Why strengthening genomic surveillance is an imperative

Subject :Science and Technology

Section: Biotechnology

Context:A recent study revealed that the rate of genetic changes in the monkeypox virus was higher than expected

Ever since it was first reported in humans in 1970, monkeypox virus infections have been largely restricted to countries in Central and Eastern Africa until recently.
Following a rapid rise in cases, the World Health Organization (WHO) on July 23, 2022 declared the 2022 monkeypox outbreak as a Public Health Emergency of International Concern (PHEIC).

Genome sequences

The accelerated use of genomics as a tool to understand outbreaks in the last half decadehas left an indelible mark during the ongoing COVID-19 pandemic and has seen a wider deployment of sequencing infrastructure across the world. Genomic surveillance of pathogens could provide unique insights to understand the outbreak better, track the spread of pathogens and provide immense opportunities for public health decision-making as well as for epidemiology.
Researchers from across the world have made available over 650 complete genome sequences of monkeypox isolates to date in public domain databases including GISAID and GenBank. This includes over 600 genomes which were sequenced this year alone from over 35 countries, including genomes of two isolates from India, collected from Kerala.

Accelerated evolution

The monkeypox virus has a DNA genome of around 2,00,000 base pairs, roughly six times larger than that of SARS-CoV-2.
Being a DNA virus, the monkeypox virus like other poxviruses was believed to have a small rate of accumulating genetic changes compared to viruses with an RNA genome like SARS-CoV-2, which have a much larger rate of mutations. For poxviruses, this rate is estimated to be as low as a couple of genetic changes every year. A recent study, however, revealed that the observed rate of genetic changes in the virus was higher than expected — average of around 50 genetic changes.

APOBEC3 protein

The study also suggests that several mutations that have been identified in the new sequences of the monkeypox virus may have emerged due to interaction between the virus genome and an important family of proteins coded by the human genome known as the Apolipoprotein B Editing Complex (or APOBEC3). These proteins offer protection against certain viral infections by editing the genome sequence of the virus while it replicates in the cell.
Monkeypox virus can infect a range of hosts, including non-human primates and rodents which could act as a natural reservoir. Infections in the reservoir could also enable continued transmission and accumulation of mutations before spilling over to cause human infections. Other studies have also suggested a continued evolution of the virus, including deletions involving genes as seen in a few genomes from the present outbreak, which could suggest newer ways in which the virus continues to evolve with sustained human-to-human transmission.

Monkeypox lineages

Clusters of genomes having common and shared mutations and a common origin are referred to as a lineage or clade. In the early 2000s, two different clades of monkeypox virus were defined in Africa where several cases of the disease have been seen — the Central African (Congo Basin) clade and the West African clade, of which the Congo Basin clade has been shown to be more transmissible and cause more severe disease.