Global disparities in SARS-CoV-2 genomic surveillance

Abstract

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.

Leveraging global genomic sequencing data to estimate local variant dynamics

“…Characterizing the growth of emerging variants and accurate nowcasting of prevalence are challenging problems. There are often long lag times from sequence collection to submission and reporting, especially in locations with limited sequencing capacity ( 20 ). Emerging variants have few sequences available and, usually, have been detected in only a few countries.…”

“…Because genomic data are often quite sparse, these methods can be challenging to apply in practice. In addition to being limited in numbers, genomic data are often concentrated into a few geographies, both for emerging variants and for many countries as a whole 20 . For example, 90% of publicly available SARS-CoV-2 sequences come from just 10% of countries (Figure 1).…”

“…For example, 90% of publicly available SARS-CoV-2 sequences come from just 10% of countries (Figure 1). These disparities are not only in the raw number of sequences available, but also in the percent of cases sequenced and the turnaround time from sample collection to sequence availability 20 . Because of the concentration of sequencing into a few countries, sample size limitations often make country-specific, regression-based approaches unreliable.…”

Global SARS-CoV-2 genomic surveillance: What we have learned (so far)

“…However, regional and temporal variation in the intensity of SARS-CoV-2 genome sequencing was primarily driven by socioeconomic disparities, as evidenced by the percentage of COVID-19 cases sequenced in countries around the world. Nearly 80% of high-income countries had more than 0.5% of their COVID-19 cases sequenced, compared to less than 50% of middle and low-income countries ( Brito et al, 2022 ). Recognising the significant opportunities afforded by genomics, there have been since the start of the pandemic major government investments in the development and implementation of whole-genome sequencing (WGS), predominantly within high-income settings.…”

Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel

“…Continental source-sink dynamics were determined by calculating the net difference between viral exportation and importation events for each country and continent (see Materials & Methods for more detail). A limiting factor of this analysis is that countries with under-reported incidence and low sequencing proportions 18 but high global connectivity would have been missed as important global or regional VOC disseminators (given the reliance of our methods on genomic data and underlying testing patterns).…”