Genomic surveillance at scale is required to detect newly emerging strains at an early timepoint

Abstract

Genomic surveillance in the setting of the coronavirus disease 2019 (COVID-19) pandemic has the potential to identify emerging SARS-CoV-2 strains that may be more transmissible, virulent, evade detection by standard diagnostic tests, or vaccine escapes. The rapid spread of the SARS-CoV-2 B.1.1.7 strain from southern England to other parts of the country and globe is a clear example of the impact of such strains. Early discovery of the B.1.1.7 strain was enabled through the proactive COVID-19 Genomics UK (COG-UK) program and the UK’s commitment to genomic surveillance, sequencing about 10% of positive samples.1 In order to enact more aggressive public health measures to minimize the spread of such strains, genomic surveillance needs to be of sufficient scale to detect early emergence and expansion in the broader virus population. By modeling common performance characteristics of available diagnostic and sequencing tests, we developed a model that assesses the sampling required to detect emerging strains when they are less than 1% of all strains in a population. This model demonstrates that 5% sampling of all positive tests allows the detection of emerging strains when they are a prevalence of 0.1% to 1.0%. While each country will determine their risk tolerance for the emergence of novel strains, as vaccines are distributed and we work to end the pandemic and prevent future SARS-CoV-2 outbreaks, genomic surveillance will be an integral part of success.

Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York

“…Genomic surveillance is a critical tool to monitor the progression of the COVID-19 pandemic and modelling suggests that sequencing at least 5% of specimens that test positive for SARS-Cov-2 in a geographic region is necessary to reliably detect the emergence of novel variants at a lower prevalence limit of between 0.1% to 1% 24 . Through the combination of increased sequencing efforts and the use of the software utility described here, we were able to identify the B.1.526 lineage and to begin to characterize its phylogenetic and phylodynamic patterns in NYC in early 2021.…”

The localized rise of a B.1.526 SARS-CoV-2 variant containing an E484K mutation in New York State

“…L452R might increase infectivity by stabilizing the spike-ACE2 receptor interaction and has evolved independently in multiple lineages (such as B.1.427; Tchesnokova et al 2021). While surveillance efforts have increased in the US, the country has not yet met the recommended sequencing of 5% of all COVID-19 cases in order to detect variants before they reach high prevalence in the population (Vavrek et al 2021).…”

Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany

“…From the beginning of last year, the world has witnessed the emergence and unprecedented spread of SARS-CoV-2 which has so far claimed at least 3.5 million lives worldwide (June 2021, WHO). Viral genome sequencing and subsequent integrated data analyses proved to be essential [ 1 , 2 , 3 , 4 ] to track the spread of the virus and to detect emerging mutations as well as variants of concern/interest (VOC/I) that can be associated with antibody escape or higher transmissibility [ 5 , 6 , 7 , 8 ].…”