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…

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More from @AndersonBrito_

7 Sep
Gente maluca de verde e amarelo na Paulista sempre me lembra as artes de @vitorcartum. Retratam bem como o Brasil chegou nesse nível de insanidade de 2013 para cá.

Facebook: facebook.com/vitorcartum/ph…
#ForaBolsonaro #7SForaBolsonaro #JailBolsonaro
Essas charges nunca envelhecem. #ForaBolsonaro 🇧🇷

Arte: @vitorcartum
Quem lembra do pato da @Fiesp? 🐥
Feliz R$ 7 de setembro!

Arte: @vitorcartum
#ForaBolsonaro 🇧🇷
Read 4 tweets
5 Sep
Uma portaria da @anvisa_oficial impõe restrições a viajantes que vêm de Reino Unido, África do Sul e Índia.



Por que esses países?
R: São os países de origem das variantes Alpha 🇬🇧, Beta 🇿🇦, Delta 🇮🇳

Mas essa medida é ilógica, já que as variantes estão em mais de 100 países.
Por semanas eu não queria crer que a @anvisa_oficial escolheu países alvo de restrições com base em locais de origem das variantes, e não com base em parâmetros de incidência da COVID-19 ou distribuição geográfica das variantes

Mas é isso mesmo. É uma regra ilógica, quase inócua
A portaria da ANVISA impõe quarentena apenas a viajantes com origem ou passagem pelos países que primeiro identificaram as variantes Alpha 🇬🇧, Beta 🇿🇦, Delta 🇮🇳

A medida deveria ter como alvo países com alta incidência de COVID e alta prevalência das variantes. Vejam os EUA.
Read 7 tweets
3 Sep
Entre as sugestões do Nextflix que recebi, já assisti ou comecei a assistir algumas: Atypical, Unorthodox, Sweet Tooth.

Agora estou assistindo o anime #Evangelion, é interessante. É uma produção bem anos 90: algumas cenas me remetem à banheira do Gugu.
Algumas cenas de Evangelion me transportam de volta para uma das viagens mais interessantes que fiz nos últimos anos, por razões óbvias. 🇯🇵⛩️🗾 ImageImageImage
Read 4 tweets
26 Aug
Any virus in circulation accumulates mutations over time. Evolution never stops. It works just like a construction of roadways: it starts small, it grows, splits…but also shrinks, gets extinct.

The Pango system of SARS-CoV-2 nomenclature aims at tracking these changes.🧵👇
When SARS-CoV-2 emerged, and caused large outbreaks in early 2020, the Pango system started by classifying the virus into two lineages: A and B.

This paper explains how this dynamic system works: nature.com/articles/s4156…
With more COVID-19 cases being reported, scientists have been sequencing SARS-CoV-2 genomes, which often have new mutations that naturally arise during infections.

We quickly identify growing, new sub-lineages, which initially get the same name as their originating lineage.
Read 12 tweets
25 Aug
Qualquer vírus em circulação acumula mutações. A evolução nunca para. É como a construção de uma via: começa pequena, se subdivide, aumenta de tamanho… mas também diminui, e se extingue.

O sistema Pango de nomenclatura do SARS-CoV-2 visa acompanhar essas mudanças. 🧵👇
Quando o SARS-CoV-2 emergiu, gerando grandes surtos no início de 2020, o sistema começou classificando o vírus em duas linhagens ('ruas'): A e B.

Este artigo explica como o sistema dinâmico funciona: nature.com/articles/s4156…
Com mais casos de COVID-19 acontecendo, cientistas vêm sequenciando genomas do SARS-CoV-2,sempre com novas mutações que surgem naturalmente durante infecções.

Logo identificamos a expansão de certas sublinhagens, que a princípio têm o mesmo nome das linhagem da qual derivam.
Read 13 tweets
4 Jul
A variante Delta (B.1.617.2, identificada na Índia) ainda levanta muitas questões sobre transmissão, gravidade da doença, impacto sobre vacinas e no controle da pandemia.

Abaixo explico um pouco do que sabemos sobre a Delta.🦠
✹ Primeiro, o que é uma variante?

No fim de 2019 existia um SARS-CoV-2 ancestral. Os coronavírus acumulam de 2 a 3 mutações por mês quando infectam seus hospedeiros. Qualquer vírus com variações genéticas em relação àqueles ancestrais é uma variante.
✹ A variante Delta é mais transmissível?

Sim. Dados epidemiológicos e moleculares apontam que a Delta tem vantagens competitivas, sendo 40-60% mais transmissível do que a variante Alpha. A Delta já é a variante dominante no Reino Unido e nos EUA

+ info: assets.publishing.service.gov.uk/government/upl…
Read 14 tweets

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