Questions and Responses W91ZLK-22-R-0005.pdf

Question and Responses W91ZLK-22-R-0005

Coronavirus Analysis in Wastewater Including Variants

1. Does it matter if the contractor uses traditional qPCR or newer digital PCR technology to do this analysis?

Response: Preference would be for digital PCR.

2. Is there a particular way that you want the variant testing handled? Some clients only want variant testing as a "reflex" afterthe initial sample is tested forCOVID. This is more cost effective because we only need to run the PCR again using a different gene target. However, some clients may wish to test for a particular variant from the start. I can explain more if needed.

Response: Ideally, we would like to know which variants are present, and extent (like a percentage, for instance) within the sample. Example: 150,000 RNA copies per liter SARS-CoV-2 within the sample (90% Omicron, 8% Delta, 2% Alpha). If a breakdown of percentages is too expensive, then presence only would be acceptable (using above example, 150,000 RNA copies per literSARS-CoV-2 within sample (Omicron, Delta, Alpha detected)). Clearly, if there is no SARS-CoV-2detected in the sample, then there will be no variants detected in the sample.

3. What is the expectation for data reporting?

a. Are you expecting a quantitative result that estimates the amount of COVI Din the sample?

We can provide this at no extra cost. Or are you looking for a simple positive/negative result?

b. What format are you expecting results in? (Excel, on line tools, etc).

Response: a. Results must be quantitative, reporting RNA copies per unit volume.

b. Report weekly analysis results, including full lab reports, to APHC EHSE within (2) calendar days of completion of sample analysis. Interpretations/notes/conclusions/comments are to be included where appropriate. Any deviations from established protocols (and response to those deviations) must be described, explained, and included in weekly lab reports. A .pdf of the results, along with lab reports, etc. is acceptable.

4. From reading the proposal, the opportunity is only requesting analysis of 108 samples (9/month). Is this accurate? Or is the proposal looking at 108 samples/location/year? To perform adequate surveillance for the presence of COVID-19 in a community, analysis should be performed at least 3 times a week. In large urban communities, samples should be obtained from 3-8 locations. Again, is this contract for only 108 samples/year?The fiscal commitment to maintain the facilities to perform variant analysis is high and would escalate the cost of performing 108 samples/year greatly.

Response: The proposal is for 108 samples per year. Two sites X 52 weeks= 104 samples. Plus a few extra for contingencies.

5. The proposal requires variant analysis for each sample. This component of the opportunity is the costliest and the description is vague. Are the contractors required to identify all novel variants of SARS- CoV-2? Are the contractors required to perform gene sequence analysis to identify the mutations of each observed variant despite the prevalence(% ottotal virus detected) in samples?

Response: Ideally, we would like to know which variants are present, and extent (like a percentage, for instance) within the sample. Example: 150,000 RNA copies per literSARS-CoV-2within the sample (90% Omicron, 8% Delta, 2% Alpha). If a breakdown of percentages is too expensive, then presence only would be acceptable (using above example, 150,000 RNA copies per literSARS-CoV-2 within sample (Omicron, Delta, Alpha detected). Clearly, if there is no SARS-CoV-2detected in the sample, then there will be no variants detected in the sample.

Complete gene sequence analysis to identify previously unidentified mutations/variants is beyond the scope of this proposal.

6. Will there be any desire to examine the presence of antibodies to COVID-19 in wastewater samples?

Response: Not at this time.

7. Does the APHC require the contractors to create a biobank of the samples obtained to allow for future analysis?

Response: No.