Metagenome sequencing is transforming pathogen surveillance

Subject :Science and technology

Section: Health

Metagenomics:

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.
Metagenomics is the study of the structure and function of entire nucleotide sequences isolated and analyzed from all the organisms (typically microbes) in a bulk sample. Metagenomics is often used to study a specific community of microorganisms, such as those residing on human skin, in the soil or in a water sample.

Metagenomics technique used in SARS-CoV-2:

Scientists didn’t go the more time-consuming microbiology route with the Covid-19 samples; instead, and in a break from tradition, they were directly subjected to genome-sequencing and bioinformatic analysis, which helped the scientists quickly identify the virus.
This new approach – called metagenomics – was not only rapid but could also be deployed directly on patient samples, without any a priori knowledge of the infectious agent.
- The scale of sequencing during the pandemic rendered SARS-CoV-2 one of the most sequenced organisms in global history.
The technique and its adoption also drastically changed the way pathogen identification would be undertaken thereafter.

Difference between traditional microbiology route and Metagenomics:

While traditional microbiologyand microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods.
Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world.
- As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.
- Recent studies use either “shotgun” or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities.

Significance of this new technique:

The national and international organizations started implementing public health policies based on the genomic data.
- GISAID, a popular repository on the internet to which SARS-Co-V-2 genome-sequence data could be submitted, is a testimony to such high-throughput genome surveillance activities.
- India also initiated a national SARS-CoV-2 genome-sequencing and surveillance program supplemented by several State government and private initiatives.
The Nigerian Centre for Disease Control applied metagenomicssequencing for pathogen surveillance and detection, and was able to identify several viruses including: Human blood-associated dicistrovirus, pegivirus C and the presence of yellow fever and mpox virus in the patients.
The study demonstrated the power of metagenomic sequencing investigations for pathogen detection and disease diagnosis, and to inform public health outbreak responses.
In 2022, the world witnessed a global mpox virus outbreak which fortunately ‘fizzled’ out majorly because the scientists were able to apply genome-sequencing technologies perfected during the COVID-19 pandemic to understanding the origin and spread of the mpox virus.
Recently, the experts have used genome sequencing technologies as frontline tools to motivate the detection and surveillance of lumpy skin disease in cattle and the emergence of drug-resistant tuberculosis, among other use-cases.

Avian Influenza:

Avian influenza viruses are another prime candidate for genome surveillance as they trigger seasonal outbreaks of avian influenza, or bird flu.
Given the highly mobile and migratory nature of their hosts – including both wild birds and poultry – avian influenza viruses are capable of causing mass death in birds and some animals, and with little warning.
They need to be complemented by a well-organised genomic surveillance programme so that scientists can identify which virus strains are circulating, as well as monitor the impact of vaccination.

Key to early response:

The genome surveillance provides the sort of information that experts can use to devise an early response strategy, identify emerging viral strains, and undertake risk-based surveillance of key animal species.
Such initiatives have also been mooted for other seasonal pathogenic viruses, including Zika and dengue.