IN THIS ISSUE
Keeping track of XBB.1.5
Nature’s Method of the year: long read sequencing
What does viral interference have to do with the Tripledemic?
Pandemic preparedness legislation got passed, after all
New and Noteworthy
The Omicron recombinant variant XBB.1.5 marches west
XBB.1.5 is still the fastest growing variant we have seen pandemic-to-date. It is also our first fully home-grown variant, identified initially in NYC. Now it’s steadily spreading westwards. As of now, XBB.1.5 represents 86.8% of NY/NJ but still only 36.7% in California and the southwest, for a national average of 49.1% of “Nowcast” sequences. Although it evades essentially all available antibody therapies, it does not evade any of the widely used EUA-authorized tests.
We shared XBB.1.5 at holiday parties this year, alas
The number of deaths from (and with) COVID nearly doubled in mid-January as XBB.1.5 reached dominance. However, that number is still only a quarter of the level we reached during the early February BA.1 peak a year ago. The vast majority of these deaths are in the oldest of citizens - testing and masking is still essential for members of this vulnerable group and folks who interact with them.
Were the Tripledemic waves a case of viral interference?
It looks like the tripledemic is receding, at least for the moment, with cases of RSV and flu on the downswing. But did you happen to notice something? RSV peaked in the middle of November. Flu peaked in early to mid-December. And it’s looking like the latest COVID surge may have peaked at the end of December (at least in reported cases). You might ask: Why didn’t they all peak at the same time? Was it just a lucky break?
Turns out it might not have been. As described in this great article from Knowable Magazine, “the presence of one virus can block another.” It’s a phenomenon called viral interference, and it can happen in individual cells, individual organisms (including us), and in whole populations. It may be part of the reason why we didn’t have a flu season or much of an RSV season during the worst of the pandemic, when Omicron arrived. (If you want to know the nuts and bolts of how the phenomenon happens, read the whole article.)
That said, viral interference is not a guarantee - it definitely is possible to be infected with more than one virus at a time, unfortunately. And on the population level, if what we saw in November through January was really viral interference, that could mean that once the current COVID surge has receded adequately, RSV could take over once again. Cross your fingers.
Pandemic preparedness legislation squeaked in while we weren’t looking
So you know that big omnibus bill that Congress passed at the end of the year to keep the federal government up and running? Guess what - a bunch of pandemic preparedness legislation was squirreled away inside it, mostly from the proposed PREVENT Pandemics Act. Some highlights:
Establishment of the White House Office of Pandemic Preparedness and Response Policy
Provisions to enhance public health data collection and response efforts at the state, local, and Tribal community levels
A requirement that the CDC “strengthen and expand . . . the use of genomic sequencing of pathogens in public health surveillance”
A directive for the HHS secretary to “support rapid, accurate, and secure sharing of laboratory test results during a public health emergency,” and improve coordination with clinical labs
Permission for HHS to contract with both public and private entities “to improve the rapid development and availability of diagnostic tests,” so that public health officials can address emerging infectious diseases more quickly.
Commentary: We applaud the effort and intent of the pandemic preparedness piece of this bill. We are 100% behind the effort and intent to create more partnerships with public AND private entities as well as broadly sharing information (especially lab results) in order to respond faster. Our concerns are the usual - is this just intent? Will it be funded appropriately, so that it can be actually implemented? We do hope that it will become functional now, before the Public Health Emergency ends. We know that money is an issue - but cheaper now than in the future if we lose control of a pathogen.
Food for Thought
Wastewater important, but needs expansion and standardization
The National Academies of Sciences, Engineering, and Medicine just released a comprehensive report about the good, bad, and ugly of wastewater testing. The good is focused on the fact that wastewater analysis works, is an effective tool to manage public health, and is not new - it has been used for community opioid detection as well as for polio and other diseases. The bad (okay, it’s really more just challenges), as we suggested here a few weeks ago, is that the US needs a standardized dashboard with consistent measures that can be used across existing and new systems, and it needs to become more representative of the nation as a whole. Second challenge is the perception and perhaps reality of privacy issues related to wastewater. Wastewater is intended to be a community wide assessment. But with some communities, might it be possible to trace a pathogen to a specific street or building? Potentially. Some think of this as great news making wastewater analysis more actionable - others throw up a huge red flag. At a minimum, education seems necessary. The piece from October 2022 explores what American know and don’t know about wastewater. The ugly . . . well, it’s wastewater testing. Do you really want a description?
Note: If you want to learn more go to COVID Data Dispatch for their compilation of wastewater dashboards - four national and 24 state and local dashboards. (Our favorite is COVIDPoops19, a global poop database with 72 countries participating).
Long read sequencing declared method of the year
Sequencing has been the frequently underestimated hero of the pandemic. Chinese scientists released the first full sequence of SARS-CoV-2 to the world on Jan. 5, 2020 (just four days after the Wuhan seafood market was closed due to an unknown respiratory disease), allowing vaccine development to begin immediately. In mid-2020 a novel, more transmissible variant (D614G) was identified that would eventually spread globally. In 2022, as wastewater became the primary pandemic marker, long read sequencing became an essential tool to identify and differentiate all the different types of DNA commingled in wastewater (humans, rodents, SARS, influenza, etc.). Although long read sequencing is critical for research and its cost is coming down rapidly, it is still too expensive for regular clinical and epidemiological purposes. This month, Nature Methods profiles this invaluable tool in a number of papers - for those interested in more, start with this hyperlinked editorial.
Quick Hits
CDC has launched a new website to help consumers find free COVID testing sites. The initiative is part of the Increasing Community Access to Testing (ICATT) program and is available for those with and without health insurance.