The importance of genomic surveillance of SARS-CoV-2 in Bangladesh
By utilizing information in a timely fashion, western countries are imposing lockdowns to reduce the spread of these variants and restricting their borders; the UK authority has already started restricting people from countries with highly infectious variants and updated the list of countries in the red regularly.
According to the weekly Covid-19 update reports, the overall new cases increased by 71.7 percent within a week as per the 55 published reports by the World Health Organization since March 15.
To know whether the increase cases of Covid-19 infection is happening due to the new variants evolved in Bangladesh or the imported variants, we need to keep track of the mutations by genomic surveillance.
Unfortunately, no sequence has been deposited since January in the public repository for SARS-CoV-2 genomes named GISAID - a global open-access platform that stores genomic data of influenza viruses and SARS-CoV-2. This stirred up our curiosity to investigate the Bangladeshi data a bit more.
After analyzing the metadata of GISAID till March 21, we found the existence of 971 sequences deposited from Bangladesh in the database, including incomplete sequences. Among them, the top three contributors are Bangladesh Council of Scientific and Industrial Research (BCSIR), DNA Solution Ltd (DNAS) and Child Health Research Foundation (CHRF) - depositing 371, 230 and 122 sequences, respectively.
According to the metadata from the same source, BCSIR collaborated with the National Institute of Laboratory Medicine and Referral Center (NILMRC) - named as the originating laboratory.
DNA solutions collaborated mainly with several institutions such as the University of Dhaka, Mymensingh Medical College and Hospital, and the Designated Reference Institute for Chemical Measurements (DRICM) as the originating laboratory. Most of the samples deposited by CHRF originated from its own sources.
For determining a highly infectious variant of the SARS-CoV-2, sequence genomes from a particular region should be kept under continuous monitoring as this can help detect the emergence of a highly infectious variant of the deadly virus.
For instance, the UK variant detected in December 2020 by monitoring sequences under the hood of Covid-19 Genomics UK (COG-UK) consortium, revealed one mutation (N501Y), detected in September under continuous monitoring, from an increasing frequency from genomic data from some regions.
From the sequence analysis of the mutation, they identified no link to foreign countries, thus announcing it as a local variant we are worrying about.
As the vaccine rolls out and the number of infections keep increasing, we need to monitor the evolution of the virus in our community with a plan. If we look at the data, no institute is monitoring viral evolution continuously.
For example, no sequences were deposited from BCSIR- NILMRC in August, September and November, 2020. Furthermore, almost all the sequences deposited in January are from Dhaka.
This is concerning, particularly because it is likely the virus has evolved from circulation and we lack regional data. A recent article published in Virus Research, an International journal of Molecular and Cellular Virology published by Elsevier BV in 1984, reports that there are 4,604 mutations, including 34 unique mutations of the local sequences among the 371 high-throughput genomic sequences deposited from Bangladesh as of November 30, 2020.
These 34 mutations are found in 14 different open reading frames of SARS-CoV-2 genomes and the spike glycoprotein has two unique mutations. The overall mutations per genome in Bangladeshi sequences was approximately 12.
So, to make a rapid public-health decision related to controlling the spread of the new local variants, like those originating in the UK and South Africa, a systematic genomic surveillance study should be in place.
By utilizing information in a timely fashion, western countries are imposing lockdowns to reduce the spread of these variants and restricting their borders; the UK authority has already started restricting people from countries with highly infectious variants and updated the list of countries in the red regularly.
Moreover, monitoring is also required for assessing the effectiveness of the vaccine against the circulating virus. At this point, we need a systematic sequencing plan that sequences a representative number of genomic sequences from different regions of the country regularly to establish the genomic surveillance of SARS-CoV-2.
We also urge to publish periodic public reports on local variants from implementing institutes.
Investing in genomic surveillance could help healthcare service providers gain a better understanding of the circulating viruses to update their decision-making process.
Md Mahbub Hasan is a PhD Candidate at Institute of Pharmaceutical Science in King's College London and Assistant Professor of Genetic Engineering at the University of Chittagong. He can be reached at mahbub.hasan@kcl.ac.uk.
Dr Khondaker Miraz Rahman is Reader in Medicinal Chemistry and Antimicrobial Research Theme Lead at Institute of Pharmaceutical Science in King's College London. He can be reached at k.miraz.rahman@kcl.ac.uk.
