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

Nov 23
What should we expect this flu season?

Here’s a forecast from a wastewater perspective (because sh*t don’t lie)

1/
Background. The 4 main kinds of influenza circulating among humans (in order of severity) are:
FluA H3N2
FluA H1N1
FluB
FluC (many don’t know this one)

2/
Last season, there was a pretty even split between H1N1 and H3N2, with a little bit of FluB late in the season. At least according to CDC patient data.
3/ Image
Read 13 tweets
Nov 21
This is wild.

Remember the NJ crytic lineage?

I posted 18 months ago that the Spike was too divergent to predict ACE2 binding, and asked if someone else could figure it out.

Some colleagues took me up on it.

Guess what they found?
1/
This preprint just came out. @wchnicholas and team reconstructed and tested the NJ Spike and found that it has the tightest ACE2 binding of any SC2 Spike ever measured.
2/
medrxiv.org/content/10.110…
We first found the NJ variant in 2023 because this sewershed from NJ with 1.5 million people because it regularly had a sequence that was a reversion to the bat sarbeco sequence, which is common in cryptics.
3/

Read 9 tweets
Oct 31
Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?

That is the question we asked in our latest pre-print.

Turns out you can.
1/
medrxiv.org/content/10.110…
We are not the first group to do unbiased sequencing of wastewater to monitor circulating viruses, but I think we are the first to ever do it at this scale.

Weekly wastewater samples for 18 months, totaling over 85 Billion sequence reads.

2/ Image
Among the ‘known’ viruses, there was a fairly even split between bacteria viruses (phages) and eukaryotic viruses.
This was just raw reads though, if you look at diversity there was considerably more species of phages.
3/ Image
Read 23 tweets
Oct 24
Help me out, I’ve got another wastewater virus mystery.

This one really blows my mind.
1/
Starting in the late 2023, + @securebio have been doing ultra-deep metagenomic sequencing of the virome from Columbia, MO wastewater.

We’ve collected and sequenced sample for over 90 consecutive weeks.
2/Lung.fish
We sequence about a billion reads per sample. That’s generated about 16TB of data from this site so far.

To put this in perspective for people my age, it would take a stack of 3.5 in floppy disks 200 miles high to store this data.
3/
Read 12 tweets
Oct 17
It looks like Coeur d’Alene, ID cryptic is gone for now, but it has still managed to answer a lot of lingering questions for me about SARS-CoV-2 evolution, and what to expect next.

Here's a whole genome summary and interpretation.
1/ Image
For a long time cryptic lineages were all from pre-Omicron lineages.

I started wondering:

Will there be Omicron cryptics?

If so, will they have the same evolutionary trajectories as the pre-Omicron cryptics?

ID shows that the answer to both questions is yes.
2/
We don’t do a lot of whole genome sequencing, so I sent 3 samples to @dho lab, who got fantastic sequences for all 3.
These samples were virtually 100% cryptic, so we have nearly complete coverage of the genome for a change.
3/ Image
Read 12 tweets
Sep 10
This really pisses me off.

I obviously knew there was some manipulation of post metrics on social media, but I really didn’t realize just how hard this platform slams the breaks on posts it doesn’t like.

Here’s my experiment.
1/
This weekend I posted 3 threads.

1. on a cryptic lineage
2. on H5N1
3. on seasonal respiratory viruses

Each time I posted the threads on X and bsky at the same time.
2/
The three threads each got roughly the same attention on bsky.
However, on X the first 2 each had hundreds of RTs and over 1k likes.
The 3rd was practically invisible. It had only 5 RTs and 28 likes after 2 days. Over 40-times fewer views.

3/
Read 7 tweets

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