Tag: virus

Warp Speed is Normal

one big reason we got vaccines so quickly was that work had already gone into coronaviruses:

That was a really good—well, not “guess,” I suppose, but a good hypothesis, right? That a coronavirus was going to be a problem?

We were hedging our bets. No one knew what the next outbreak would be. It could have been a variant of influenza; it could have been one of a number of pathogens. But yeah, the short answer is, if you look at a list of outbreaks over the last 20 years, if 2 of the viruses on the list are in the coronavirus family, then you shouldn’t be shocked that it comes up again. SARS was 2002. MERS was 2012. In pandemic history, that’s a pretty short timeframe.

So we did some work with Moderna on designing MERS vaccines—all early, preclinical—so we were able to test how our mRNA worked, and we could test some designs on what the RNA should teach the body to make an immune response against. We had a lot of groundwork already laid when we found out the new virus was a coronavirus.

to prepare for the next pandemic:

It took nearly 20 years to understand coronaviruses well enough to work on. But what if the next one’s not a coronavirus?

There’s a reasonable possibility that a virus could emerge from a different virus family, and we would not be as prepared. We know that there are ~20 major virus families in the world that infect humans, and almost every outbreak we’ve seen in the past 50 years or more has come from one of those 20 virus families. What if we made a concerted effort to study every family in detail, to make vaccines to every family, and do what we did for coronavirus? Make some prototypes. So that if a cousin in that family emerges, a virus we’ve never seen before, we at least have laid some groundwork for vaccine design. One could, for $20m per virus family, make a prototype vaccine and test in the clinic. You’re talking a few billion $ over 5 years for that kind of project. That used to seem like it wouldn’t be tenable. But now it’s like, well, if I could be prepared for the next pandemic, that’s probably a really good investment.

Genomic epidemiology

We believe this may have occurred by the WA1 case having exposed someone else to the virus in the period between Jan 15 and Jan 19 before they were isolated. If this second case was mild or asymptomatic, contact tracing efforts by public health would have had difficulty detecting it. After this point, community spread occurred and was undetected due to the CDC narrow case definition that required direct travel to China or direct contact with a known case to even be considered for testing. This lack of testing was a critical error and allowed an outbreak in Snohomish County and surroundings to grow to a sizable problem before it was even detected.

this is a great summary of the state of the art on using mutations to reconstruct how a disease spreads.

COVID-19 Scenarios

One unlikely but possible scenario is that this “novel” virus is not really novel. Because its symptoms are generally mild and very similar to other symptoms from flu and other viruses, it may have been circulating around the globe for a while, without a name. It can be transmitted by people who have no symptoms at the time or even while they have the virus. If the majority of people infected don’t ever get sick, but easily pass it on, then it can spread widely unseen. But a few are susceptible to it and die. Because the symptoms are not unique to it, this illness is assumed to be flu or something else. Then something happened in China to produce notice — maybe someone created a test for it — and then as people died, the new test found many people positive.

Ambigram Viruses

Occasionally, sections of a genome will have overlapping sequences that code for different proteins. But in narnaviruses, the entire genome is an overlapping sequence: It can be read in its “reverse complementary” orientation. That is, the RNA is like an ambigram, a stylized script that still says something when flipped upside down.

Life In Our Phage World

The world of phages is more than a little scary. They have been evolving for billions of years, their numbers are so vast every writer in this anthology resorts to scientific notation, and their generation time is as low as minutes, making for dizzying amounts of selection pressure and optimization – phages seem to have explored every possible way of attacking, subverting bacteria, replicating faster, compacting and making themselves more efficient, and won every arms-race bacteria started with them.

2023-01-12: And the reverse

A species of plankton that populate freshwater worldwide is the world’s first known organism that survives and thrives by dining on viruses alone, an advance that sheds new light on the role of viruses in the global food web. This virus-only diet – “virovory” – is enough to fuel the growth and reproduction of a species of Halteria, a single-celled organism known for the minuscule hairs.

2025-09-18: Viable AI-mutated phages

the researchers mixed all 16 AI-generated phages with ΦX174 and then threw them into a tube with E. coli cells. Because the phages were forced to compete for the same host cells, the variants that reproduced fastest would dominate. By sequencing the phages over time, the researchers could track which phages were gaining ground and which were falling behind. Several of the AI phages consistently outperformed wild ΦX174, with one variant (called Evo-Φ69) increasing to 65x its starting level.

Ultimately, these 16 AI-generated phages were not only viable; in many cases, they were more infectious than wildtype ΦX174 despite carrying major genome alterations that a human would be unlikely to rationally design.

Multipartite viruses

Some viruses can replicate without passing all their genes into any 1 cell.

A classical view in virology assumes that the viral replication cycle occurs within individual cells. But in the case of this “multipartite” virus, it seems that this is not true. The segments infect cells independently and accumulate independently in the plant host cells. It really shows that the virus doesn’t work at a single-cell level, but at a multicellular level.