The National Genomic Surveillance initiated to track SARS-CoV-2 variants

15 SEP 2021

Bangladesh observed significant surges in the COVID-19 infection since March 2021, fueled by some highly contagious variants. According to the World Health Organization (WHO), these variants cause more infections and spread faster than early forms of SARS-CoV-2. Therefore, it is important to scale up whole-genome sequencing (WGS) capacity by following a systematic approach to support the epidemic preparations of the country. In this context, the National SARS-CoV-2 Variant Surveillance (NSVS) consortium was formed recently comprised of four leading institutes - Institute of Epidemiology, Disease Control and Research (IEDCR); icddr,b (formerly International Centre for Diarrhoeal Disease Research, Bangladesh); Child Health Research Foundation (CHRF); and Institute for Developing Science and Health Initiatives (ideSHi). These institutes are working closely to monitor genomic variants of SARS-CoV-2 across the country. The consortium will continue sequencing SARS-CoV-2 genomes in the next 12 months. The Bill and Melinda Gates Foundation (BMGF) has been supporting this initiative.

The overall goal of the NSVS is to identify variants of SARS-CoV-2 in Bangladesh through institutional collaborative efforts and a systematic approach. The NSVS will also strengthen the capacity for genomic surveillance through enhancing genome sequencing and analysis. It will also implement a strategic sequencing approach to maximise information regarding the virus evolution within the country by identifying SASR-CoV-2 variants. And finally, it will share data with national and international stakeholders who can use these data to find a broad range of pathogen threats in the future, leading to building a sustainable platform for epidemic surveillance in Bangladesh.

Genomic sequencing process

The IEDCR receives representative samples from 17 donor labs across the country, of which 13 are located outside of Dhaka, and four labs are within Dhaka city to cover all eight divisions of Bangladesh. The IEDCR then shares the specimens with the consortium institutions. The institutions extract SARS-CoV-2 RNA from the samples, convert it to complementary DNA, and load it into the next-generation sequencing equipment - Illumina MySeq, NextSeq, and Nanopore MinION. Specimens are sequenced, and data is collected from sequencers following quality control measures. The raw data is processed and turned into sequence data. After curing, all sequence data are immediately submitted to the public database GISAID.ORG, an open platform from which all the stakeholders can avail genetic data of the contemporary variants as and when required. Published data are openly accessible for analysis for scientists around the world.

 

Findings

A total of 179 samples were collected and sequenced between 01 July to 31 July 2021; of which 178 samples were Delta or B.1.617.2  (99.4%), and 1 (0.6%) was of Beta (B.1.351) variant. Different lineages of Delta variant such as Delta B.1.617.2-like, Delta AY.1, AY.4, AY.10, AY.12, AY.16, AY.19, AY.20, AY.21, and AY.25 were identified (Table 1).

Table - Total number of confirmed cases by variant and region (1-31 July 2021)

NextStrain build of SARS-CoV-2 variant distribution in Bangladesh (1-31 July 2021)

A phylogenetic tree was constructed with the 179 complete genomes of variants (collected between 1-31 July 2021) sequenced by the consortium using NextClade (clades.nextsrain.org). Phylogenetic analysis reveals that there have been multiple introductions of Delta variants across the country (Figure 1). Until 31 July 2021, no variant unique to Bangladesh has been detected. Interestingly, 1 Beta variant, which was mostly detected during March-June, 2021, still exists in one Division (Mymensingh).

Figure - Phylogenetic tree of the 179 SARS-CoV-2 Bangladeshi variants (collected 01-31 July 2021) sequenced by the consortium

The infrastructure and capacity built during this collective initiative will not only provide timely and practical information to guide COVID-19 response but also will create the framework to conduct surveillance and respond to future epidemic threats.

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MR