Collaboration Launches to Assess the Prevalence of Coronavirus Variant

A collaboration agreement to augment national surveillance infrastructure in the USA to track the emergence and prevalence of novel strains of SARS-CoV-2 was announced.

With support from the US Centers for Disease Control and Prevention (CDC), llumina, Inc., and Helix announced the combination of sequencing technology, expertise, and a national COVID-19 testing footprint would significantly expand the USA’s existing surveillance efforts to detect and characterize emerging variants of the SARS-CoV-2 betacoronavirus.  

According to a press release issued on January 5, 2021, the collaboration has already demonstrated results in the USA by identifying 51 of the first 54 cases of B.1.1.7, the highly transmissible variant first found in the United Kingdom (UK).

The UK’s Public Health England confirmed on December 21, 2020, this novel variant had been identified spreading rapidly within the UK.

In a non-peer-reviewed study published on December 23, 2020, in the three most heavily affected England regions (South East, East of England, and London), researchers estimated that B.1.1.7 - VOC 202012/01 is 56 percent more transmissible (95% credible interval across three regions 50-74%) than preexisting variants of SARS-CoV-2.

Over the past several weeks, Helix has analyzed recent positive samples and identified those with ‘S gene dropout’ on their diagnostic PCR assay, indicating the potential presence of the emerging B1.1.7 variant in different regions in the USA. 

Illumina then sequenced a subset of these ‘S gene dropout’ samples using Illumina’s COVIDSeq Test, which identified the B.1.1.7 variant in 4 samples from California and Florida.

“Genomic surveillance is essential in fighting the pandemic. Illumina is pleased to partner with the CDC and Helix to provide accurate sequencing that can contribute to rapidly scaling genomic surveillance in the US to better understand the presence of B.1.1.7 and other variants as they emerge in our communities,” stated Dr. Phil Febbo, M.D., Chief Medical Officer of Illumina, in the press release.

“Having a robust surveillance effort in place is critical to understanding how the SARS-CoV-2 virus is evolving, and how our public health response needs to adapt,” added Dr. James Lu, M.D., Ph.D., co-founder and President of Helix. 

“By bringing together the strengths of Helix, Illumina, and the CDC, we were able to quickly evaluate the prevalence of this new variant and take learnings from this effort to better and more proactively characterize future strains that will emerge.”

During April 2020, a study's findings suggested that the virus is evolving and European, North American, and Asian strains might coexist, each of them characterized by a different mutation pattern. These researchers characterized (8) novel recurrent mutations of SARS-CoV-2, with 2891, 3036, 14408, 23403, and 28881 positions predominantly observed in Europe, whereas those located at positions 17746, 17857, and 18060 are exclusively present in North America.

The World Health Organization published an analysis on June 2, 2020, which found several variants of the SARS-CoV-2 genome exist and that the D614G clade has become the most common variant since December 2019. The evolutionary analysis indicated structured transmission, with the possibility of multiple introductions into the population.

Helix and Illumina are expanding the scope of their collaboration to examine a higher volume of samples on an ongoing basis for both the presence of B.1.1.7 and new strains. This effort will empower public and private entities to react quickly to any potential changes in pathogenicity of the virus or the effectiveness of diagnostics, therapeutics, and vaccines.

Click here to learn more about Illumina. Click here to learn more about Helix.

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