Global disparities in SARS-CoV-2 genomic surveillance

Abstract

The COVID-19 pandemic has revealed the importance of virus genome sequencing to guide public health interventions to control virus transmission and understand SARS-CoV-2 evolution. As of July 20th, 2021, >2 million SARS-CoV-2 genomes have been submitted to GISAID, 94% from high income and 6% from low and middle income countries. Here, we analyse the spatial and temporal heterogeneity in SARS-CoV-2 global genomic surveillance efforts. We report a comprehensive analysis of virus lineage diversity and genomic surveillance strategies adopted globally, and investigate their impact on the detection of known SARS-CoV-2 virus lineages and variants of concern. Our study provides a perspective on the global disparities surrounding SARS-CoV-2 genomic surveillance, their causes and consequences, and possible solutions to maximize the impact of pathogen genome sequencing for efforts on public health.

Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

“…The substantial number of sequences and spatiotemporal distribution of B.1.628 major might normally be interpreted as evidence of an earlier emergence compared to B.1.627, B.1.631 and B.1.634. However, sampling intensity and the relative frequency of different lineages in the region require careful consideration , particularly given the considerable disparities in sampling intensity in the context of genomic surveillance (Brito et al, 2021) , 2021). Given the differences in genome sampling and sequencing intensity between the two countries during the months preceding the detection of these lineages (6.3% of confirmed cases were sequenced in the USA during the last week of March 2021, compared to 1.6% for Mexico; Brito et al, 2021), it is likely that early cases of the B.1.628 major were not detected by genomic surveillance.…”

“…However, sampling intensity and the relative frequency of different lineages in the region require careful consideration , particularly given the considerable disparities in sampling intensity in the context of genomic surveillance (Brito et al, 2021) , 2021). Given the differences in genome sampling and sequencing intensity between the two countries during the months preceding the detection of these lineages (6.3% of confirmed cases were sequenced in the USA during the last week of March 2021, compared to 1.6% for Mexico; Brito et al, 2021), it is likely that early cases of the B.1.628 major were not detected by genomic surveillance. However, the regional distribution of the lineages does suggest the recombinant lineage emerged in North America between late 2020 and early 2021.…”

Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific real time reverse transcription PCR

“…There is also evidence that infection with the Delta variant is associated with higher viral loads, more severe disease, and a greater risk of hospitalisation [7] . It is, therefore, important to monitor the spread of the Delta variant globally to inform public health policies and interventions [8] . The gold standard methodology for identifying Delta is full genome sequencing.…”

Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13

“…Currently, the identification of viral mutations and tracking of circulating SARS-CoV-2 variants is performed by viral genomic sequencing and a small number of mutation-specific RT-qPCR tests [27][28][29] . However, the lack of infrastructure and expertise have made routine genomic surveillance difficult to perform outside of specialized genomic centers 30 . CRISPR-Dx are uniquely suited to detect VOCs for routine surveillance applications.…”