Georgia WWSCAN Biweekly Newsletter Update 4/12/24

Welcome to the bi-weekly update for WWSCAN partners in Georgia! The samples provided up through 4/8/24 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.

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 19,000 and 210,000 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 have been declining.

As of 4/12/24, Little River is in the HIGH (2 sites) Wastewater category. Columbus, Utoy Creek, College Park, Johns Creek, and South River are in the MEDIUM (5 sites) category. RM Clayton and Big Creek are in the LOW (2 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 30); 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 (93.9%).

Influenza A: IAV RNA concentrations have been below 23,000 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 within the middle third level. As of 4/12/24, South River and Johns Creek are in the HIGH (2 sites) Wastewater category. Despite this, these levels are far below the peak this January. RM Clayton, Columbus, and Big Creek are in the MEDIUM (3 sites) category. Utoy Creek, College Park, and Little River are in the LOW (3 sites) category.

Influenza B (IBV) RNA concentrations are below 13,000 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. Based on the trend line in the chart below, IBV wastewater concentrations continue to decline in Georgia. As of 4/12/24, College Park, Columbus, Johns Creek, and Little River are in the HIGH (4 sites) Wastewater category, while RM Clayton, South River, Utoy Creek, and Big Creek are in the LOW (4 sites) category.

Respiratory syncytial virus (RSV) RNA concentrations were below 8,500 copies/gram over the last two weeks. 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 are at the bottom of the middle third level of all concentrations measured in the last year.

As of 4/12/24, most Georgia sites are in the LOW (7 sites) Wastewater category and Big Creek is the only site in the MEDIUM (1 site) category. Non-detections at College Park, Little River, RM Clayton, South River, and Utoy Creek indicate the end of RSV season.

HMPV (human metapneumovirus) RNA concentrations in wastewater are between 5,000 and 93,000 copies/g. Based on the heat map below, HMPV has been detected more frequently 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. Concentrations appear to be declining now but seem to have recently peaked with levels similar to the most recent peak in November 2023. The pattern is similar to last year, when HPMV peaked in the spring. RM Clayton, Utoy Creek, College Park, Columbus, Big Creek, Johns Creek, and Little River are in the HIGH (7 sites) Wastewater Category, as of 4/12/24. South River is in the LOW (1 site) category.

EV-D68 RNA was only detected at the Columbus 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 4/12/24, all Georgia sites are in the LOW (8 sites) Wastewater category.

Parainfluenza RNA has been detected in the wastewater at low concentrations over the last two weeks at all Georgia sites with RM Clayton having the highest concentrations of them all, based on the heat map below. Parainfluenza concentrations have been below 81,000 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 4/12/24, RM Clayton, South River, Utoy Creek, College Park, Johns Creek, and Little River are in the HIGH (6 sites) Wastewater category. Columbus and Big Creek are in the MEDIUM (2 sites) category.

Norovirus GII (HuNoV GII) RNA concentrations range between 6,000,000 - 29,000,000 copies/g, and the population-weighted average line for the 8 Georgia sites remains within the upper third level. HuNoV GII RNA wastewater concentrations continue to decline in Georgia, based on the trend line in the chart below. However levels are still quite high and as of 4/12/24, South River, Utoy Creek, College Park, South Columbus, Big Creek, Johns Creek, Little River are in the HIGH (8 sites) Wastewater category. And RM Clayton is in the MEDIUM (1 site) category.

Rotavirus RNA concentrations have been between 95,000 and 9,100,000 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 4/12/24, most Georgia sites are in the HIGH (7 sites) Wastewater category and RM Clayton is the only site in the MEDIUM (1 site) 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 4/12/24.

Candida auris DNA has been detected at the College Park and Columbus sites in the last two weeks, based on the heat map below. As of 4/12/24, all Georgia sites are in the LOW (8 sites) Wastewater Category.

Hepatitis A RNA has not been detected at any of the 8 Georgia sites over the last two weeks, according to the heat map. As of 4/12/24, all Georgia sites are in the LOW (8 sites) Wastewater 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, May 10th @ 12 PM EST. You can use this zoom link to join. Hope to see you there!