This has now happened a second time: an Ebola outbreak has occurred due to transmission from a persistently infected person of a virus that has barely changed in years.

This hints at an unknown and completely novel persistence mechanism for an RNA virus.
virological.org/t/oct-2021-evd…
This Ebola virus diverges from the most closely related genome by only 6 nucleotides. That virus was sampled from a deceased EVD patient in July 2019, meaning that in over 2 years, this virus has barely changed.

Which is really, really weird.
RNA viruses famously have a very high mutation rate, The RNA-dependent RNA polymerase (RdRp) that copies the viral genome can't proofread & correct "typos" during replication. Thus, you can count the typos—mutations—as a measure of evolutionary time if you know the mutation rate.
For Ebola, we'd expect to see that a virus which is persistently replicating—even at low levels—would acquire many more than 6 mutations in 28 months. This suggests the persistent virus isn't replicating much, if at all.
And because RNA is unstable, it's thought that RNA viruses can't really persist in a truly latent state like herpesviruses (which are DNA viruses) can. Herpes latency involves the genome basically shutting down and just existing in a host cell until it becomes reactivated.
So RNA viruses generally don't achieve latency. Chronic RNA virus infections typically involve low level persistent replication. (HIV is an exception, as it makes a DNA copy of its RNA genome that then integrates into the host genome as a provirus. But Ebola cannot do that).
Some RNA viruses, like hepatitis C virus, are capable of persistent infection for years. But chronic HCV infection is the result of low-level replication that flies under the radar of the host's immune system. It seemed like that's also happening with Ebola until this year.
After the 2014-2016 epidemic, Ebola persistence in immunologically privileged sites (eyes, testes) was well documented. But this was thought to be like HCV: low-level replication.

This case & the ones from March upend that.
And that's why this is so stunning and scientifically fascinating. If these cases have acquired so few mutations, that suggests these viruses weren't really replicating at all in persistently-infected Ebola survivors.

It suggests an unknown mechanism for RNA virus "latency".
Though I am never enthusiastic to hear about new Ebola case(s) in places that have been devastated by this terrible virus, I will be following this with great interest. Understanding the risk of silent, persistent Ebola infection will be essential to stopping these outbreaks.

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More from @angie_rasmussen

24 Sep
Much respect for Dr. Gilbert but I don’t agree with this. Viruses don’t always become attenuated (less virulent). When they do, it’s because there is an evolutionary selection pressure driving it. No such pressure exists for SARS-CoV-2.
An example of this type of selection pressure would be a virus that is so virulent, it kills its host before it can be transmitted to another one.

A virus is essentially a machine programmed to make more viruses. To do that, it needs to be spread to new hosts.
So variants that are so virulent they kill a host before that host can pass it along, that is under negative selection pressure. The more virulent viruses won’t be passed on. But attenuated variants will. They are under positive selection.
Read 8 tweets
21 Sep
Fellow J&J recipients: big press release out on impact of boosters. While the confidence intervals are huge, there’s evidence that boosting with a 2nd shot (of J&J) increases effectiveness.

jnj.com/johnson-johnso…
We need to see the full dataset but hopefully when it’s examined in detail, it will support a recommendation for those who got J&J to get a second shot. All the data (for any COVID vaccine) suggests there’s substantial benefit to boosting.
And I’m not sure where we are at with J&J supply, but last I saw, there wasn’t a lot. ACIP/FDA should consider recommending heterologous (mix and match) boosting with a mRNA vaccine. There’s data with AstraZeneca + mRNA that supports the safety of this approach.
Read 4 tweets
17 Sep
Yesterday my spouse said that we need to be both extra careful and hopeful. We can’t get in a car accident or appendicitis or anything that would require hospital care. There’s simply no capacity because of COVID.

I wish this had happened earlier but better late than never.
On July 11, all restrictions were lifted. I mostly go to work or run essential errands. I always wear a mask despite being fully vaccinated. We’ve gone out for dinner or drinks a handful of times and sat outside each time. Yet everywhere (except work) the scene is the same.
The majority of people are unmasked. Last Friday I picked up a bottle of wine. I was the only masked person in the long TGIF line at the liquor store. Distancing was not observed at all. A person in front of me merrily told another customer she was stocking up for a party.
Read 6 tweets
2 Sep
My excellent colleague @akelvinlab has this right: we will have more variants as long as SARS-CoV-2 continues to replicate.

Also worth pointing out that we don't know much yet about C.1.2, but we do know that it's not "mutating faster." That wouldn't even necessarily be bad.
C.1.2 is an emergent lineage of variants, meaning it's actually a cluster of several different variants. Here's the preprint describing it, by @CathrineSch07 and colleagues:
medrxiv.org/content/10.110…
Misinterpretation of panel C in the above figure led to 🚨MUTATES TWICE AS FAST 🚨 insanity a few days ago. That's wrong.

The amino acid substitution rate (new mutations that result in a change in a protein) is on par with other emerging variants.
Read 19 tweets
31 Aug
Just came back to Canada after being a groomsman in the wedding of one of my dearest friends. This trip was a joyous occasion but also a stark reminder of how badly the US has failed in its COVID responses, and continues to fail.
1. US requires an antigen test to reenter. In Canada, you can get a company to come to your home to administer a proctored test at your convenience for about $75 US. We were asked to show our test results multiple times at YXE & YVR. US CBP did not ask for our test results.
2. At the wedding, I learned to my chagrin that there were going to be some eligible attendees who refused vaccination. The wedding was fully outdoors, but I was still concerned. I thought maybe I could provide rapid tests for all guests as a gift to the couple.
Read 13 tweets

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