Marc Johnson Profile picture
Apr 12 25 tweets 7 min read Read on X
Last month there was an announcement that I thought was a major advancement in world health, but it got little attention.
I thought I would tell you all a little bit about it and why it is so important.
1/25
This breakthrough has to do with HIV, which was a zoonotic pathogen. The progenitor of HIV infects chimpanzees in Cameroon.

No one knows exactly when or how HIV crossed into humans, but the first undisputed HIV patient sample (discovered retrospectively) was from 1959 in what is now the Democratic Republic of Congo.Image
HIV smoldered for decades before becoming widespread in the early 80s.
At the time, being diagnosed with an HIV infection was a death sentence.
There was no real cure (still isn’t) and no treatment. By any measure, HIV was one of the worst diseases of the last century.
3/
nature.com/articles/d4158…Image
Throughout the 80 and 90s many antivirals were developed, but they all were doomed to fail. HIV mutated so fast that it quickly developed resistance to every drug we threw at it.
4/
The breakthrough came in 1996 when HIV researchers such as David Ho found that they could treat HIV if patients received a cocktail of antivirals all at once.
HIV went from being a death sentence, to being a life-long treatable disease.
5/ Image
BTW, David Ho still maintains a very active research lab at Columbia University, which apparently now has all of its NIH grants frozen.

Let no good deed go unpunished.
6/
science.org/content/articl…
Although HIV became treatable in 1996, the world death rate from HIV didn’t start to go down until almost a decade later. Why then?

A big part of the reason was the program PEPFAR, which was launched by George W. Bush in 2003. This program focused on getting lifesaving drugs in the hands of people who needed them.
7/Image
BTW, earlier this year PEPFAR activities were abruptly halted.
8/
nytimes.com/2025/01/27/hea…
While some of this funding has been restored, the future of PEPFAR remains quite uncertain.

9/thinkglobalhealth.org/article/pepfar…
Plus, a lot of NIH grants studying HIV that had foreign collaborators are also being terminated.

10/science.org/content/articl…
Anyway, back to the breakthrough stuff.
For the last few decades, HIV drugs have continued to improve. Patients now take fewer drugs, less often, and with fewer side effects.

11/ fight.org/hiv-medication…Image
However, HIV hasn’t gone away.

People still get infected, and they then require treatment for the rest of their lives.

There are more people living with HIV today than ever before (over 40 million), and the number keeps going up.
12/ Image
Once people are undergoing treatment, they are unlikely to pass on the virus.
The problem is the spread that occurs before people know they are infected.
What we really need is a fool-proof way of preventing people at high risk from becoming infected in the first place.
13/
About 15 years ago groups started working on what is called pre-exposure prophylaxis (PrEP) where people at high risk can take HIV antivirals that could prevent them from being infected in the first place.
14/
However, PrEP was expensive, and not always practical.

What we really needed is a vaccine (we’re not even close), or an effective, long-lasting prophylactic.
15/
Until very recently, almost all of the drugs that blocked HIV targeted one of its enzymatic proteins: RT, IN, or PR.
However, for decades numerous HIV researchers (myself included) studied the process of HIV assembly (CA protein) with the idea that it would be a better target for blocking the virus.
16/
This dream recently became a reality with the development of the drug lenacapavir, a capsid inhibitor where a single dose could last as long as 6 months.
17/
science.org/content/articl…
However, the news got even better last month when it was announced that lencapavir could be used for PrEP with as little as one treatment per year.

That is a treatment that could actually work!
18/
aidsmap.com/bulletin/confe…
That’s the good news.
Please indulge me for a moment to get on my soap box to tell you why we should really care about continuing to fight the war on HIV, even though not that many people are dying of HIV in the US.
19/ Image
The first is simply the forest fire analogy. Forest fires, like pathogens, don’t respect national borders.

HIV started in Africa, but it didn't stay there.

If you live in a forest, it really makes sense to fight the fire before it’s on your property.

20/
But there is a reason that is even more important. Patients with untreated HIV become severely immune suppressed, and immune suppressed patients are breeding grounds for new pathogens and variants.
21/
Using COVID as an example, in early 2021 we had a vaccine, cases were dropping, and it seemed like the pandemic was almost over.
Then began a series of new waves which were each driven by a new COVID variant.
22/ Image
These variants were not the result of gradual changes acquired by circulating lineages.

They were each, wildly different variants.

We are all but certain these new variants were all derived from individuals (presumably immune compromised) with long persistent infections.

23/
Persistent infections are training grounds for pathogens.

People worry about ‘gain of function’ work, but failing to continue treating the 40+ million people in the world living with HIV would be the largest and most dangerous gain of function ‘experiment’ in history.
24/ Image
I’ll get off my soapbox now. Thanks for reading.
25/25

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More from @SolidEvidence

Apr 6
I briefly thought the SA BA.3.2 was in the US, but it turns out the virus was just messing with me again.

This was kind of interesting though.
1/
We've been screening all of the new wastewater data a few times a week for signs of BA.3.2.

One of the many screens we have is looking for reads that have C21846T+T21864C together, which are in BA.3.2 but no current lineages (it works better to look for pairs of changes).

2/
This week we had a hit. This was the genotype of the read:

C21621A|(S:T20N) A21626G|(S:T22A) T21657C|(S:F32S) T21695C|(S:S45P) A21712T|(S:S50S) CATGCTAT21758-21765del C21767-21767del C21846T|(S:T95I) T21864C|(SI101T) TTA21890-21892del|

3/
Read 9 tweets
Mar 17
Here is this week's analysis. One mutation popped out as increasing in frequency in the last data set.

S:G842S

Wonder what that is from.

1/ Image
Not a very common mutation. Mostly associated with with XEC.11*
2/
cov-spectrum.org/explore/United…Image
If that's really from XEC.11*, then we should see other mutations from that lineage increasing.

So I looked up the mutations that differentiate XEC.11 from XEC:

Orf1a:V2090F
S:K182N
SV1264L
Orf3a:L85F

3/ Image
Read 8 tweets
Mar 17
I’m very pleased to announce the launch of our LungFish Data Explorer dashboard for tracking SARS-Cov-2 lineages from wastewater.

1/
inkfishmedical.github.io/wastewater-das…
Here’s the problem we hope this dashboard will help solve.  SARS-CoV-2 remains very prevalent in the US.

However, sequence surveillance from patients has plummeted. In addition to fewer samples, the average sequence takes >3 weeks to be reported (and it’s getting slower).

2/ Image
Fortunately, we have wastewater surveillance (primarily through CDC NWSS), which covers a large chunk of the population and has a fairly fast turnaround (<2 weeks).

3/ Image
Read 16 tweets
Mar 1
So what's happening with medical research in the US? This is the cumulative award count from the NIH for the year.

Doesn't look so good.

But it gets worse.
1/ Image
Before grants are awarded, they have to be evaluated in meetings called study sections.

Before a study section can meet, it has to be listed in the federal registry for at least 15 days.

These are the new study section meetings listed in the federal registry this year.
2/ Image
Meetings can't even be scheduled, none of the committed funds are going out.

About 300,000 scientists are wondering if they are going to keep their jobs, and the most vulnerable are the students and postdocs.
3/
Read 4 tweets
Feb 28
There something new on the SARS-CoV-2 landscape, and I’m not sure what it is.
1/ Image
S:S31F and S:K182N are on the rise.

The two aren’t on the same sequencing strand, but I confirmed that they are generally appearing together in the same samples.

2/
The samples are from across the country (CA, WY, LA, CT, PA, WI, etc) and more than one sequencing group, so it’s probably not a sequencing error.

3/
Read 5 tweets
Feb 11
Brief update on the new cryptic lineage we found from Petersburg City, Virginia.

We went back and screened all of the samples from that sewershed since the beginning of 2024 and learned a few things about it.
1/ Image
First, I think I was wrong about the lineage being JN.1 derived. I thought it was JN.1 because it had 22926C (455S), but it looks like it only acquired that recently.

In samples as recent as December the lineage lacked 455S and 456L.
2/ Image
That would mean the lineage is BA.2.86-derived, which suggests it was acquired probably early 2024.

Caveat, as @LongDesertTrain points out, persist infections hate 455S. It’s possible that the lineage was JN.1, but reverted at 455, but then gained 2 nt creating 455A.
3/ Image
Read 8 tweets

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