Thread by @andersonfbrito_

Do you know that only ~6% of the SARS-CoV-2 genomes submitted to GISAID (up to July 20th) came from low- and middle-income countries? 🌎🧬



In this study we discuss the causes, consequences and possible solutions for disparities in SARS-CoV-2 genomic surveillance. 🧵👇

The emergence of VOCs and VOIs (Variants of Concern/Interest) in late 2020 led countries to intensify genomic surveillance, especially high income countries, which sequence >5% of reported cases each week.

This threshold, however, cannot be achieve by most countries (see below)

The overall percentage of sequenced cases, and the frequency of sampling also reveal disparities. And when we contrast weekly incidences and % sequenced cases, we see that few countries sequence >5% of cases when incidence is high (>100 cases/100,000 pop), as they reach capacity.

The rapid public sharing of data is essential for genomic surveillance.

The median turnaround time (time between sample collection and genome submission) varied greatly across geographic regions, with extremes of 19 days in Northern Europe, and 78 days in Eastern/Central Africa.

With the worsening of the pandemic, and high COVID-19 incidences, few countries were able to maintain fast and deep genomic surveillance, especially low- and middle-income countries, which generated few or no sequences in many weeks in 2020-2021.

Disparities in national wealth, in investment in R&D, and national coordination impact the ability of countries to perform genomic surveillance. Below we show how the % sequenced cases and turnaround time correlate with socioeconomic factors.

How the % of sequenced cases and the turnaround time affect a country’s ability to detect a previously-identified variant?

First, our results show that countries sequencing low % of cases and few genomes tend to detect less SARS-CoV-2 lineage diversity in circulation.

Using binomial confidence intervals, we estimated that when the prevalence of a rare lineage is 2%, 300 cases would need to be sequenced for at least one genome of that lineage to be detected with 95% probability. Rapid turnaround time is also essential for quick detection.

In this study we identified that Denmark has one of the best genomic surveillance programs, with quick turnaround (<18 days) and high % of sequenced cases (>32%). The lineage diversity in Denmark is large. Countries with low surveillance may be missing many circulating variants.

Local public health labs should strengthen their local capacity to sequence at least 0.5% of cases per week, when incidence is high (100 cases/100,000 pop.). 📈

In this scenario of peak incidence, such threshold can be achieve by sequencing 1 genome for every 200,000 habitants.

Socioeconomic, epidemiological, and political factors (coordination) impact genomic surveillance capacity and timeliness. As a result, genomic surveillance in many countries is sparse, and do not meet the minimum threshold of 0.5% of sequenced cases per week.

In order to maintain constant and rapid genome sequencing, local coordination, adequate staffing/training, and appropriate analytical tools are essential for enabling rapid responses to emerging infectious disease threats to public health.

Efforts must be made to provide funds, training, and logistic support for low- and middle-income countries to improve their local genomic surveillance capacity, to allow public health decision making in regions where resources may be scarce.

In the link below you can find more details about our findings (under peer-review) about the global disparities in SARS-CoV-2 genomic surveillance. 🌎🦠🧬
medrxiv.org/content/10.110…