Genome sequencing of coronavirus in sewage can help detect local variants

20 Janvier, 2021, 17:55 | Auteur: Yves Courtet
  • ImmunityBio Simulations give clue to why South African strain of SARS-CoV-2 is rapidly spreading

The ability to track SARS-CoV-2 mutations in wastewater could be particularly useful for tracking new variants, like the B.1.17 strain that is now widespread in the United Kingdom and has already been introduced in the U.S.

Enhanced affinity of S RBD for hACE2 very likely underpins the greater transmissibility conferred by the presence of either E484K or N501Y; while the induction of conformational changes may provide an explanation for evidence that the 501Y.V2 variant, distinguished from the B.1.1.7 United Kingdom variant by the presence of E484K, is able to escape neutralization by existing first-wave anti-SARS-CoV-2 antibodies and re-infect COVID-19 convalescent individuals. By sampling wastewater, we can get information on infections for a whole population, ' explained study co-author Kara Nelson from the University of California (UC)-Berkeley in the US. "Sampling wastewater is a very efficient way to get information". It is also a less biased source of information, because we can get information from all individuals in the sewershed, whether or not they are being tested in a clinic. "We know that there are individuals that have asymptomatic infections that may never get tested".

In the new study, researchers developed and used a novel method for sampling wastewater.

When scientists sequence genetic material concentrated and extracted from wastewater samples, the study noted that there may be many different strains present as there are many individuals contributing to the sample. However, it is challenging to distinguish the SARS-CoV-2 genetic signal from the billions of bacteria and viruses people excrete every day.

"The way that we need to process the sequence information is complex". One contribution of this paper is the ability to prepare samples for sequencing from wastewater, ' Nelson said.

Instead of directly sequencing everything present, the researchers used a new approach in which they first tried to enrich the viral RNA. "You can't get any more sensitive than that".

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In the study, the scientists sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate whole and almost complete SARS-CoV-2 genomes.

In the first study, "Millisecond-scale molecular dynamics simulation of spike RBD structure reveals evolutionary adaption of SARS-CoV-2 to stably bind ACE2" using exceptionally long-duration millisecond scale MD simulation, ImmunityBio scientists revealed the evolutionary adaptation of spike RBD for binding to ACE2, and the regions of RBD that strongly bind ACE2.

The researchers also detected variants with very small differences in the genetic material that had only been reported from elsewhere in the USA or globally.

On the basis of their findings, Nelson and her team suggested that wastewater sequencing can provide evidence for new viral lineages before clinical sequencing.

In the new study, MD simulation was applied to the highly concerning new strains of SARS-CoV-2 including the predominating variant in South Africa 501Y.V2 and the United Kingdom variant B.1.1.7.

'Of everyone who gets tested, only a fraction of those samples even get sequenced. You can't get any more sensitive than that, ' Nelson said. Therefore, the organisation has stressed the importance of improving genomic sequencing in order to identify and respond to new variants early on. It provides a network for scientists in academia, industry and clinical settings. ASM's mission is to promote and advance the microbial sciences. It enhances laboratory capacity around the globe through training and resources. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.

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