Rapid identification and tracking of SARS-CoV-2 variants of concern

In the past few months, we have seen emergence of clinically important mutations that alter infectivity, severity, or immune susceptibility of SARS-CoV-2.¹ Prominent examples include Asn501Tyr, His69_Val70del, and Glu484Lys mutations in the spike protein that have emerged independently in many global strains, such as those from the UK, South Africa, and Brazil, possibly driving resurgence of the pandemic when it appeared to be coming under control.² Some of these variants are likely to be resistant to vaccines and capable of reinfections. Future public health policy and pandemic response will need knowledge of the presence of such variants in the local population and their rapid identification on introduction into communities. This is not possible without local sequencing capacity, which is scarce in many vulnerable parts of the globe, where lockdown regulations are not strictly enforced and movement is unrestricted.³ Even in those low-income and middle-income countries where such capacity is present and high alert is in place, the delay between positive diagnosis and sequencing results leads to an opportunity for a new variant to become established. Hard quarantine, involving strict confinement and isolation for all people with a positive test for SARS-CoV-2 who are at risk of carrying clinically important new variants, until cleared by sequencing, is a public health measure that is difficult to implement. This difficulty arises because long turnaround times that are associated with sequencing might lead to extra pressure on health-care authorities for institutional quarantine or follow-up after release in the event of variant detection in an individual. Diagnostic platforms that are based on sequencing and are suitable for use at the point of care, such as pore-based technologies, are anticipated to contribute substantially to this process in the near future, being capable of diagnosis, variant calling, genealogy, and novel mutant detection. Until then, we propose an alternative approach for low-resolution, yet accurate, early detection of specific variants of concern through clustered interspaced short palindromic repeats (CRISPR) diagnostics, which rely on the specific DNA interrogation properties of enzymes, such as FnCas9, Cas12, or Cas13, to identify variants of concern through fluorescence or paper strip-based diagnosis (appendix).⁴ Such tests are rapid, inexpensive, and especially suited for low-income countries. Even where sequencing is being done, CRISPR diagnostics can help to isolate variants in the first instance, which can then be sequenced to validate and map coexisting mutations (appendix). We have used this approach to identify the Asn501Tyr variant of concern, starting from RNA.⁵ The variant detection strategy (ie, rapid variant assay) can be readily combined with a CRISPR diagnostics platform that is already approved as an equivalent diagnostic method to quantitative real-time PCR in India, providing diagnosis and identification of one variant of concern in less than 90 min from sample to result, at a test cost of less than US$15.

The coming months present a challenging scenario: tracking and controlling the spread of such variants and simultaneously understanding their effects on the pandemic. Large-scale sequencing efforts and tailor-made diagnostic solutions, such as CRISPR diagnostics will be crucial.