–Not a typo in the title: Ebola is back. Guinea, whom you may recall as one of the most affected countries during the West Africa outbreak, officially declared an Ebola outbreak after the virus was confirmed in an outbreak of hemorrhagic fever. There are five confirmed or suspected deaths so far and there are at least 220 known contacts under surveillance, most of whom attended the same event recently (a funeral). There are over 11,000 doses of vaccine on their way there. Assuming the contact tracing is accurate and they get very liberal with the vaccines, the 6 weeks that Guinea has targeted to control this outbreak is very feasible.

–The rest of this will be brief this week, bordering on terse. My son is back in COVID jail due to contact with a kid in his class who has apparently tested positive. In a rule change from last semester, negative tests for COVID will NOT get you out of quarantine jail so there is no point in testing at all now absent symptoms. That, coupled with a lot of snow earlier this week has absolutely wrecked my usual window for writing these.

–Case numbers continue to trend down across the US, and much of the rest of the world.

–Variants of particular concern continue to spread worldwide. In the US, the B.1.1.7 variant first described in South Africa has now been found 8 states, and a confirmed case is in a hospital in NYC (having transferred in from Connecticut). But all of the variants of concern, including those first described in the UK and Brazil, are turning up across the world.

–Yet, cases continue to decline. That epidemiology suggests that most of these new variants do NOT re-infect patients with sufficient immunity from either previous infection or vaccination.

–“Most” is not all though. The 501Y.V2 (the variant first described in South Africa) continues to show some troubling trends.

a) First, we heard from our South African correspondent (and thank you for asking around). Anecdotally, they were seeing re-infections with B.1.351 (aka 501Y.V2). What is not clear is the rate of those re-infections. The data exists–South Africa has been very much on the ball throughout the pandemic, including catching and describing this variant. But there has not been publication of it yet that either of us can find. The re-infections were memorable to health care friends because a number of them were severe cases requiring hospitalization, even though the patient’s first case of COVID was pretty mild.

b) That fits with a pre-publication case report out of France, where they boldly proclaim the very first re-infection with 501Y.V2, the variant first described in South Africa. “Very first” is a pretty bold claim given the Novavax study in South Africa and anecdotal accounts there, but, okay, it’s at least the first the French have published. That patient had a mild initial case of COVID months ago, but is now hospitalized with severe disease with this variant.

c) Two publications in the New England Journal of Medicine this week, separately looking at the effectiveness of the mRNA vaccines (Moderna and Pfizer) against the variants first described in Brazil, the UK and South Africa. The variant first described in the UK is handled by both vaccines. The antibodies from patients who got the vaccines are less effective against the other variants, particularly the variant first described in South Africa.

HOWEVER, all the variants were neutralized completely by the antibodies, and at titers frequently seen after successful vaccination. For example, the antibody level I had one week after the second dose of the vaccine was more than 10 times the neutralizing titer in the Pfizer paper above. Again, enough antibodies are being provoked into production to win by sheer force of antibody numbers, even if they are individually less effective.

–And again, T-cells may have a lot more to do with immunity than antibodies–although a wall of effective antibodies will certainly help.

–That said, Moderna and Pfizer both suggested this week that they would be developing boosters, and that the boosters may be aimed to cover some of the defining spike mutation changes in these variants.

–Speaking of vaccines, AstraZeneca’s vaccine in South Korea got a caution from their FDA in patients over 65 years of age due to a lack of data in South Koreans in that age group (worth noting–it worked in that age group in South Africa, but underwhelmed in younger patients and less severe disease there).

–The US FDA is still reviewing the AZ vaccine.

–Johnson and Johnson has a single shot vaccine that has been looking good, although early reports are that manufacturing will take some time to ramp up.

–Finally, a note on nomenclature. I am going to follow tradition and generally refer to strains of the virus based on where they were first isolated and identified. This is common–a good example is Ebola Zaire, first identified in Zaire. The outbreaks in the DRC we just finished covering were the Ebola Zaire variant. What the “Zaire” part tells me is that this is the version of Ebola that is most common and most deadly, with 60-80% mortality untreated. That’s unlike, say Ebola Sudan, which has mortality of about 50-60% untreated, and fewer and generally smaller outbreaks. It also tells me this is the version that spreads mostly by contact with infected fluid (unlike Ebola Reston, named for the city in Virginia where it was identified, where there is good reason to suggest Ebola Reston may have been airborne–this version was only symptomatic in monkeys, and humans who went on to develop antibodies to Ebola Reston never knew they had it).

In short, location where it was first identified is an easy short-hand to remember specific clinical features of a variant. Much easier than the hierarchical clustering of sequencing results that give rise to the B.something names or the various short hands for amino acid substitutions that have been used, like 501Y.V2. How much easier? I deliberately misidentified one of the strains up above there. Did you catch it?

Willing to bet not.

If you’re wondering, it was the first time I mentioned the variant first identified in South Africa. I called it B.1.1.7–that’s the “B” name of the UK variant. The South Africa variant is B.1.351.

Most of you just read the “South Africa” part and knew that I was talking about the SARS-CoV-2 strain with a certain set of mutations that appear to make it more contagious, resists vaccines and some treatments in petri dishes and in at least one clinical vaccine trial, and does appear to be re-infecting some patients.

For ease, I will try to keep calling that the “South Africa” variant, even though it is worldwide now.

Similarly, the Brazil variant was first identified in Brazil, and has limited anecdotal evidence it may cause re-infection, and also shows some petri dish resistance to some treatments and vaccines. While the UK variant was first ID’d in the UK, and appears to be more contagious, but so far seems to be susceptible to vaccines already on the market.

Some have asked why I keep using the location for the variants–that is why. Location is also used to introduce the three SARS-CoV-2 variants in both New England journal papers above, so at least I use them colloquially in good company.

–We will be watching for data on the rate of re-infections by these variants, the South Africa variant in particular. Epidemiology trends still look good, and re-infection may still be uncommon to rare. BUT, we will still give it a couple months as these variants continue to spread around the world. -If- they can break out again (and a big -if- as more and more people are vaccinated on top of those already immune from having caught SARS-CoV-2 already), a couple months is plenty of time for them to get critical mass to do so.

–Your chances of catching Ebola are equivalent to my excitement level at the prospect of another COVID vaccine booster after the last one.

–Your chances of catching coronavirus are equivalent to the chances I would get the booster anyways.

<Paladin>