Non-invasive SARS-CoV-2 genome surveillance and its utility in resource-poor settings during the Delta wave of the COVID-19 pandemic
Khairnar, K.; Tomar, S. S.
Show abstract
Voluntary participation of the public in disease surveillance can be encouraged by deploying user-friendly sample collection processes that can minimise the discomfort to the participants. This study evaluated the suitability of saline gargle-based sample collection for genomic surveillance of SARS-CoV-2, which included 589 SARS-CoV-2 positive samples collected from Nagpur city in central India from March to December 2021. The SARS-CoV-2 positive samples were subjected to whole genome sequencing (WGS) using the oxford nanopore technologies next-generation sequencing platform. Out of 589 samples, 500 samples qualified for the WGS, and the results revealed eight different clades of SARS-CoV-2 encompassing 37 different Pango-lineage types. The mutation mapping analysis of the variants identified in this study showed six mutations of interest and one mutation of concern E484K in the spike glycoprotein region. Our findings indicate that non-invasive gargle-based genomic surveillance is scalable and does not need significant changes to the existing workflow post-sample collection.
Matching journals
The top 8 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Evaluating diagnostic accuracies of Panbio ™ COVID-19 rapid antigen test and RT-PCR for the detection of SARS-CoV-2 in Addis Ababa, Ethiopia using Bayesian Latent-Class Models (BLCM) 97%
- SARS-CoV-2 detection in multi-sample pools in a real pandemic scenario: a screening strategy of choice for active surveillance 96%
- Comparative Genomic Study for Revealing the Complete Scenario of COVID-19 Pandemic in Bangladesh 96%
Similar papers in this journal
- Genomic diversity of SARS-CoV-2 in Pakistan during fourth wave of pandemic 96%
- Evaluation of seven different rapid methods for nucleic acid detection of SARS-COV-2 virus 96%
- Detection of Lumpy Skin Disease Virus Reads in the Human Upper Respiratory Tract Microbiome Requires Further Investigation 96%
Similar papers in this journal
- Evaluation of three rapid lateral flow antigen detection tests for the diagnosis of SARS-CoV-2 infection 95%
- Rapid and simultaneous identification of three mutations by the Novaplex™ SARS-CoV-2 Variants I Assay kit 94%
- Investigating the genomic landscape of novel coronavirus (2019-nCoV) to identify non-synonymous mutations for use in diagnosis and drug design 94%
Similar papers in this journal
- Epidemiological and phylogenetic analyses of public SARS-CoV-2 data from Malawi 94%
- Respiratory virus infection dynamics and genomic surveillance to detect seasonal influenza subtypes in wastewater: a longitudinal study in Bengaluru, India 94%
- Epidemiological and virological factors determining dengue transmission in Sri Lanka during the COVID-19 pandemic 94%
Similar papers in this journal
- SARS-CoV-2 IgG antibody responses in rt-PCR positive cases: first report from India 95%
- Whatman FTA(R) cards versus plasma specimens for the quantitation of HIV-1 RNA using two Real-Time PCR assays 94%
- First hybrid complete genome of Aeromonas veronii reveals chromosome-mediated novel structural variant mcr-3.19 from human clinical specimen 92%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.