Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Dec 12;13(12):e0078924.
doi: 10.1128/mra.00789-24. Epub 2024 Nov 12.

Genomic surveillance of SARS-CoV-2 in Nepal

Binod Khadka  1 , Rajindra Napit  1   2 , Kathie A Mihindukulasuriya  3   4   5 , Smita Shrestha  1 , Ramanuj Rauniyar  1 , Eans T Tuladhar  1   6 , Lindsay Droit  3   4 , Anne M Paredes  4 , Runa Jha  7 , Roji Raut  1   2 , Bimalesh K Jha  7 , Scott A Handley  4   5 , Annie Elong-Ngono  8 , Sujan Shresta  8 , David Wang  3 , Krishna D Manandhar  1
Affiliations

Genomic surveillance of SARS-CoV-2 in Nepal

Binod Khadka et al. Microbiol Resour Announc. .

Abstract

During the COVID-19 pandemic, Nepal, like other countries, faced emerging SARS-CoV-2 variants. To evaluate the circulating variants, 278 samples collected between September 2021 and March 2022 were sequenced in the country. From these, 229 high-quality genomes were obtained (82.97% Omicron and 17.03% Delta) highlighting the genomic diversity of SARS-CoV-2 in Nepal.

Keywords: COVID-19; Illumina; coronavirus; whole-genome sequencing.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig 1
Fig 1
Phylogenetic analysis of complete SARS-CoV-2 genome sequences using GTR substitution model. The phylogenetic analysis showed a distinct clustering pattern among the circulating variants where the tree shows distinct clustering of Delta (red) and Omicron (blue).
See this image and copyright information in PMC

References

    1. Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ. 2020. Coronavirus disease 2019-COVID-19. Clin Microbiol Rev 33:e00028-20. doi:10.1128/CMR.00028-20 - DOI - PMC - PubMed
    1. Rayamajhee B, Pokhrel A, Syangtan G, Khadka S, Lama B, Rawal LB, Mehata S, Mishra SK, Pokhrel R, Yadav UN. 2021. How well the government of Nepal is responding to COVID-19? An experience from a resource-limited country to confront unprecedented pandemic. Front Public Health 9:597808. doi:10.3389/fpubh.2021.597808 - DOI - PMC - PubMed
    1. Bastola A, Sah R, Rodriguez-Morales AJ, Lal BK, Jha R, Ojha HC, Shrestha B, Chu DKW, Poon LLM, Costello A, Morita K, Pandey BD. 2020. The first 2019 novel coronavirus case in Nepal. Lancet Infect Dis 20:279–280. doi:10.1016/S1473-3099(20)30067-0 - DOI - PMC - PubMed
    1. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. 2021. Twelve years of SAMtools and BCFtools. Gigascience 10:giab008. doi:10.1093/gigascience/giab008 - DOI - PMC - PubMed
    1. Wilm A, Aw PPK, Bertrand D, Yeo GHT, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N. 2012. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res 40:11189–11201. doi:10.1093/nar/gks918 - DOI - PMC - PubMed

LinkOut - more resources