First off - viruses mutate all the time, creating "variants". The vast (and I mean vast!) majority do nothing, so when you hear SARS-CoV-2 variant/lineage/mutate, Don't Panic! #42. A lot has been said about this already - here's a great article:https://www.nature.com/articles/s41564-020-0690-4 …
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Number one priority - there's a desperate need for coordination and regulation when it comes to SARS-CoV-2 variants. The UK and South Africa showed us how to do this and
@WHO just came out with working definitions too. https://www.who.int/publications/m/item/covid-19-weekly-epidemiological-update …pic.twitter.com/5Hj1q5lVtc
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I think it's important for the US to have a system in place - managed and overseen by e.g.,
@CDC_AMD with an external committee. I see the need for four main classifications: Variant Variant of Interest (VOI) Variant under Investigations (VUI) Variant of Concern (VOC)Show this thread -
The need for coordination is critical. Too many examples lately of scientists finding something (they find) interesting and then heading straight to the media - with limited data, no studies available, and no coordination with local health departments. Don't do this. Seriously.
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It's key to remember that there is often a big difference between what's *interesting* vs what's *unusual*. If unusual, there's a difference between what's unusual vs what's *important*. Often, what's seen as interesting, isn't unusual, and unusual isn't necessarily important.
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So when it comes to variants, what's both unusual and important? SARS-CoV-2 variants of concerns (VOCs) that have increased transmission, increased virulence, or can evade immunity (whether vaccine-derived or natural) and public health measures, including diagnostics and drugs.pic.twitter.com/STMzy6i1tm
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We have only three variants that fall into the "VOC" category - those first identified in the UK (B.1.1.7), Brazil (P.1), and South Africa (B.1.351). I have already talked about these a lot, so head over to this thread if you're interested:https://twitter.com/K_G_Andersen/status/1355689990487896065?s=20 …
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Now, recent "Variants of Interest" (VOIs). There are many, incl. those identified in California (B.1.429/427) and New York (B.1.526). VOIs are about identifying variants that *may* be important - which is different than monitoring the ones we *know* are important (the VOCs).
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To move from VOI
VOC requires evidence. A lot of evidence. The UK provides a stellar example of how exactly to go from VOI
VUC
VOC.
Investigate, investigate, and continue to investigate - while accurately communicating importance and uncertainty through the process.Show this thread -
Importantly though, as soon as you have enough evidence - which is never going to be perfect - move. And move fast. Which, again, the UK did. That requires coordination - and should never be done at the level of individual scientists.pic.twitter.com/81jjo4ZEhx
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So what should alert us to a VOI: 1. Variant with a lot of mutations (sidenote, not just spike - e.g., ORF1b P314L
)
2. A variant with mutations we know are important
3. Rapid increase in frequency
4. Convergent evolution
5. Spread in areas of high levels of immunitypic.twitter.com/Wdr7TZtlJd
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Let's look at the two recent CA/NY variants (NOT VOCs!!) - all sloppy science and bad reporting, or is there something to it? I think there's something there - and consider both VOIs. The CA may be slightly more transmissible (~10-15%?) and the NY evade some immunity
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"California" variant / B.1.429/427. - Key mutations - L452R and possibly W152C - Originated in summer, 2020 - Rose in frequency, beginning in November (around the time of surge) - Two independent lineagespic.twitter.com/IIUEFZwb3P
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Here are the two lineages, sharing a common ancestor ~summer. Also, a number of mutations split the two lineages (B.1.429 and B.1.427). Tree can be accessed here: https://nextstrain.org/groups/spheres/ncov/california?c=pangolin_lineage …pic.twitter.com/QhBPEEoFBk
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Here you can see the increase over time of B.1.429 and B.1.427. The surge in California actually starts *prior* to these lineages increasing in relative frequency. https://outbreak.info/situation-reports?country=United%20States&division=California&pango=B.1.429&selected=California&selectedType=division … https://outbreak.info/situation-reports?country=United%20States&division=California&pango=B.1.427&selected=California&selectedType=division …pic.twitter.com/RlkeeeQni7
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So what's going on here? Probably the surge is the primary driver of increasing frequency, but possibly also helped along by a slight increase in inherent transmissibility. The data is not conclusive though. Also, association with virulence and immunity = null. = VOI.
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"New York" variant (B.1.526) - this one is more interesting to me and likely of importance. - Two sub-lineages - one with E484K and one with S477N (known to be important) - Rapid rise in frequency of both - High levels of immunity in New York (high attack rate last spring)pic.twitter.com/VD5x5eifcH
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Here are the two sub-lineages - again, one with E484K ("Eek") and one with S477N ("Sean"). Tree can be accessed here: https://nextstrain.org/groups/spheres/ncov/new-york?c=pangolin_lineage …pic.twitter.com/C1jPnEk8HF
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Here you can see the increase over time of B.1.526 - full lineage + sub-lineages carrying E484K or S477N. Note, "Eek" increasing more rapidly than "Sean" - as we might expect, based on functional data. https://outbreak.info/situation-reports?country=United%20States&division=California&division=New%20York&pango=B.1.526&selected=New%20York&selectedType=division … https://outbreak.info/situation-reports?country=United%20States&division=California&division=New%20York&pango=B.1.526&muts=S%3AE484K&selected=New%20York&selectedType=division … https://outbreak.info/situation-reports?country=United%20States&division=California&division=New%20York&pango=B.1.526&muts=S%3AS477N&selected=New%20York&selectedType=division …pic.twitter.com/5XoMDk0owN
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Like the "CA" variant, terrible reporting, however, given the rapid increase in frequency of two independent sub-lineages carrying mutations that we know can evade some Ab immunity, in a part of the country with high levels of immunity
= VOI that should immediately
VUI.Show this thread -
In summary, we need to be *much* better at communicating research around SARS-CoV-2 variants - whether known or novel - especially as it relates to data, findings, interpretations, and importance. Finally, a collaborative and coordinated effort


to
confusion and
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ARRRRGGHHHH, I forgot the corgi! Sorry tweeps. Since
@EvolveDotZoo informed me that he holds the copyright on Twitter corgis, I have something better for you today. Here's Noodle's (a) opinion on recent scariant reporting, and (b) her plan for the weekend.
pic.twitter.com/8yGGiykDii
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End of conversation
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