The feasibility of targeted test-trace-isolate for the control of SARS-CoV-2 variants

William Bradshaw,Alun Lloyd,Jonathan Huggins,Kevin Esvelt

doi:10.12688/f1000research.51164.1

Abstract

The SARS-CoV-2 variant B.1.1.7 reportedly exhibits substantially higher transmission than the ancestral strain and may generate a major surge of cases before vaccines become widely available, while the P.1 and B.1.351 variants may be equally transmissible and also resist vaccines. All three variants can be sensitively detected by RT-PCR due to an otherwise rare del11288-11296 mutation in orf1ab; B.1.1.7 can also be detected using the common TaqPath kit. Testing, contact tracing, and isolation programs overwhelmed by SARS-CoV-2 could slow the spread of the new variants, which are still outnumbered by tracers in most countries. However, past failures and high rates of mistrust may lead health agencies to conclude that tracing is futile, dissuading them from redirecting existing tracers to focus on the new variants. Here we apply a branching-process model to estimate the effectiveness of implementing a variant-focused testing, contact tracing, and isolation strategy with realistic levels of performance. Our model indicates that bidirectional contact tracing can substantially slow the spread of SARS-CoV-2 variants even in regions where a large fraction of the population refuses to cooperate with contact tracers or to abide by quarantine and isolation requests.

Highlights

The frequency of the B.1.1.7 variant of SARS-CoV-2 has grown rapidly from its initial detection in October 2020 to become the dominant strain in southeastern England by the start of 2021
Given the current low prevalence of the variants in most jurisdictions and the ability to identify cases of the new variant using existing testing infrastructure, we hypothesized that TTI programs dedicated to controlling them could substantially reduce the harm inflicted prior to widespread vaccination of populations later in 2021, especially if vaccine reformulation is needed
Such programs could be enhanced through incorporation of bidirectional tracing[10]

Summary

Introduction

The frequency of the B.1.1.7 variant of SARS-CoV-2 has grown rapidly from its initial detection in October 2020 to become the dominant strain in southeastern England by the start of 2021. Early reports suggest that current vaccines[3] and prior SARS-CoV-2 exposure[4] may be less protective against the B.1.351 and P.1 variants common in South Africa and Brazil. All three variants share an otherwise rare del11288–11296 mutation in orf1ab that can be detected using a single RT-PCR reaction[5]; B.1.1.7 can be distinguished with the TaqPath diagnostic test[6], twenty million of which are manufactured weekly[7]. As such, existing COVID-19 testing infrastructure can be used to track the transmission of the new variants. Samples testing positive by other kits can be re-screened[8] without an emergency use authorization

Methods

Results

Conclusion