Nationwide WWSCAN Update 4/28/23

Hi everyone,

This newsletter contains updates on the WastewaterSCAN program with wastewater data processed by the lab through Monday April 24, 2023. Below you will find information on the program in terms of participating partners, review of targets being measured, as well as trends in concentrations of infectious disease targets.

Enjoy your weekend,

Ali & Marlene

Participants:

• 151 plants sampling
• 154 plants onboarded
• 10.68% US population represented (35,750,716 people)
• 29 states represented

Welcome, New Plants!

• Hilo, HI
• Bridgwater, NJ

The methods for our assays are in the public domain. You can access them using these QR codes:

In late January 2023 we started testing for XBB* and these results are now available to view by selecting 'SARS-CoV-2 View by Variant' on data.wastewaterscan.org. See the example plot for Garland, TX below. The N gene (present in all variants) is shown in red, XBB* mutations are shown in yellow, and the HV69-70 mutation (present in the BA.4, BA.5 and BQ* sublineages) is shown in green. You can see that in the month of February, the yellow line is increasing and is approaching the red line, while the green line is falling off to non-detect. This can be interpreted to mean that more of the SARS-CoV-2 genomes in wastewater solids from this site have the XBB* mutations than the mutation characteristic of the BA.4, BA.5, and BQ* variants. This is consistent with what we know from recent sequencing of clinical specimens, which is that XBB* (and XBB.1.5 in particular) has replaced other variants.

The ratio of the XBB* mutations/N across all WWSCAN plants is shown in the chart below on the left. As the ratio reaches 100%, it suggests that all the SARS-CoV-2 genomes in wastewater have the XBB* mutations. These data indicate that the average ratio XBB* mutations/N is ~60% but some places show levels as high as 70-90%, and there is an increasing trend. This suggests 60%-80% of infections across the communities are caused by XBB or XBB.1.5 and the percentage is increasing. The chart on the right shows the ratio of the BA.5, BA.4, and BQ* mutation/N across all WWSCAN plants. It can be read the same way as the XBB* chart. The average ratio is about 10-20% and has a decreasing trend. Note that our XBB* assay will also detect XBB.1.16, XBB.1.9, and FD.2 (XBB.1.5.15.2*).

Below are the SARS-CoV-2 N gene concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country (left panel), those in HHS Region 4 - Southeast US (middle panel), and those in HHS Region 5 - Midwest US (right panel). Evident in the data are relatively high concentrations around the start of the year with lower levels presently observed.

Below is the trend analysis for the SARS-CoV-2 RNA concentrations (N gene concentrations normalized by PMMoV) in wastewater solids at all participating plants. Red indicates a significant upward trend, blue is a significant downward trend, and dark grey is no trend. Yellow indicates that there were not enough data points to calculate a trend (we required 3 points over the last 21 days). You can read about our methods for trend analysis here. In short, we test for linear trends between log10-transformed concentration (target/PMMoV) and time; the trend must be classified as statistically significant (p<0.1). Of the 152 sites, 2 show an upward trend, 119 show no trend, and 30 show a decreasing trend. The remaining 1 does not have enough data to calculate a trend. This can be interpreted to mean that over the last 21 days, that concentrations of SARS-CoV-2 RNA have generally not changed at most sites.

Influenza A (IAV) RNA concentrations (normalized by PMMoV) are generally lower now than they were at the height of Influenza A cases earlier this winter at most sites. The median concentration across all sites over the last 21 days is 0 copies/gram (non-detect). Examples below are from all participating sites across the nation (left panel), California (middle panel), and those in San Mateo County, CA (right panel).

Below is the trend analysis for the IAV RNA concentrations (normalized by PMMoV) in wastewater solids at all participating plants. Red indicates a significant upward trend, blue is a significant downward trend, and dark grey is no trend. Yellow indicates that there were not enough data points to calculate a trend. Of the 152 sites, 0 shows an upward trend, 147 show no trend, and 4 show a decreasing trend. The remaining 1 does not have enough data to calculate a trend.  

Influenza B (IBV) RNA concentrations are mostly non-detect at WWSCAN sites. There have only been 290 positive samples out of 1,489 samples during the past 21 days. Below is a heat map showing IBV detections at all the plants in WWSCAN in New Jersey. Each location is a row, and the date is a column. White indicates no sample, blue indicates non-detect, and the orange to red show variable concentrations if IBV. You can see how IBV RNA is occasionally detected since we began measuring it in mid December 2022 at these sites.

RSV RNA concentrations had decreased quite bit from the winter. The median concentration across all sites over the last 21 days is 0 copies/gram. Example charts below are from all participating sites across the country (left panel), Fulton County, GA (middle panel), and Marin County, CA (right panel).

Below is the trend analysis for the RSV RNA concentrations (normalized by PMMoV) in wastewater solids at all participating plants. Red indicates a significant upward trend, blue is a significant downward trend, and dark grey is no trend. Yellow indicates that there were not enough data points to calculate a trend. Of the 152 sites, 0 shows an upward trend, 148 show no trend, and 3 show a decreasing trend. The remaining 1 does not have enough data to calculate a trend.  

Human metapneumovirus (HMPV) RNA is consistently detected at WWSCAN sites, unlike RSV and Influenza A RNA.  The median concentration across all sites over the last 21 days is 12,005 copies/gram. Examples below show HMPV RNA at participating sites across the country (left panel), HHS Region 1 - New England (middle panel), and HHS Region 3 - Northeast US (right panel). The weighted average lines in these plots are trending down.

Below is the trend analysis for the HMPV RNA concentrations (normalized by PMMoV) in wastewater solids at all participating plants. Red indicates a significant upward trend, blue is a significant downward trend, and dark grey is no trend. Yellow indicates that there were not enough data points to calculate a trend. Of the 152 sites, 4 show an upward trend, 117 show no trend, and 30 show a decreasing trend. The remaining 1 does not have enough data to calculate a trend.

‌Norovirus GII (HuNoV GII) RNA has been consistently detected at the sites.  The median concentration across all sites over the last 21 days is 17,002,009 copies/gram. Example charts showing concentrations (normalized by PMMoV) in wastewater solids below are from all participating sites across the country (left panel), Kansas (middle panel), and Texas (right panel).

Below is the trend analysis for the Norovirus GII RNA concentrations (normalized by PMMoV) in wastewater solids at the plants. Red indicates a significant upward trend, blue is a significant downward trend, and dark grey is no trend. Yellow indicates that there were not enough data points to calculate a trend. Of the 151 sites, 7 show an upward trend, 118 show no trend, and 26 show a decreasing trend. The remaining 1 does not have enough data to calculate a trend.

We rarely detected mpox DNA in samples from any site over the past three-weeks. Below you can see, in red, there have only been 2 positive samples out of 1,489 samples during the past 21 days. Outbreaks seem to be under control, but we will continue to monitor so that public health departments can respond if we see consistent detections and increases in concentrations in any sites. The chart below shows every plant in WWSCAN (approximately 151) as rows, and the last 21 days as columns (labeled at the bottom axis). White indicates no samples, blue is non-detect for mpox DNA and red is detect for mpox DNA.