Georgia WWSCAN Biweekly Newsletter Update 4/26/24

Welcome to the bi-weekly update for WWSCAN partners in Georgia! The samples provided up through 4/24/24 have been processed in the lab and data are on the site at data.wastewaterscan.org.

A new "Publications" page is now available within the Resources section on the data dashboard that provides a detailed overview of the program’s peer-reviewed scientific literature organized by topics and themes. Click here to read!

We launched the categorization system for the more recently onboarded 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.

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 9,300 and 120,000 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 within the lower third level of all concentrations measured in the last year. Nationally and in the Southern region, SARS-CoV-2 RNA concentrations continue to decline.

As of 4/26/24, Columbus, Big Creek, Johns Creek, and South River are in the MEDIUM (4 sites) category. Utoy Creek, Little River, and RM Clayton are in the LOW (3 sites) category. There was not enough data to calculate a category for College Park.

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 (dark purple) made up the largest proportion of the lineages detected at both sites (100% at RM Clayton, and 97.8% at College Park). Note that the most recent data are from two weeks ago (through Apr 6 at RM Clayton & Apr 13 at College Park); 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 (73.3%).

Influenza A: IAV RNA concentrations have been below 15,000 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 is approaching the upper third level. As of 4/26/24, South River, Columbus, and Big Creek are in the HIGH (3 sites) Wastewater category. RM Clayton and Johns Creek are in the MEDIUM (2 sites) category. Utoy Creek and Little River are in the LOW (2 sites) category. There was not enough data to calculate a category for College Park.

Influenza B (IBV) RNA concentrations are below 4,500 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. As of 4/26/24, most Georgia sites are in the LOW (7 sites) Wastewater category. There was not enough data to calculate a category for College Park.

Respiratory syncytial virus (RSV) RNA concentrations were below 29,000 copies/gram over the last two weeks. However, since Apr 17, none of the 8 Georgia sites detected RSV. The chart below includes the raw data for each site since 2023. The aggregated line below is at zero showing that RSV RNA concentrations among Georgia sites remain at the bottom of the middle third level of all concentrations measured in the last year.

As of 4/26/24, most Georgia sites are in the LOW (7 sites) Wastewater category. There was not enough data to calculate a category for College Park.

HMPV (human metapneumovirus) RNA concentrations in wastewater are below 61,000 copies/g. Based on the heat map below, HMPV continues to be frequently detected at all Georgia locations within the last two weeks at lower concentrations. HMPV RNA concentrations in Georgia remain within the upper third level of all concentrations measured in the last year. RM Clayton, Columbus, Big Creek, Johns Creek, and Little River are in the HIGH (5 sites) Wastewater Category, as of 4/26/24. South River and Utoy Creek are in the LOW (2 sites) category. There was not enough data to calculate a category for College Park.

EV-D68 RNA was only detected at the College Park site over the last few weeks, 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 4/26/24, all Georgia sites are in the LOW (7 sites) Wastewater category. There was not enough data to calculate a category for College Park.

Parainfluenza RNA has been detected in the wastewater at all Georgia sites over the last two weeks with RM Clayton continuing to have the highest concentrations of them all, based on the heat map below. Parainfluenza concentrations have been below 135,000 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 4/26/24, RM Clayton, Big Creek, and Johns Creek are in the HIGH (3 sites) Wastewater category. Columbus, South River, Utoy Creek, and Little River are in the MEDIUM (4 sites) category. There was not enough data to calculate a category for College Park.

Norovirus GII (HuNoV GII) RNA concentrations range between 5,500,000 - 21,000,000 copies/g, and the population-weighted average line when the data is normalized by PMMoV for the 8 Georgia sites is within the upper third level. HuNoV GII RNA chart below also shows the raw data. As of 4/26/24, South River, Utoy Creek, Columbus, Big Creek, Johns Creek, and Little River are in the HIGH (6 sites) Wastewater category. And RM Clayton remains in the MEDIUM (1 site) category. There was not enough data to calculate a category for College Park.

Rotavirus RNA concentrations have been between 24,000 and 900,000 copies/g over the last two weeks. The chart below shows the population-weighted average line is shown in black plus the raw data for each site. As of 4/26/24, RM Clayton, South River, and Utoy Creek are in the HIGH (3 sites) Wastewater category. Columbus, Big Creek, Johns Creek, and Little River are in the MEDIUM (4 sites) category. There was not enough data to calculate a category for College Park.

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. Most Georgia sites are in the LOW (7 sites) Wastewater Category as of 4/26/24. There was not enough data to calculate a category for College Park.

Candida auris DNA has been detected only at the Columbus site in the last two weeks, based on the heat map below. As of 4/26/24, most Georgia sites are in the LOW (7 sites) Wastewater Category. Columbus is in the MEDIUM (1 site) category. There was not enough data to calculate a category for College Park.

Hepatitis A RNA has not been detected at Big Creek and South River over the last two weeks, according to the heat map. As of 4/26/24, most Georgia sites are in the LOW (7 sites) Wastewater category. Big Creek is in the MEDIUM (1 site) category. There was not enough data to calculate a category for College Park.

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, May 10th @ 12 PM EST. You can use this zoom link to join. Hope to see you there!