. Therefore, since its first case in December 2019, five variants of concern (VOC) have evolved -Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) (2,10). Within a span of two years Delta and Omicron variants have become dominant VOCs due to their increased transmissibility and decreased neutralization with vaccine or naturally acquired antibodies (2,(11)(12)(13)(14).…”

Section: Introductionmentioning

confidence: 99%

Genomic perspectives of SARS CoV-2 in liver disease patients with its clinical correlation: A single centre retrospective study

Bhugra

Agarwal

Gautam

et al. 2023

Preprint

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Background: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2), is a causative agent of current global pandemic of Coronavirus disease-19 (COVID-19). Due to propagated outbreak and global vaccination drive an immense immunological selection pressure has been exerted on SARS CoV-2 leading to evolution of new variants. This study was performed to compare the mutational and clinical profile of liver disease patients infected with different variants of SARS CoV-2. Methodology: This was a single-centre, retrospective, cohort study in which clinicogenomic analysis of liver disease (LD) patients infected with SARS CoV-2 was performed. Complete demographic and clinical details were retrieved from Hospital Information System (HIS). QC-threshold passed FASTA files containing sequences from COVID-19 patients (n=174) were compared with a reference genome of SARS-CoV-2 isolate named Wuhan-Hu-1 (NCBI Reference Sequence: NC_045512.2) for mutational analysis. Results: Out of 232 finally analysed patients 137 (59.1%) were LD-CoV (+) and 95 (40.9%) were LD-CoV(-). LD patients with comorbidities were affected more with COVID-19 (p=0.002). On comparing the outcome in the terms of mortality, LD-CoV (+) had 2.29 times (OR 2.29, CI 95%, 1.25-4.29) higher of odds of succumbing to COVID-19 (p=0.006). Multivariate regression analysis revealed, abdominal distention (p=0.05), severe COVID-19 pneumonia (p=0.046) and the change in serum bilirubin levels (p=0.005) as well as Alkaline phosphatase (ALP) levels (p=0.003) to have an association with adverse outcome in LD patients with COVID-19. In Delta (22%) and Omicron (48%) groups, Spike gene harboured maximum mutations. On comparing the mutations between LD-CoV(+/D) and LD-CoV(+/O) a total of nine genes had more mutations in LD-CoV(+/O) whereas three genes had more mutations in LD-CoV(+/D). Conclusion: We concluded that LD patients are more susceptible to COVID-19 as compared to a healthy adult with associated adverse clinical outcomes in terms of mortality and morbidity. Therefore this special group should be given priority while devising and introducing new vaccination and vaccination policies. The infection with different variants did not result in different outcome in our group of patients. Keywords: COVID-19, SARS CoV-2, Delta, Omicron, Liver disease

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A comprehensive profile of SARS-CoV-2 variants spreading during the COVID-19 pandemic: a genomic characterization study from Chhattisgarh State, India

Negi,

Sharma,

Bhargava

et al. 2024

Arch Microbiol

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SARS-CoV-2 Lineage Tracking, and Evolving Trends Seen during Three Consecutive Peaks of Infection in Delhi, India: a Clinico-Genomic Study

Abstract: Genome surveillance of the Delhi data provides a more detailed picture of diverse circulating lineages. The added value that the current study provides by clinical details of the patients is of importance.

Cited by 5 publications

References 27 publications

Genomic Profiling of Sars-Cov-2 Strains Circulating in South Eastern Region of India During Three Waves of Pandemic

Genomic Profiling of Sars-Cov-2 Strains Circulating in South Eastern Region of India During Three Waves of Pandemic

Genomic perspectives of SARS CoV-2 in liver disease patients with its clinical correlation: A single centre retrospective study

A comprehensive profile of SARS-CoV-2 variants spreading during the COVID-19 pandemic: a genomic characterization study from Chhattisgarh State, India

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