Bay Area SCAN weekly update 12/29/22

All samples picked up by the couriers as of 12/27/22 have been processed and their data are on the site: wbe.stanford.edu.  Data from samples picked up yesterday will be on the site later today.

Note that the website changed in that now all non-SARS-CoV-2 pathogens can be found on one page with more control over the visualizations. Check it out here.

COVID-19
There are different trends in SARS-CoV-2 RNA among the plants over the last two weeks. In some locations concentrations are steady, falling, or rising. An example of a plant with steady levels is Sacramento, and an example with rising levels is Silicon Valley Clean Water in San Mateo County. In general, concentrations are similar to what they were in the last BA.2/BA.5 surge.

The HV69-70 mutation present in BA.5 and B.Q* sublineages is still present in the majority of circulating SARS-CoV-2 found in wastewater. You can see that in this chart from Davis showing the HV69-70 mutation concentration (purple line) mostly following the blue lines (N and S gene concentrations).

But as we have pointed out previously, the ratio of HV69-70/N has been slowly decreasing across the plants as shown in this chart of the HV69-70/N ratio over time at all the plants. If the ratio is at 100%, it suggests that all the SARS-CoV-2 genomes have the mutation (and we infer that all genomes are from BA.5 or BQ.*). The grey symbols are from all the plants in SCAN (you can access the plot and play around with it here). The current regional ratio of HV69-70/N appears to be  about 75%, the same as it was last week.

This suggests 25% of circulating SARS-CoV-2 in wastewater does not have the HV69-70 mutation. XBB and BA.2.75 are among circulating variants that do not have the mutation. The CDC variant tracker nowcast for our region (HHS region 9) predicts that nearly 25% of circulating variants for last week (ending 12/24/22) are those without this mutation (including XBB and BA.2.75). We do not have wastewater sequencing data this week but will have 2 weeks worth of data to report on next week.

Influenza A (IAV) RNA concentrations continue to drop across the plants over the last week suggesting contributions from infected individuals into the wastewater are also declining. The exceptions are the plants in San Francisco County were the concentrations have been steady for the last two weeks.

We look at the positivity rates across the State of California for influenza from the CDPH website which are updated on a weekly basis (see chart below). It is hard to tell from the positivity rate data if there is a downward trend yet due to delays in test result reporting. The most recent data are for the week ending of 12/17/22. Note that these data are aggregated across the state and there are likely regional differences in positivity rates and disease occurrence not captured by these data.

Influenza B (IBV) RNA concentrations are non-detect in most samples over the approximate 6 weeks we have been measuring it. When it is detected, it is mostly at quite low concentrations (except the one measurement in San Jose). Example data from Oceanside are below from the drill down page (here). The units on the y-axis are copies per gram dry weight of solids.

RSV RNA concentrations are falling at the Santa Clara County plants (see example of Palo Alto below). Otherwise, RSV RNA concentrations are mostly steady across the last 2 weeks (see example from Sacramento), or rising in the case of Silicon Valley Clean Water in San Mateo County.

Here is a chart of the weekly RSV positivity rate data across the entire state of California from the CDPH website, also showing a recent decline in RSV case positivity. The most recent data are for the week ending 12/17/22. Note that these data are aggregated across the state and there are likely regional differences in positivity rates and disease occurrence not captured by these data.

HMPV (human metapneumovirus) RNA concentrations have a diversity in trends over the last two weeks across the plants from strongly increasing (Sacramento) to strongly decreasing (Palo Alto) to steady (San Jose). HMPV infections may be more localized than influenza A or RSV. This will be interesting to look into once we have more data from all the sites to compare.

Norovirus RNA concentrations have been measured for about 6 weeks now at all the SCAN plants. We have observed concentrations between 10^4 cp/g and 10^8 cp/g.  Data appear to be hovering near high levels; trends are mixed across plants. Here is an example from the drill down page for Oceanside. The concentrations on the y-axis are on a linear scale and are in units of copies per gram dry weight. Another example from the non-COVID page on the website (here) is shown for San Jose. Note that the assay we use targets human norovirus GII which is a common genotype of norovirus, but GI can also circulate.

MPXV We are seeing  non-detects in the past 2 weeks for MPXV DNA. The only exception is for Southeast where we still have detections at low levels, 3 of the last 12 samples were positive). Here are charts of the MPXV DNA data from Southeast showing the 5-d trimmed, centered averages of PMMoV normalized MPXV DNA over the last 6 months.