Georgia WWSCAN Biweekly Newsletter Update 3/15/24

Welcome to the bi-weekly update for WWSCAN partners in Georgia! The samples provided up through 3/11/24 have been processed in the lab and data are on the site at data.wastewaterscan.org.

We have now launched the categorization system for the more recently onboard pathogens, including Rotavirus, Parainfluenza, EV-D68, Candida auris, and Hepatitis A. When you visit data.wastewaterscan.org, you will now find that the map view includes information on Wastewater Categorization for all of the pathogen’s WastewaterSCAN monitors. For more information on the Wastewater Categorization methodology, please refer to the About page on the website here.

We also want to share a couple new resources with you! First, a new paper from our team, "Observations of respiratory syncytial virus (RSV) nucleic-acids in wastewater solids across the United States in the 2022-2023 season: Relationships with RSV infection positivity and hospitalization rates" gives insight into the use of RSV data from wastewater.  

We also have an Influenza A Fact Sheet now available that provides a summary of our November 2023 paper exploring similar insight from influenza A data in wastewater across the country.

If you notice any bugs on the site or have any comments about it, please continue to send your feedback via email wwscan_stanford_emory@lists.stanford.edu. We thank you for your partnership!

The methods for our assays are in the public domain and links for these are provided at the end of the newsletter.

SARS-CoV-2 RNA concentrations have been between 40,000 and 250,000 copies/gram in the last two weeks. The chart below shows the raw data over the last 365 days and the population-weighted aggregated trend line for all 8 Georgia sites when the data is normalized by PMMoV. The aggregated line and the National Levels benchmarks illustrate that SARS-CoV-2 N gene RNA concentrations among Georgia sites are now within the middle third level of all concentrations measured in the last year. Across the South, SARS-CoV-2 RNA concentrations remain high but with a downward trend over the last few weeks.

As of 3/15/24, College Park, Columbus, Little River, Big Creek, and Johns Creek are in the HIGH (5 sites) Wastewater category. RM Clayton, Utoy Creek, and South River are in the MEDIUM (3 sites) category.

Sequencing of SARS-CoV-2 from wastewater is available for RM Clayton and College Park (Camp Creek). The plots below show the relative proportions of different variants inferred from sequencing the entire genome of SARS-CoV-2 (Note: the sequencing variant plots are now available on the website, so the plots that are shown below are linked above if you want to interact with them). Results are based on sequencing of 2 samples per week, combined to provide a weekly value. Please note that the large gap of "no data" for College Park is because we had data available from preliminary testing while finalizing site selection for sequencing, and then began weekly sequencing in the middle of December.

In the most recent samples, JN.1 (bright red) made up the largest proportion of the lineages detected at both sites (100% at RM Clayton, and 100% at College Park). Note that the most recent data are from two weeks ago (through Mar 2); sequencing data are always from samples taken between 1- 2 weeks ago.

Sequencing data is now also available in aggregate across all sites in WWSCAN with sequencing data. That plot is shown below and also suggests that JN.1 is the most abundant variant across all sites (99.3%).

Influenza A: IAV RNA concentrations have been below 25,000 copies/gram in the last two weeks. The chart below shows the raw data and the population-weighted aggregated trend line for all 8 Georgia sites when the data is normalized by PMMoV. As of 3/15/24, College Park, Columbus, South River, Big Creek, Johns Creek, and RM Clayton are in the HIGH (5 sites) Wastewater category. Utoy Creek, Johns Creek, and Little River are in the LOW (3 sites) category.

Influenza B (IBV) RNA concentrations range between 2,100 and 32,000 copies/gram. The chart below shows IBV RNA concentrations raw data and the population-weighted aggregated trend line for all 8 Georgia sites when the data is normalized by PMMoV. The trend line recently peaked in February, and it appears that IBV wastewater concentrations are declining in Georgia. As of 3/15/24, all Georgia sites are in the HIGH (8 sites) Wastewater category.

Respiratory syncytial virus (RSV) RNA concentrations were below 17,000 copies/gram over the last two weeks. The chart below includes the raw data for each site since 2023. The aggregated line below is within the dark shaded area, showing that RSV RNA concentrations among Georgia sites are within the middle third level of all concentrations measured in the last year. Concentrations are low and continue to decrease to levels below the recent winter peak.

As of 3/15/24, RM Clayton, South River, Utoy Creek, South Columbus, Johns Creek, and Little River are in the LOW (6 sites) Wastewater category. Detections at South River and Utoy Creek indicate the end of RSV season. Camp Creek and Big Creek are the only sites in the HIGH (2 sites) category.

HMPV (human metapneumovirus) RNA concentrations in wastewater are below 27,000 copies/g. Based on the heat map below, HMPV has been detected at all Georgia locations within the last two weeks at low concentrations. HMPV RNA concentrations in Georgia remain within the upper third level of all concentrations measured in the last year. Columbus and Johns Creek are in the HIGH (2 sites) Wastewater Category, as of 3/15/24. RM Clayton, South River, Utoy Creek, College Park, Big Creek, and Little River are in the LOW (6 sites) category.

EV-D68 RNA is rarely detected at Georgia sites. Over the last two weeks, there was a single EV-D68 detection at Little River, according to the heat map below. As a reminder, the color blue means the sample was non-detect for EV-D68 RNA and the colors get darker with higher concentrations. As of 3/15/24, all Georgia sites are in the LOW (8 sites) Wastewater category.

Parainfluenza RNA has not been detected over the last two weeks at a couple of sites (College Park and Utoy Creek), based on the heat map below. Parainfluenza concentrations have been less than 18,000 copies/g. The chart below shows the raw data and the population-weighted aggregated trend line for all 8 Georgia sites when the data is normalized by PMMoV.

As of 3/15/24, RM Clayton, South River, Utoy Creek, Camp Creek, Big Creek, and Littler River are in the LOW (6 sites) Wastewater category. Johns Creek is in the MEDIUM (1 site) category. Columbus is in the HIGH (1 site) category.

Norovirus GII (HuNoV GII) RNA concentrations range between 5,400,000 - 29,000,000 copies/g, and the population-weighted average line for the 8 Georgia sites is within the upper third level. HuNoV GII RNA wastewater concentrations in Georgia are increasing, based on the trend line in the chart below. As of 3/15/24, all of the Georgia sites are in the HIGH (8 sites) Wastewater category.

Rotavirus RNA concentrations have been between 220,000 - 20,000,000 copies/g over the last two weeks and have been detected at higher concentrations at Little River. The chart below shows the population-weighted average line is shown in black plus the raw data for each site. As of 3/15/24, all of the Georgia sites are in the HIGH (8 sites) Wastewater category.

Mpox DNA results have been non-detect at all Georgia sites in the last 21 days. This heat map shows data since July 2022. Sites are labeled in the rows and each date a sample was collected as a column. The color blue means the sample was non-detect for mpox DNA and the color maroon means Mpox DNA was detected. White indicates no sample was collected. All Georgia sites are in the LOW (8 sites) Wastewater Category as of 3/15/24.

Candida auris DNA has not been detected at any of the Georgia sites in the last two weeks, based on the heat map below. As of 3/15/24, all Georgia sites are in the LOW (8 sites) Wastewater Category.

Hepatitis A RNA continues to be detected in samples collected from Columbus and RM Clayton over about the last two weeks, according to the heat map. As of 3/15/24, most Georgia sites are in the LOW (6 sites) Wastewater category, while Columbus and RM Clayton are in the MEDIUM (2 sites) category.

Protocols (Pre-analytical methods and SARS-CoV-2 analytical methods including controls):

• High Throughput RNA Extraction and PCR Inhibitor Removal of Settled Solids for Wastewater Surveillance of SARS-CoV-2 RNA
• High Throughput pre-analytical processing of wastewater settled solids for SARS-CoV-2 RNA analyses
• Quantification of SARS-CoV-2 variant mutations (HV69-70, E484K/N501Y, del156-157/R158G, del143-145, LPPA24S, S:477-505, and ORF1a Del 141-143) in settled solids using digital RT-PCR
• High Throughput SARS-COV-2, PMMoV, and BCoV quantification in settled solids using digital RT-PCR

Pre-prints and peer-reviewed publications provided WWSCAN methods: 

• SARS-CoV-2 
• Influenza, Human metapneumovirus, Respiratory syncytial virus, Human parainfluenza
• Mpox
• Norovirus GII
• Adenovirus group F, Rotavirus, Candida auris, Hepatitis A
• Enterovirus D68

A complete list of peer-reviewed publications utilizing the WWSCAN data is available here!

The next stakeholder meeting will take place Friday, April 12th @ 12 PM EST. You can use this zoom link to join. Hope to see you there!