Nationwide WWSCAN Update 5/26/23

Hi everyone,

This newsletter contains updates on the WastewaterSCAN program with wastewater data processed by the lab through May 23, 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:

• 160 plants sampling
• 11.5% US population represented (38,590,140 people)
• 31 states represented

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 available to view by selecting 'SARS-CoV-2 View by Variant' on data.wastewaterscan.org. See the example plot for Coeur d'Alene, ID below. The N gene (present in all variants) is shown in blue, XBB* mutations are shown in red, and the HV69-70 mutation (present in the BA.4, BA.5 and BQ* sublineages) is shown in orange. You can see that in the month of February, the red line is increasing and is approaching the orange line, while the pink 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*  has replaced other variants.

The ratio of the XBB* mutations/N across all WWSCAN plants is shown in the chart below on the right. 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 ~75% but some places show levels as high as 80-100%. This suggests the majority of infections across the communities are caused by XBB* . The chart on the left 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%. 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 US Census Region - South (middle panel), and those in Alabama (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 160 sites, 13 show an upward trend, 123 show no trend, and 21 show a decreasing trend. The remaining 3 sites do not have enough data to calculate a trend.

When we look at the 21-day trends at the US Census Region level, no regions show an upward trend, the Northeast and South regions show no trend, and the Midwest and the West show decreasing trends.

Influenza A (IAV) RNA concentrations (normalized by PMMoV) are very low signaling the end of influenza season. 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), HHS Region 5 - IL, IN, MI, MN, OH (middle panel), and Indiana (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 160 sites, 0 shows an upward trend, 156 show no trend, and 1 show a decreasing trend. The remaining 3 sites do not have enough data to calculate a trend.

When we look at the 21-day trends at the US Census Region level, all 4 regions (Midwest, Northeast, South, and West) show no trend for IAV.

Influenza B (IBV) RNA concentrations are mostly non-detect at WWSCAN sites. There have only been 248 positive samples out of 1,293 samples during the past 21 days (~19% detection rate), all at low concentrations. Below is a heat map showing IBV detections at all the plants in WWSCAN in Florida. 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 are low signaling the end of RSV season. 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), the Greater San Francisco Bay Areas sites, and Orange County, FL(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 160 sites, 0 shows an upward trend, 157 show no trend, and 0 show a decreasing trend. The remaining 3 sites do not have enough data to calculate a trend.

When we look at the 21-day trends at the US Census Region level, the Midwest, Northeast, South and West show no 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 3,798 copies/gram, which is about twice our lower limit of detection. Examples below show HMPV RNA at participating sites across the country (left panel), California (middle panel), and Maine (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 160 sites, 5 show an upward trend, 130 show no trend, and 22 show a decreasing trend. The remaining 3 sites do not have enough data to calculate a trend.

When we look at the 21-day trends at the US Census Region level, no regions show an upward trend, the South show no trend, and the Midwest, Northeast and West show decreasing trends.

‌Norovirus GII (HuNoV GII) RNA has been consistently detected at the sites.  The median concentration across all sites over the last 21 days is 10,788,324 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 Minnesota (right panel). The weighted average lines in these plots are trending down.

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 160 sites, 7 show an upward trend, 112 show no trend, and 38 show a decreasing trend. The remaining 3 sites do not have enough data to calculate a trend.

When we look at the 21-day trends at the US Census Region level, no regions show an upward trend, the Northeast and South show no trend, and the Midwest and West show decreasing trends.

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 1 positive samples out of 1,293 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 160) 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. As a reminder, you can access our paper in New England Journal of Medicine about how mpox wastewater monitoring compares to clinical reports of infectious here.

Please join us for our usual all stakeholder meeting on June 9. We'll send out the usual update in advance of the meeting and will be taking the time to focus on demonstrating different features of the website and answering questions about its use. If you have questions about the website or anything else, submitting them in advance here will help us plan to address everything. We hope to see you there!