The next pandemic, and what you shouldn’t do about it

As I’ve written before, I didn’t really get turned onto learning until a 4th year university virology course in 1984 (I half since seen the prof several times and thanked him profusely).

John Oliver and his writing staff have done everything I’ve tried to do, but he has better writers who are also paid better.


Hand washing only spiked temporarily during pandemic, hospital finds

European Cleaning reports that a US hospital study has revealed that while healthcare hand hygiene compliance soared early on in the pandemic, it fell back to pre-pandemic levels after just four months.

Woman washing her hands at the kitchen sink. There are vegetables out of focus in the background.

The University of Chicago Medical Centre used an automated hand hygiene monitoring system to track how often staff washed their hands or used sanitiser when entering and exiting a patient’s room between September 2019 and August 2020. Compliance trends were then analysed by researchers at the hospital.

In September 2019, baseline monthly hand hygiene compliance levelled out at 54.5 per cent across all units, peaking at 75.5 per cent. On March 29, 2020 – when anxiety about the pandemic was running high – hand hygiene compliance hit a daily peak of 92.8 per cent across all hospital units. And it hit 100 per cent across those units that were temporarily given over for the exclusive use of COVID-19 patients.

However just four months later in August 2020, monthly compliance levels had dropped back to 56 per cent, researchers found.

The results of the study, published in JAMA Internal Medicine, considered various factors that may have contributed to the March 2020 jump in compliance including staff members’ increased awareness of the importance of hand washing during the pandemic.

Bump in foodborne botulism in Colorado

The pandemic brought a rise in home canning and food preservation as evidenced by a scarcity of canning supplies on store shelves and from online retailers, perhaps driven by a bountiful harvest by those who planted home gardens in the spring during the early lockdown period.

The Journal Advocate reports improperly canned food is behind at least some of the several cases of confirmed and suspected foodborne botulism that the Colorado Department of Public Health and Environment (CDPHE) has investigated in the state since September, according to a release from CDPHE Wednesday. Testing from the Centers for Disease Control and Prevention confirmed four of the cases, one is still under investigation, and two test results are pending. All of the confirmed cases occurred along the Front Range, and one of the unconfirmed cases occurred in the Western Slope.

A majority of the cases appear to be unrelated as no common food item was identified. The last two confirmed cases were the result of an improperly canned shared food made in the same household, prompting a warning from CDPHE about home food safety.

 “Botulism does not spread from person to person, so there is no risk to the public. However, these cases are a good reminder of how important it is to properly preserve and handle food in the home,” said Nicole Comstock, deputy branch chief, communicable disease branch.

Global norovirus pandemic emergence: maybe it’s in the polymerase

The perfect human pathogen has fantastic fitness because of lots of things: small hearty virus particles, millions of particles shed per gram of feces/vomit; induces projectile vomiting and according to new research in mSphere, fa_polymerase_figure4maybe the lack of fidelity in norovirus polymerase increases transmission between hosts.

Viruses are awesome.

Norovirus Polymerase Fidelity Contributes to Viral Transmission In Vivo 




A. Arias, L. Thorne, E. Ghurburrun, D. Bailey and I. Goodfellow

Intrahost genetic diversity and replication error rates are intricately linked to RNA virus pathogenesis, with alterations in viral polymerase fidelity typically leading to attenuation during infections in vivo. We have previously shown that norovirus intrahost genetic diversity also influences viral pathogenesis using the murine norovirus model, as increasing viral mutation frequency using a mutagenic nucleoside resulted in clearance of a persistent infection in mice. Given the role of replication fidelity and genetic diversity in pathogenesis, we have now investigated whether polymerase fidelity can also impact virus transmission between susceptible hosts. We have identified a high-fidelity norovirus RNA-dependent RNA polymerase mutant (I391L) which displays delayed replication kinetics in vivo but not in cell culture. The I391L polymerase mutant also exhibited lower transmission rates between susceptible hosts than the wild-type virus and, most notably, another replication defective mutant that has wild-type levels of polymerase fidelity. These results provide the first experimental evidence that norovirus polymerase fidelity contributes to virus transmission between hosts and that maintaining diversity is important for the establishment of infection. This work supports the hypothesis that the reduced polymerase fidelity of the pandemic GII.4 human norovirus isolates may contribute to their global dominance.

IMPORTANCE Virus replication fidelity and hence the intrahost genetic diversity of viral populations are known to be intricately linked to viral pathogenesis and tropism as well as to immune and antiviral escape during infection. In this study, we investigated whether changes in replication fidelity can impact the ability of a virus to transmit between susceptible hosts by the use of a mouse model for norovirus. We show that a variant encoding a high-fidelity polymerase is transmitted less efficiently between mice than the wild-type strain. This constitutes the first experimental demonstration that the polymerase fidelity of viruses can impact transmission of infection in their natural hosts. These results provide further insight into potential reasons for the global emergence of pandemic human noroviruses that display alterations in the replication fidelity of their polymerases compared to nonpandemic strains.

US waits to react to flu discovery in Canadian pigs

As a backlog of state and federal lab test results reached the Centers for Disease Control and Prevention (CDC), the total number of confirmed cases of H1N1 in the US climbed to 244 in 34 states, the Associated Press reported this weekend.

The Globe and Mail reported numbers from the World Health Organization, stating, “Canada, for its part, has tallied 101 cases in seven provinces.”

When news broke that a Canadian swine herd was found suffering from a flu thought to be H1N1, the U.S. Department of Agriculture (USDA) issued a statement assuring that, “this detection does not change the situation here in the United States.”

The statement continued:

“Today’s discovery will not impact our borders or trading with Canada. As prescribed by the World Organization for Animal Health guidelines, any trade restrictions must be based on science so at this time, we are awaiting confirmatory test results before considering any action."

Additionally, while the CDC works on a H1N1 vaccine for humans, the USDA announced it is trying to develop a vaccine for swine. But that’s just standard protocol when a new virus appears.

It seems they’re taking no rash action until there’s evidence to suggest it’s necessary. That sounds like a wise use of resources to me.

The World Health Organization is similarly waiting for evidence before sounding the alert to a pandemic. As reported by the New York Times,

“The World Health Organization announced an increase in the number of confirmed cases of swine flu on Saturday, but said there was no evidence of sustained spread in communities outside North America, which would fit the definition of a pandemic.”

“Dr. Michael J. Ryan, the director of the World Health Organization global alert and response team, said in a teleconference from Geneva, ‘We have to expect that Phase 6 (the level of a pandemic) will be reached. We have to hope that it is not.’”

The public should be made aware of existing risks and what’s being done to manage them. But, there is no good reason to waste resources pretending to manage imaginary risks.

Act on what you know and seek out what you don’t–for the good of the public.