Genetic Epidemiology of New and Emerging Infections in India

COVID-19 Genome Analysis Summaries

  • Genomic variants in SARS-CoV-2 isolates from India and its impact on diagnostic assays - what we need to know We catalogued a total of 132 primers or probes sequences from the literature and the public domain. Our analysis revealed a total of 125 unique genetic variants in 80 either ...
    Posted Aug 20, 2020, 11:34 PM by Vinod Scaria
  • GENETIC DIVERSITY OF INDIAN SARS-NCOV-2 ISOLATES 15/05/2020 Credits:  Inforgraphics: Bani Jolly Data Source: GISAID Acknowledge data submitted from NIMHANS Bengaluru, NCDC Delhi, ICMR NIV Pune, NIBMG Kalyani, GBRC Gandhinagar and Gandhi Medical College, Secunderabad Methods and Resources ...
    Posted May 14, 2020, 8:20 AM by Vinod Scaria
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COVID-19 Resources
The COVID-19 resources at GenePI are listed below. A comprehensive listing is available at the COVID-19 Open Research, Data and Resources page.


COVID-19 Genomepedia is a c comprehensive searchable resource for SARS-nCoV-2 genomes from across the world


Gupta, V., Bhoyar, R. C., Jain, A., Srivastava, et al, 
Clinical Infectious Diseases (2020) ciaa1451, 

Banu S, Jolly B, Mukherjee M, Singh P, Khan S, Zaveri L, Shambhavi S, Gaur N, Mishra RK, Scaria V, Sowpati DT 

Poojary M, Shantaraman A, Jolly B, Scaria V 

Jain A, Rophina M, Mahajan S, Krishnan BB, Sharma M, Mandal S, Fernandez T, Sultanji S, Mathew S, Sivasubbu S, Scaria V 
Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays International Journal of Infectious Diseases 

Bhoyar RC, et al, High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing bioRxiv 2020.08.10.242677; doi: [Preprint]

Radhakrishnan C, Divakar MK, Jain A et al, 
Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions bioRxiv 2020.09.09.289892; doi: [Preprint]

Yadav S,Thakkar D,Bhoyar R,Jain A,Wadhwa T,Imran M,Jolly B,Divakar M,Kapoor R,Rastogi N,Sharma D,Sehgal P,Ranjan G,Sivasubbu S,Sarma S,Scaria V
Asymptomatic Reactivation of SARS-CoV-2 in a Child with Neuroblastoma Characterised by Whole Genome Sequencing. Authorea. October 12, 2020. DOI: 10.22541/au.160253792.25165912/v1  [Preprint]

Sivakumar S, Vimal S, Majeed SA, Kumar SS, Taju G, Madan N, Rajkumar T, Thamizhvanan S, Shamsudheen KV, Scaria V, Sivasubbu S, Hameed ASS
A new strain of white spot syndrome virus affecting Litopenaeus vannamei in Indian shrimp farms
J Fish Dis. (2018) ;1–18 DOI: 10.1111/jfd.12811

Jalali S, Kohli S, Latka C, Bhatia S, Vellarikal SK, Sivasubbu S*, Scaria V*, Ramachandran R*
Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach

Patowary A, Chauhan RK, Singh M, Shamsudheen KV, Periwal V, Kushwaha KP, Sapkal GN, Bondre VP, Gore MM, Sivasubbu S and Scaria V
De novo identification of viral pathogens from cell culture hologenomes
BMC Research Notes 2012, 5:11