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.
As more sub-lineages (new ‘roads’) emerge, at some point it's necessary to give them new names, to avoid confusion.

The team of volunteers at @PangoNetwork, an initiative I’m a member, is in charge of tracking and assigning names to new lineages.
New lineages always come up, increase or decrease in frequency, and eventually get so rare that they are no longer detected (and eventually may disappear).

Users of Pango submit daily requests for designation of new lineages via a GitHub system.
As explained above, virus evolution is very dynamic: researchers are always detecting new lineages when they sequence viral genomes from COVID samples.

Using the Pango nomenclature system, all lineages described so far are described at cov-lineages.org
SARS-CoV-2 lineages are named following an alphanumeric format, up to its 4th level, when new alias of 1st level may be assigned. That is what happened recently with lineages of Delta:

B → B.1 → B.1.617 → B.1.617.2 (Delta) →→→ AY

More information: pango.network/new-ay-lineage…
This dynamic evolution explains why we have so many lineages today, such as: B.1.1.7, B.1.617.2, P.1 (descending from B.1.1.28.1)

This alphanumeric system is well-suited to accommodate phylogenetic patterns. It's neutral, and prevents stigma (“Indian variant”, “UK variant”, etc)
By tracking viral evolution closely, and providing a neutral, systematic nomenclature for new SARS-CoV-2 lineages, we can avoid inadequate names, which may cause unnecessary confusion and anxiety, such as “Delta Plus”, which is meaningless.
technologyreview.com/2021/08/13/103…
Currently there are 3 main systems of SARS-CoV-2 nomenclature.

Pango: pango.network
Nextclade: clades.nextstrain.org
WHO: who.int/en/activities/…

They have similarities, and share a common objective: to guide ourselves along the complex evolutionary path of viruses.
The Pango system is mainly managed by volunteer researchers from @PangoNetwork: pango.network/committees/com…

In this article you can learn more about the work done by these researchers, which provide daily updates about new SARS-CoV-2 lineages.
technologyreview.com/2021/07/26/103…
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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
27 Aug
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.
Read 14 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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