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How Helix rapidly scaled to provide national viral surveillance and what’s still needed in 2022

In September 2020, researchers in the UK first detected a SARS-CoV-2 variant that was more transmissible and deadly than the original strain. Later designated as the Alpha variant by the World Health Organization (WHO), the surge in cases caused by this variant led to England declaring a third national lockdown just a few months later. By January 2021, more than 50,000 people in the UK had died, presumably from Alpha.

On the other side of the Atlantic, Nicole Washington, Director of Research at Helix noticed a new trend in Helix’s COVID-19 diagnostic test results. COVID-19 positive tests exhibiting ‘S-gene dropouts’, an indirect way of detecting the Alpha variant in qPCR-based tests, were starting to appear.

“team. we are seeing the new covid variant,” wrote Washington on the company’s slack on December 22nd, 2020, just before the company was ready to take off for the winter holidays. Thus began a sequence of events – driven by quick-thinking Helix team members making the right decisions at the right time – that ultimately led to today’s viral surveillance program.

Thanks to a research protocol for viral sequencing that was already in place, Helix was able to confirm four cases of the Alpha variant, announcing the news in a blog post published on December 31st, 2020, just nine days after Washington’s original observation. Helix continued to monitor for the variant and ultimately detected 51 of the first 54 cases of Alpha in the US.

Helix identified 51 of the first 54 cases of Alpha in the US

In parallel, Washington’s team quickly published the early detection of Alpha in a preprint, which eventually broadened into a collaboration with scientists at Scripps Research and included viral sequencing data from 212 patients who had been infected. This data demonstrated for the first time that the new strain was roughly 50 percent more transmissible than other lineages, and that the share of US cases was increasing by about 7.5 percent daily. These findings were published just one month later as the cover story in Cell.

Meanwhile, the CDC had already begun to recognize that expanded viral sequencing and national surveillance would be a key strategy to mitigate the virus’ spread in order to help local hospitals prepare for surging caseloads. Helix’s quick actions demonstrated the need for increased surveillance of SARS-CoV-2 variants and that it was perfectly positioned to help meet those goals. This effort was solidified into a partnership with the CDC and Illumina, marking the first public-private partnership for viral sequencing in the US. After bringing sequencing in-house, Helix would later renew this partnership with the CDC in late 2021.

The start of Helix’s involvement in COVID-19 response efforts

From June to November 2020, Helix went from a testing capacity of a few hundred tests per day to tens of thousands per day.

Before SARS-CoV-2 had arrived in the US, Helix was primarily a human genomic sequencing company. In response to the virus, we quickly pivoted our large-scale human sequencing platform to become one of the largest and most capable labs in performing high-throughput diagnostic testing nationally. This pivot was made possible due to quick decision-making by members of Helix’s laboratory and operations teams, and was primarily supported by Rapid Acceleration of Diagnostics (RADx) funding from the National Institutes of Health (NIH). Over the course of mere months, from June to November 2020, Helix went from a testing capacity of a few hundred tests per day to tens of thousands per day.

Helix’s high-volume national testing footprint is what allowed our researchers to be able to first spot the signal for the Alpha variant. But the S-gene dropout would need sequencing to confirm its relevance. Despite having a process in place to regularly sequence humans, doing so for the SARS-CoV-2 virus would initially be very manual. Only a few hundred samples could be set aside for sequencing per day and multiple hand-offs between teams were required.

Moreover, the viral sequencing work was burgeoning at the same time as the 2020 winter COVID-19 surge, adding more responsibilities to Helix’s already stretched laboratory staff. But, as it became clear that Helix was uniquely positioned to provide data of such public health importance, our leadership team quickly pulled scientists from all over the company to provide dedicated help for COVID-19 sequencing and data analysis.

One shift of scientists working five days a week in the laboratory soon swelled to three, working around the clock every day of the week. Eventually, engineering and bioinformatics teams automated much of the viral sequencing pipeline, creating data infrastructures that could quickly analyze sequencing information internally. And by March 2021, the viral sequencing assay itself was moved in-house in order to centralize and expand our capabilities. These workflows enabled Helix to continue to identify new variants, such as Delta and Omicron, and to share these essential findings as quickly as possible with the CDC. At one point Helix’s data accounted for more than 20 percent of all SARS-CoV-2 viral sequencing in the US, and our predictions about how variants were trending would be reported in the Wall Street Journal.

Ready for what’s next

As our team of researchers coalesced around COVID-19 sequencing efforts, we’ve also been able to contribute to a wide range of projects that investigate the role of genetics in viral infection and severity.

To ensure that every person infected with SARS-CoV-2 could identify their unique variant, we established methodologies early on with the NIH for their Genotyping Program. More recently, Helix contributed approximately 90 percent of the sequenced confirmed biobank samples to evaluate new diagnostics as part of the RADx program that could help enable providers to receive rapid variant reporting in the near-hospital setting to improve decision-making for treatments like monoclonal antibodies. All of this data has been used to provide faster insights into the rates that variants are spreading through a community.

We have also contributed data to global projects with the COVID-19 Host Genomics Initiative and the COVID Human Genetic Effort. These consortia aim to understand genetic variants that confer immunity to the virus or how the host genome impacts disease progression and symptoms. Each collaboration has spawned several peer-reviewed papers. One published in Nature helped uncover 13 genomic loci associated with severe cases of COVID-19, several of which have known roles in lung and inflammatory diseases.

Finally, we’ve played a key role in understanding vaccine reactions and vaccine effectiveness against SARS-CoV-2 variants. In November, by combining our human genome sequences with self-reported COVID-19 phenotypic information on 17,000 patients, our scientists were able to determine that people with the HLA-A3*03:01 serotype had a two-fold higher risk for severe reactions when given the Pfizer-BioNTech vaccine. We also leveraged the sequencing we’ve done on the virus itself to help understand the effectiveness of the Moderna and Pfizer vaccines against specific variants through a contract with Kaiser Permanente. Each of these studies have revealed important insights that can be used to enhance future vaccine and drug development.

We urge the federal government to rapidly establish a national real-time viral surveillance ecosystem so that we can deliver more effective public health responses and outcomes for all.

While we have seen significant advancements in science these past two years specifically in the realm of viral surveillance through genetic epidemiology, we must now make sure we leverage these learnings so we are prepared to respond to the next COVID variant, or even worse, the next inevitable “Pathogen X.” We urge the federal government to rapidly establish a sustainable, national real-time viral surveillance ecosystem that includes genomic sequencing so that we can deliver more effective public health responses and outcomes for all.

Helix has proven our ability to respond quickly and make important decisions in the name of public health, and we look forward to continuing to advance the infrastructure, data systems and technology needed to further scale and connect genomic surveillance to a broader network for improved outcomes.