COVID-19 control needs faster submission of genome sequence to public portal
doi:10.1038/nindia.2021.111 Published online 17 August 2021
Control of the COVID-19 pandemic requires not just sequencing the genomes of the virus strains in positive cases, but “accelerated submission” of the sequenced genomes to the open access platform GISAID (Global Initiative on Sharing All Influenza Data), scientists say1.
The scientists, from the Institute of Bioinformatics and Applied Biotechnology (IBAB) in Bengaluru, say their statistical analysis of the data for the 1,718,035 COVID-19 strains submitted to GISAID (as of 27 May 2021) by various countries suggest that the time lag between collection and submission per strain varies from one day to over one year.
They note that several new Covid-19 variants were first identified using GISAID data, which is accessible to researchers worldwide. These include B.1.1.7 (in the United Kingdom), B.1.351 (South Africa), B.1.1.28 (Brazil), B.1.617.2 and B.1.617.1 (India), P.3 (Philippines), and B.1.427 and B.1.429 (United States).
Discussing why several countries, including India, are taking more time in identifying new variants, the report says that in countries with a longer time lag, such as India, the new variants may have enough time to establish themselves across a region if quick tracking, tracing and actions to stop transmission are not undertaken.
“Therefore, this issue must receive urgent attention and bottlenecks that prevent a lower time lag must be addressed,” the report says. “This will enable researchers across the globe to track the evolved variants and their mutations, epidemiology and biological consequences, which will provide crucial inputs for appropriate and effective public health policies.”
The absence of a strong system for sample collection, a paucity of funds or restrictions on importing reagents and equipment that use newer sequencing technologies would also add to the delay in submission.
“One does not know the extent of various problems in each country, causing a delay in sequencing and submission,” says Gaurav Sharma, corresponding author. “It is important to remove these obstacles.”
1. Kalia, K. et al. The lag in SARS-CoV-2 genome submissions to GISAID. Nat. Biotechnol. Doi: 10.1038/s41587-021-01040-0