u/KaleMunoz

Link: https://journals.sagepub.com/doi/abs/10.1177/0034673X241256659

DOI: 10.1177/0034673X241256659

There has been a lot of discussion about a 2020 study of the 2018 to 2019 outbreak at Epuyén. This is cited as a caution to what’s often been said about the symptomatic spread and the necessity of prolonged physical contact.

The authors emphasize how social the interactions were a lot more than people here recognize, but still, it was clearly more infectious at social gatherings than previous household-based studies had suggested.

But there’s something weird here. More than 80 healthcare workers treated patients, performing high risk procedures, with almost none of healthcare workers wearing PPE. Not one healthcare worker got sick (a few non-employees did).

"Although several high-risk medical procedures were performed in patients with ANDV hantavirus pulmonary syndrome, including orotracheal intubation and cleaning of bodily fluids such as vomit, diarrhea, and other secretions, no nosocomial infections were reported among health care workers who had been in direct or close contact with the patients at the health care fa cilities (Hospital Esquel Zonal and Epuyén Rural Hospital). Approximately 82 health care workers were exposed to symptomatic patients with confirmed ANDV infection at Hospital Esquel Zonal from December 2 to December 13, 2018. Of the 45 persons who worked in the intensive care unit and emergency department, only a small number used any form of personal protective equipment (including N95 respirators \[N100 respirators for intubations and cleaning\], goggles, and disposable laboratory coats) while they were in direct contact with an infected patient. Nonetheless, we identified one secondary nosocomial transmission event that occurred at Hospital Esquel Zonal, which is an advanced health care facility. Two additional nosocomial transmission events occurred at the smaller Epuyén Rural Hospital, for which information on the use of standard personal protective equipment was not available."

One possibility is that the uniqueness of this event is more about the individuals than the strain. If you read the report carefully, the authors only refer to super spreader individuals, not events. Those indiciduals characterized as super spreaders shared a unique symptom profile and unusually high viral loads and interleukin-1β. The authors note:

"These correlations suggest that person-to-person spread was related to a high viral load and more compromised liver function in the infected patient."

There is obviously precedent for this in previous outbreaks. For these occasional significant outbreaks, it’s worth thinking as much about the people as it is the virus itself.

https://www.nejm.org/doi/full/10.1056/NEJMoa2009040

There has been a lot of discussion about a 2020 study of the 2018 to 2019 outbreak at Epuyén. Most of the time I see this cited, it is to point out that ANDV was, at least once, more transmissible than some popular discourse suggests. But digging into the report reveals something weird. More than 80 healthcare workers were exposed to patients, performing risky procedures, and most were not using PPE.

What gives? One thing I noticed is that the study only refers to individuals at Epuyén as superspreaders rather than events as superspreaders. Maybe I am being pedantic here, but is it possible that this is more about variance in hosts than the virus itself? That ANDV can spread (somewhat more) efficiently through the occasional individual, and that the HCAs were not exposed to said individuals? The study also mentions that viral load and levels of interleukin-1β were positively associated with the likelihood of infecting another person, and that the three superspreader individuals had a different symptomatic profile than everyone else.

"Although several high-risk medical procedures were performed in patients with ANDV hantavirus pulmonary syndrome, including orotracheal intubation and cleaning of bodily fluids such as vomit, diarrhea, and other secretions, no nosocomial infections were reported among health care workers who had been in direct or close contact with the patients at the health care fa cilities (Hospital Esquel Zonal and Epuyén Rural Hospital). Approximately 82 health care workers were exposed to symptomatic patients with confirmed ANDV infection at Hospital Esquel Zonal from December 2 to December 13, 2018. Of the 45 persons who worked in the intensive care unit and emergency department, only a small number used any form of personal protective equipment (including N95 respirators [N100 respirators for intubations and cleaning], goggles, and disposable laboratory coats) while they were in direct contact with an infected patient. Nonetheless, we identified one secondary nosocomial transmission event that occurred at Hospital Esquel Zonal, which is an advanced health care facility. Two additional nosocomial transmission events occurred at the smaller Epuyén Rural Hospital, for which information on the use of standard personal protective equipment was not available."

To my earlier point:

"These correlations suggest that person-to-person spread was related to a high viral load and more compromised liver function in the infected patient."

https://www.nejm.org/doi/full/10.1056/NEJMoa2009040

I’ve never liked failing students, but doing what’s necessary always got easier with time. I don’t typically struggle with this any more.

Maybe it’s just the nature of the kind of year I’ve had, but I’m feeling pretty glum about two Fs that need to go out.

One girl I’ve taught before in a different class. She barely passed. She has some mental health issues that I know or authentic that make work hard for her. I don’t like giving people bad grades under those circumstances, but some do the work and some don’t, so it’s usually that simple.

What got me this time is her group dynamic. I inherited a class I didn’t want that is primarily graded on group work. She has an F because she didn’t turn in any of her individual work. But she did excellent work for her group all throughout the semester. I witnessed this firsthand and her group all vouched for her. She was one of the better contributors. I don’t know, it’s something about her being unable to advocate for herself but unwilling to let others down is kind of hitting me in my feels.

The other student I’ve had before. Failed the first time. Probably a D or a C the second time. Doesn’t turn in work.

This time around, she didn’t turn in work the first half of the class but did decent work the second half. I’ve also learned a lot about her family dynamics. And, yikes. Abject poverty, nine siblings, former IDP. The degree will turn her family trajectory around (I know what you’re thinking, but she has a job and isn’t flakey there). Our once admirable SLAC is looking more like a sinking ship, and I’m struggling to jeopardize her future to defend the honor of the degree, as we lower our standards again and again and again. I am her advisor and see on her transcript that she passes most classes. She fails something most semesters, but she probably will graduate if one colleague and I don’t stand in her way.

Edit: to clarify, these aren’t the only people failing. A reliable percentage fail every semester. Don’t love it, but am never torn up about it. They move on. These two just hit different right now.

“Across all three hantavirus genome segments, the closest relatives are consistent with one another, which suggests the virus has not undergone reassortment which is a process where segmented viruses exchange genome segments with another strain, potentially creating a novel variant.  The absence of evidence for reassortment implies the outbreak virus likely emerged from a single, relatively stable viral lineage rather than from a recent mixing event between different hantaviruses.”

“At present, there is no clear evidence from this single genome of major genetic shifts, unusual evolution, or reassortment.”

“The available phylogenetic and sequence data nevertheless suggest that the Swiss patient isolate represents a relatively typical naturally circulating ANDV lineage originating from the established rodent reservoir in Chile/Argentina, rather than a highly divergent or newly emerged variant.  Across all three genomic segments (S, M, and L), the virus clusters consistently with known South American Andes virus strains, including lineages frequently associated with human infections, without evidence of segment incongruence that would suggest recent reassortment.  Additional sequence comparisons likewise do not reveal any striking or unusual mutations beyond the degree of variation expected for a wildlife-associated RNA virus lineage evolving in its natural reservoir.  The relatively short branch lengths and close phylogenetic relationship to previously described human and rodent isolates further support the interpretation of a recent transmission event from the natural rodent reservoir to a human host — the expected and well-established route of primary Andes virus infection — rather than prolonged cryptic evolution or major adaptive divergence.  Importantly, while these genomic findings do not indicate the emergence of a fundamentally novel Andes virus strain, the genomic data alone cannot distinguish between direct zoonotic acquisition and secondary human-to-human transmission in this case, both of which remain biologically plausible for Andes virus.”

tl;dr - human outbreaks are serious and global pandemic potential is still low. It is wrong to describe the Andes variant as “barely transmissible,” but correcting people on this does not establish broad pandemic risk.

"Looks like a likely spillover from the O. longicaudatus rodent Argentina/Chile natural reservoir from a clade of Andes hantavirus that frequently infects humans."
"...suggesting there hasn’t been reassortment"