Georgia WWSCAN Biweekly Newsletter Update 2/2/24

Welcome to the bi-weekly update for WWSCAN partners in Georgia! The samples provided up through 1/29/24 have been processed in the lab and data are on the site at data.wastewaterscan.org.

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 140,000 and 760,000 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 upper third level of all concentrations measured in the last year.

As of 2/2/24, RM Clayton, College Park, Columbus, Big Creek, Johns Creek, Little River, and South River are in the HIGH (7 sites) category. There was not enough data to calculate a category for Utoy Creek.

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 (83.4% at College Park, and 85.1% at RM Clayton). Note that the sequencing data are always from samples taken between 1- 2 weeks ago. The most recent data are from last week (through Jan 27).

Sequencing data is now also available in aggregate across all sites in WWSCAN with sequencing data. That plot is shown below, and also suggest that JN.1 is the most abundant variant across all sites.

Influenza A: Retrospective data (1 Oct 2023 to approximately 11 Jan 2024) are actively being uploaded to the website as samples get reanalyzed. We expect the entire time series to be filled in by early next week, and as more data becomes available on the website, trends will become clearer. IAV RNA concentrations have been between 20,000 and 98,000 copies/gram in the last two weeks. The chart below shows the raw data from November 21st, 2023, and the population-weighted aggregated trend line for all 8 Georgia sites when the data is normalized by PMMoV. With this data now available, it appears that influenza A peaked in wastewater in the end of December/beginning of January in Georgia.

Influenza B (IBV) RNA continues to be detected frequently at all Georgia sites at low up to high concentrations, as shown in the heat map below. IBV RNA concentrations are below 80,000 copies/gram. As of 2/2/24, RM Clayton, South River, College Park, Columbus, Big Creek, and Johns Creek have had an onset of IBV in wastewater and are in the HIGH (6 sites) Wastewater Category. Little River is in the LOW (1 site) category. There was not enough data to calculate a category for Utoy Creek. IBV RNA wastewater concentrations in the Southern region are high and do not appear to have peaked.

Respiratory syncytial virus (RSV) RNA concentrations were below 25,000 copies/gram over the last two weeks. The chart below includes the raw data for each site since February 2023. The aggregated line and the National Levels benchmarks illustrate that RSV RNA concentrations among Georgia sites are within the upper third level of all concentrations measured in the last year but have come down rgom a peak in December. RM Clayton, College Park, Columbus, Little River, Big Creek, and Johns Creek are in the HIGH (6 sites) Wastewater Category as of 2/2/24. South River is in the LOW (1 site) category. There was not enough data to calculate a category for Utoy Creek.

HMPV (human metapneumovirus) RNA concentrations in wastewater are below 12,000 copies/g. Based on the heat map below, HMPV has not been detected at South River or Utoy Creek within the last two weeks. HMPV RNA concentrations in Georgia are much lower in comparison to this time last year. Most Georgia sites are in the LOW (7 sites) Wastewater Category, as of 2/2/24. There was not enough data to calculate a category for Utoy Creek.

EV-D68 RNA has not been detected at any Georgia sites within the last two 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. Because this is a newer target, there is no category assigned and we are still establishing what an expected baseline amount of detection will be.

Parainfluenza RNA has been frequently detected at lower concentrations in samples collected from most Georgia sites. Utoy Creek has not detected parainfluenza RNA in the last two weeks. Concentrations have been less than 60,000 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. Because this is a newer target, there is no category assigned and we are still establishing what an expected baseline amount of detection will be.

Norovirus GII (HuNoV GII) RNA concentrations range between 7,000,000 - 75,000,000 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 the Southern region are high with an upward trend over the last 21 days. Marlene notes on an anecdotal level that the school age crowd seems to have been stricken with stomach bugs over the past couple weeks, so this shouldn't be surprising to any of you with kids in school!

As of 2/2/2024, RM Clayton, College Park, Columbus, Little River, South River, Big Creek, and Johns Creek are in the HIGH (7 sites) Wastewater Category. There was not enough data to calculate a category for Utoy Creek.

Rotavirus RNA concentrations have been between 460,000 - 6,500,000 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. Because this is a new target, there is no category assigned and we are still establishing what an expected baseline amount of detection will be.

Mpox DNA results have been non-detect at most Georgia sites in the last 21 days except for a single detection on 1/21/24 at Utoy Creek. 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. There are 7 Georgia sites in the LOW Wastewater Category as of 2/2/24.

Candida auris DNA has only been detected at the South River site in the last two weeks, based on the heat map below. Because this is a new target, there is no category assigned and we are still establishing what an expected baseline amount of detection will be.

Hepatitis A RNA has not been detected in the last two weeks. Because this is a new target, there is no category assigned and we are still establishing what an expected baseline amount of detection will be.

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

The next stakeholder meeting will take place Friday, February 9th @ 12 PM EST. You can use this zoom link to join. Hope to see you there!