There is an interesting contrast between the way Pandemics begin and end. This is certainly true in the modern age of instant global communication, when there is no doubt in anyone’s mind about the beginning. You may argue about a few weeks or a month— did the Chinese hide something in the month of November or late October, hoping the outbreak would peter-out like a mini SARS-1, and go unnoticed—but that’s splitting hairs on the time line, if not the ethics front. The end is pretty clear in the case of a disease that runs its course and disappears; but quite murky for a novel disease like SARS2-COV19 (COVID) which has morphed into an endemic pathogen likely to be with us in perpetuity. The US Administration has declared an end to the Public Health Emergency for May 11th. That will bring all sorts of practical changes for the bulk of Americans; vaccines will no longer be free when the current government stock runs out, current antiviral treatments will similarly become expensive when the pre-paid stash is exhausted, testing which was possible to obtain free, will very quickly become relatively more expensive on the open market. Ashish Jha has suggested the free vaccines and treatment will run out perhaps as soon as the early summer. The limited Federal programs which until now continued to provide monetary assistance to some will go away. It’s impossible to say how many Americans will be dying everyday by May 11th, hopefully far fewer than the 500/day now, but that is not the metric the government wants us to focus on. America of course is just one place in a Pandemic world. China looks ready to declare an end as well—just as soon as all the wagons proclaiming, “Bring out your dead”, get back to the crematoriums, which of course are functioning on a normal holiday schedule with, “nothing to see here”.
Regular readers will know I’ve been very interested in the technology and practical utility of waste water surveillance of human pathogens. An interesting, and as far as I am aware, novel application of this has just come to light—but there is also another side to the story. There is a polio vaccine/laboratory in Bilthoven, Netherlands. In a demonstration of excellent forethought, they have been monitoring the waste water of the surrounding communities for polio virus. In November they detected wild type Polio Virus3 in the waste water. So this was not an example of detecting asymptomatic shedding of the weakened vaccine virus, which occurs with regularity after oral polio vaccine, but the fully virulent virus which is extinct in the Netherlands—except in this laboratory. The workers in the lab (all vaccinated of course) were quickly screened, and one was found to have been infected by the virus in the laboratory. That apparently normal person continued to excrete polio virus in their stools for 55 days. The waste water surveillance program was brilliant, and identified the problem quickly. The inconvenient fact remains that this is yet another example of a dangerous viral pathogen leaking from a high level bio-containment lab, and in a country were we have high expectations of superior technology and adherence to good practices (at least higher than China). No breaches in protocol or accidents were identified in the extensive follow up evaluation of the laboratory. Luckily, this is a GI pathogen which got leaked into a population with very high vaccination levels. It would be a completely different story if this was a novel respiratory virus, with incredibly high transmissibility, which leaked into a dense urban environment where people had zero baseline immunity. It wouldn’t matter if this novel virus was recovered de novo from a wild animal, or if it had been tweaked by intrepid virologists to increase its infectivity for humans, in order to study exactly how such a virus could be countered, (Gain of Function Research). The net result would potentially be same either way, and there would be no active surveillance program of the surrounding waste water for an as yet “unknown virus”. This remarkable story was just published in: EUROSURVEILLANCE #28 issue 5, 2 Feb 2023.
Wild poliovirus type 3 (WPV3)-shedding event following detection in environmental surveillance of poliovirus essential facilities, the Netherlands, November 2022 to January 2023
The last word today is going to focus on the inter-species spread SARS2-COV19 between humans and animals, in particular the eastern White Tailed deer As you are aware, the virus has infected a large number of mammal species, in some producing lethal infection, primates and big cats, and in others apparently largely asymptomatic infection. There is concern of course, that virus which has jumped from humans to an animal species, may undergo unique mutations during adaptation to the animal, and may potentially cross back to humans. This was observed in the Netherlands early on in the Pandemic, when cases were documented of SARS2-COV which had infected farmed mink crossed back to humans, and triggered the killing of millions of mink. Eastern White Tailed deer have been recognized as a species infected with the virus from contact with humans. A recent article in PNAS is the most comprehensive investigation of the extent of this epidemic. Over a two year period ending in December 2021, 5400 deer from New York State were autopsied. During the first year 0.6% of the deer were infected, during the second year 21.2% were infected. They were found to have COVID viral lineages now basically extinct in humans, Alpha, Beta, Gamma, but with many unique combinations of mutations not recognized in humans, and the result of viral adaptation to the unique physiology of the deer. Given that rate of growth, it’s a fair bet that the virus has by now infected the majority of the millions of deer in NY. Whether a reverse transfer event of a unique virus with the potential for rapid human spread or a change in clinical severity will occur is anybody’s guess.
White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern
Leonardo C. Caserta https://orcid.org/0000-0003-1643-8560, Mathias Martins https://orcid.org/0000-0002-8290-5756, Salman L. Butt https://orcid.org/0000-0002-4565-0125, +5, and Diego G. Diel https://orcid.org/0000-0003-3237-8940 dgdiel@cornell.eduAuthors Info & Affiliations
Edited by Xiang-Jin Meng, Virginia Polytechnic Institute and State University, Blacksburg, VA; received September 2, 2022; accepted December 12, 2022
January 31, 2023
120 (6) e2215067120
https://doi.org/10.1073/pnas.2215067120
Thanks for your time today. The post was short since I am exhausted from scanning the sky for giant “Weather Balloons” and other celestial harbingers of the end of the world. If you find these updates informative, please pass along to your friends. Just for the record, I am no longer representing Sam Bankman-Fried at this time, we had severe differences regarding appropriate court attire, the contacting of witnesses and my FTX statement.
Waste water surveillance really exploded with COVID. I don't know about the Netherlands, (I assume it's similar) but in the US there was no standing nationwide program to do surveillance for any pathogen. On a local basis, if a problem arose, like the polio case in NY state, then local state authorities would set up ad hoc testing. In the case of the Netherlands, the only reason they were doing this testing was because there was a Polio lab in that area. In the past waste water testing had been used mostly in third world locations to monitor pathogens which normally are not present, but can cause epidemics sporadically, like Cholera and Polio. Across the US, COVID water testing started in a few metropolitan areas and University campuses which had access to labs with quick turn around times. In Telluride the program we set up was paid for by the local county and administered by the Department of Health. All the data analysis was done by myself and a colleague pro bono. Eventually after more than a year the State of CO subsumed our program into a state wide program. The CDC eventually (took much too long) began collecting the data from all the independent local and state Public Health Departments, and displays the aggregate data on their web site, but the programs depend on local support ,and many are winding down now.
Jeffrey,
A few questions about wastewater surveillance...how does the determination of which pathogens to look for differ between the Netherlands and the US? Which agency in the US is responsible for that decision? Keep up the good work!
Debbie Frankfurt