Thread by @andersonfbrito_

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…

This thread was originally written in Portuguese, and can be found below.

https://twitter.com/AndersonBrito_/status/1430627349255577609