A pc-generated rendering of a complete influenza (flu) virus, in semi-transparent blue with a navy-blue background.
| Photo Credit: Dan Higgins/CDC
If we’re to outline one world life-altering occasion of our era, COVID-19 is more likely to prime the checklist. All of us witnessed the devastation that the COVID-19 pandemic wrought, at a scale so unprecedented that individuals nearly in every single place paused what they had been doing and began looking for solutions collectively to finish it shortly.
One of the preliminary breakthroughs within the definitive identification of SARS-CoV-2 because the causative agent of COVID-19 got here from the applying of unbiased genome sequencing applied sciences to contaminated affected person samples. Scientists didn’t go the extra time-consuming microbiology route with these samples; as a substitute, and in a break from custom, they had been instantly subjected to genome-sequencing and bioinformatic evaluation, which helped the scientists shortly determine the virus.
This new strategy – referred to as metagenomics – was not solely fast however is also deployed instantly on affected person samples, with none a priori information of the infectious agent. Indeed the size of sequencing through the pandemic rendered SARS-CoV-2 one of the vital sequenced organisms in world historical past. The approach and its adoption additionally drastically modified the best way pathogen identification can be undertaken thereafter.
Genomic tech to the frontline
Scientists in nations worldwide have since developed scores of applied sciences based mostly on genome-sequencing – together with the very talked-about CovidSeq assay – spawning a number of nationwide and worldwide SARS-CoV-2 genome surveillance actions. GISAID, a well-liked repository on the web to which SARS-Co-V-2 genome-sequence information could possibly be submitted, is an affidavit to such high-throughput genome surveillance actions.
(‘High-throughput’ refers to sequencing methods that may parse massive portions of DNA on the identical time, together with a complete genome directly.)
The significance and affect of the best way SARS-CoV-2 was being surveilled additionally turned evident when nationwide and worldwide organisations began implementing public well being insurance policies based mostly on the genomic information. India additionally initiated a nationwide SARS-CoV-2 genome-sequencing and surveillance program supplemented by a number of State authorities and personal initiatives.
The success has offered a template for making use of refined genomic applied sciences as frontline instruments to surveil recognized and unknown organisms and to monitoring rising pathogens in an unbiased and high-throughput method.
The Nigerian examine
In an August 4 paper in Nature Communications, scientists from the Nigerian Centre for Disease Control utilized metagenomic sequencing for pathogen surveillance and detection in three cohorts of sufferers. They investigated 593 febrile Nigerian people with unbiased sequencing.
The first cohort represented population-level surveillance of people presenting with signs in line with Lassa fever, a viral haemorrhagic fever brought on by the Lassa virus endemic to West African nations. The second cohort consisted of individuals from outbreaks with suspected infectious aetiologies. The third cohort consisted of individuals with clinically difficult however undiagnosed circumstances.
The scientists had been in a position to determine 13 distinct viruses afflicting the people. The genomic strategy additionally helped them pinpoint the second and third documented instances of human blood-associated dicistrovirus, which the workforce named the human blood-associated dicistrovirus 2, among the many cohorts.
The scientists additionally recognized pegivirus C as a typical co-infection in sufferers with Lassa fever in addition to that the presence of pegivirus C was related to a decrease viral load in sufferers. Further investigations revealed the presence of yellow fever virus and mpox virus in sufferers.
As it occurred, the metagenome-sequencing strategy additionally allowed the scientists to rule out viral infections in some people and hyperlink their signs to pesticide poisoning as a substitute.
The examine demonstrated the ability of metagenomic sequencing investigations for pathogen detection and illness prognosis, and to tell public well being outbreak responses.
Tracking avian influenza
In 2022, the world witnessed a world mpox virus outbreak. It was attributed to a super-spreader occasion and threatened the planet with one other epidemic, however which luckily ‘fizzled’ out. One cause is that scientists had been in a position to apply genome-sequencing applied sciences perfected through the COVID-19 pandemic to understanding the origin and unfold of the mpox virus.
Avian influenza viruses are one other prime candidate for genome surveillance as they set off seasonal outbreaks of avian influenza, or chicken flu. Given the extremely cellular and migratory nature of their hosts – together with each wild birds and poultry – avian influenza viruses are able to inflicting mass demise in birds and a few animals, and with little warning. These outbreaks pose a danger to human well being in addition to human livelihoods and biosecurity.
In the final decade, avian influenza viruses have additionally unfold quickly to people. While fast detection kits and vaccines for these viruses are extensively obtainable, they must be complemented by a well-organised genomic surveillance programme in order that scientists can determine which virus strains are circulating, in addition to monitor the affect of vaccination.
The worldwide deployment of large-scale genome sequencing infrastructure through the COVID-19 pandemic is now holding us in good stead, by permitting us to conduct avian influenza genomic surveillance at supply. For instance, scientists working on the Institut Pasteur du Cambodge, Cambodia, demonstrated earlier this 12 months the ability of such surveillance once they efficiently decoded the total genome sequence of the Cambodian H5N1 virus in below 24 hours.
Key to early response
Such initiatives have additionally been mooted for different seasonal pathogenic viruses, together with Zika and dengue. More just lately, consultants have used genome sequencing applied sciences as frontline instruments to encourage the detection and surveillance of lumpy pores and skin illness in cattle and the emergence of drug-resistant tuberculosis, amongst different use-cases.
It is heartening that a number of initiatives worldwide are profiting from the pace, accuracy, and high-throughput nature of superior genome sequencing applied sciences to detect pathogens from numerous environmental sources, comparable to wastewater, air, soil, and animals.
Since genome surveillance gives the kind of data that consultants can use to plan an early response technique, determine rising viral strains, and undertake risk-based surveillance of key animal species, genomic applied sciences are more likely to develop into mainstays of our arsenal towards pathogens of the longer term.
The authors are former scientists on the CSIR Institute of Genomics and Integrative Biology. All opinions expressed listed below are private.
