When research goes viral: Funding on COVID-19 variants is misdirected

As designed, the Canadian Institutes of Health Research’s (CIHR) funding opportunities to study the emergence of COVID-19 Variants of Concern (VoCs) are unlikely to achieve actionable results in a timeframe that could save lives.

The COVID-causing virus is evolving quickly, popping out new VoCs associated with increased infectivity (B.1.1.7) and immune avoidance (B.1.351). Emergence of these and other VoCs has been recognized as a major threat and, via their increased attack rates and longer periods of infectivity, spread quickly even as overall case numbers may appear to drop.

The tragic case of Roberta Place Long Term Care Home in Barrie, Ont., where all 129 of the residents along with 105 staff members contracted COVID-19, focused attention on VoCs in early February. Subsequent testing identified the B.1.1.7 variant as a significant culprit in the deaths of 69 residents.

A coordinated effort to address VoCs is urgently needed. On Jan. 29, responding to a call from the federal government, CIHR (and Genome Canada’s CanCOGen initiative) announced three funding programs for VoC research to the tune of $25 million for eligible CIHR researchers. The first program supplements already funded COVID-19 CIHR research projects for variant analysis; the second funds extra, but already submitted, project grants on VoC research; and the third funds the establishment of a national network called the Network for Emerging Variants Research. 

On the surface this looks good: responding to an emerging threat with a need to move fast. The timelines for applications are short and funding starts March 1. But while these funding opportunities are marketed as a responsive, coordinated effort to address VoCs, restricting the grants and funding to CIHR researchers who were funded in last year’s rapid COVID-19 competitions is unlikely to lead to results when and where they are needed most.  

The call is strikingly similar to the one last February, when the CIHR launched a rapid response competition to fund research into this emerging new disease. Despite a dearth of coronavirus research support in Canada since the SARS outbreak in 2003, 227 applications were submitted within an eight-day window. A second competition was launched in April with a 19-day application window, resulting in nearly 1,500 applications.

Through these two competitions, funds were rapidly dispersed to about 400 new investigations of one or two years in duration. This was, at the time, quite a pivot for CIHR given the paucity of investment in prior virology research in general and covered clinical trials, new testing methodologies, epidemiological studies and other areas of pandemic science. Time has yet to tell if the rapid injection of federal funds into COVID-19 research has altered the Canadian course of the pandemic but good science is being done.

The fundamental problem is that funding research, and the research itself, takes time and if shortcuts are taken, as is necessary in rapid response mode, it often leads to misplaced effort. The window of greatest need for VoC control is likely the next three to four months. By then, large scale vaccination should be impacting caseloads. That’s not to say we won’t need to continue surveillance. Indeed, as selective pressures on the virus increase, it becomes even more important to identify new variants. We absolutely will need to be thinking about pathogen surveillance – long after SARS-CoV-2 is a memory.

To avoid being labelled as performative, VoC identification will require rapid analysis and public health reporting, not only the observational studies and cataloguing that will be the likely output of the new funding. While full genomic sequencing is the gold standard and provides insights into patterns of spread and identification of new mutations, it is also expensive and relatively slow. The fastest tests, producing results in hours, are based on polymerase chain reactions but require a separate assay for each variant and normally can’t individually discern subtypes. Other tests have and are being developed that scan mutational hotspots, providing partial sequence and yield results in 24-to-48 hours. That is the timeframe needed for actionable results – for reporting VoC infections to public health units to allow for urgent, focused track and tracing. A week is a lifetime in viral infection terms.

Likewise, determining more viral sequences is highly doable but most will generate limited new information. Polio was conquered by using a new strategy, the Salk vaccine, not by building more iron lungs. In this case, restricting opportunities to scientists already funded for COVID-19 work eliminates those who may have better ideas and/or who have recently pivoted to work on VoCs.

The virus is mutating and so should our thinking. Why not run a VoC identification race where the winner is the group that accurately detects the most VoCs in the fastest time? The group’s reward is to teach its approach to the rest of the country’s labs.

The virus is nimble; we must be nimbler. Why have we still not yet learned that lesson? Here is my unsolicited advice: Send the money to public health labs across the country now, where VoC data can be acted upon, and have them adjudicate the technology race we need to win.