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
. 2020 May;151(5):474-478.
doi: 10.4103/ijmr.IJMR_1253_20.

Mapping the genomic landscape & diversity of COVID-19 based on >3950 clinical isolates of SARS-CoV-2: Likely origin & transmission dynamics of isolates sequenced in India

Hina Singh  1 , Jasdeep Singh  1 , Mohd Khubaib  1 , Salma Jamal  1 , Javaid Ahmed Sheikh  2 , Sunil Kohli  3 , Seyed Ehtesham Hasnain  4 , Syed Asad Rahman  5
Affiliations

Mapping the genomic landscape & diversity of COVID-19 based on >3950 clinical isolates of SARS-CoV-2: Likely origin & transmission dynamics of isolates sequenced in India

Hina Singh et al. Indian J Med Res. 2020 May.
No abstract available

PubMed Disclaimer

Conflict of interest statement

None

Figures

Fig. 1
Fig. 1
Whole-genome-based t-SNE clustering of 3968 clinical isolates. (A) Comparative genome-based clustering of Indian isolates (red) with Chinease isolates (blue). (B) Comapartive genome-based clustering of Indian isolates (red) and Chinese isolates (blue) with rest of the world (green). (C) Diversity in clinical isolates showing three distinct clustering using hierarchical clustering on the t-SNE clusters. (t-SNE: https://github.com/jdonaldson/rtsne).
Fig. 2
Fig. 2
Position of various Indian isolates with other nations. (A-E) Clustering of SARS-CoV-2 genome sequences from India (red) with other nations around the globe. Indian samples clustered with samples from different nations – China, Kuwait, Canada, USA and Spain in whole-genome-based clustering. Figures were generated using FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).
Fig. 3
Fig. 3
Sequence similarity and mutation analysis of open reading frames. (A) Comparison of mean sequence similarity for open reading frames between Indian and global isolates with Wuhan strain. (B) Qualitative analysis on type of mutations occurring in non-conserved open reading frames (ORFs) of Indian isolates compared to Wuhan strain.
See this image and copyright information in PMC

References

    1. World Health Organization. Coronavirus disease 2019 (COVID-19) Situation report-94. Geneva: WHO; 2020.
    1. Kimball A, Hatfield KM, Arons M, James A, Taylor J, Spicer K, et al. Asymptomatic and presymptomatic SARS-CoV-2 infections in residents of a long-term care skilled nursing facility - King county, Washington, March 2020. MMWR Morb Mortal Wkly Rep. 2020;69:377–81. - PMC - PubMed
    1. Mandal S, Bhatnagar T, Arinaminpathy N, Agarwal A, Chowdhury A, Murhekar M, et al. Prudent public health intervention strategies to control the coronavirus disease 2019 transmission in India: A mathematical model-based approach. Indian J Med Res. 2020;151:190–9. - PMC - PubMed
    1. Gupta N, Praharaj I, Bhatnagar T, Thangaraj JWV, Giri S, Chauhan H, et al. Severe acute respiratory illness surveillance for coronavirus disease 2019, India, 2020. Indian J Med Res. 2020;151:236–40. - PMC - PubMed
    1. Yadav PD, Potdar VA, Choudhary ML, Nyayanit DA, Agrawal M, Jadhav SM, et al. Full-genome sequences of the first two SARS-CoV-2 viruses from India. Indian J Med Res. 2020;151:200–9. - PMC - PubMed

MeSH terms