Pooled Surveillance Testing

Pooled Saliva Surveillance Program

(see our FAQ for questions about vaccines and testing)

UAlbany researchers conduct COVID-19 pooled surveillance  testing at the RNA Institute on Wednesday, September 2, 2020. (photo by Patrick Dodson)

Surveillance testing is one way to check the health of our overall community and get ahead of a potential outbreak. Testing large numbers of people who do not have COVID-19 symptoms allows us to better understand how many people in total — not just those who have been diagnosed — have the infection. In UAlbany’s pooled testing program, saliva samples are diluted, heat inactivated, processed by the testing facility, grouped into pools of four, and tested to determine whether the pool is positive for the presence of viral RNA. When a pool is positive, each individual sample is retested to identify the presumptive positive individual. The individuals in each pool are randomly selected to protect confidentiality and scientific validity. Samples tested are also only identified by the unique barcode on the tube to protect the privacy of the participants.

If a pool tests negative, no further action is required. Please remember that you could have been exposed to the virus after submitting your saliva sample, which means a negative result is not a guarantee that you are currently negative. Participating in pooled surveillance testing is not a substitute for mask wearing, hand washing, physical distancing, staying home when sick, and all other safety protocols.

If a pool tests positive, at least one of the people in that group has the virus. Each individual sample in the positive pool is then retested to identify the presumptive positive individual. An authorized representative will then be in contact with the presumptive positive individual with further instructions for a diagnostic testing.

Our testing program

An RNA Institute team member analyzes saliva samples from the University's pooled surveillance testing program. Photo by Patrick Dodson.

UAlbany’s saliva test is a hybrid of Yale SalivaDirect and the University of Illinois test, which both directly test saliva for the presence of SARS-CoV-2 viral RNA. Both of these tests report a very high accuracy rate, with SalivaDirect reporting an accuracy of 94% at the time of publication and the Illinois test reporting a specificity of 99.8-99.9%, with very few false positives. A combination of high specificity combined with frequent testing makes saliva-based testing extremely accurate. Additionally, both methods directly test saliva without extensive sample processing, reducing the supply chain burden, and simplifying the testing process.

Why is a follow-up diagnostic test required?

While our program uses the same principle and process as diagnostic PCR testing, our testing facility is not certified by the regulatory agency that oversees diagnostic labs (New York State Department of Health Clinical Laboratory Evaluation program). Regulated diagnostic labs, or CLIA-certified labs, have to undergo extensive regulatory paperwork, validation procedures, and are limited in terms of the reagents and processes they can use. Due to the current COVID-19 pandemic, the oversight agencies are allowing non-certified laboratories to perform surveillance testing to help combat the spread of SARS-CoV-2. To confirm the presumptive positive results and to ensure that the Department of Health is notified of any positive individuals, we highly recommend all presumptive positive individuals identified by our surveillance program undergo a confirmatory diagnostic test.

Frequently Asked Questions
I was vaccinated, should I participate in saliva testing?

Yes! Each COVID-19 vaccine behaves differently, but the current vaccines in use in New York State from Pfizer and Moderna are RNA vaccines which do not contain the actual virus, but rather a part of the viral spike protein.   Our saliva test assay, and most of the assays on the market, do not target the spike protein or its associated gene for detection and therefore are free of potential interaction with the vaccines. It is still possible for future vaccines or assays to interact but getting vaccinated now will not cause you to be positive by our saliva assay. The CDC has a pretty clear answer to the question of “After getting a COVID-19 vaccine, will I test positive for COVID-19 on a viral test?

No. Neither the recently authorized and recommended vaccines nor the other COVID-19 vaccines currently in clinical trials in the United States can cause you to test positive on viral tests, which are used to see if you have a current infection. ​

Additionally, it is important to remember the following about the vaccine

  • It takes time to build up immunity.  Current Moderna and Pfizer vaccines require two doses given several weeks apart and it takes several weeks after the 1st dose for immunity to start to build and the 2nd dose to receive the full effects of the vaccination. 
  • The vaccines are highly effective but not 100% effective. It is still possible for you to get infected even after you have been fully vaccinated. Immunity is different between individuals and the CDC is recommending that individuals not assume they are completely immune from infection after having been vaccinated.
  • Vaccinate individuals can still be infected and transmit by the virus. Even if you have immunity from the virus it is still possible for the virus to reside in your nasal passages and for you to transmit the virus to other people. There are still a lot of unanswered questions about the SARS-CoV-2 virus, especially in asymptomatic individuals, so the CDC is recommending that vaccinated people still utilize all the tools available to them, which includes social distancing, masks and testing.
I was previously positive, should I participate in saliva surveillance testing?

It depends on your employer and testing program.  For participants associated with UAlbany, the University’s recommendation is that “If you are currently experiencing symptoms of COVID-19, received a positive PCR diagnostic test result within the past 90 days, or were diagnosed as positive for the virus by a physician within the past 90 days, you should not participate in pooled testing.”

Since our saliva surveillance program detects the viral RNA and not the live virus, it is possible to remain presumptive positive even after you have been infected and cleared the recommended 14-day quarantine period.  The body continues to shed virus and viral RNA for some period of time after the person is no longer considered infectious. This continued viral shedding is one of the reasons why the CDC stopped recommending a negative test for infected people to exit quarantine. Based on the experience of our testing program, most people are still positive in our saliva test 5-10 days after the quarantine period ends. Additionally, while re-infection with a different strain of the virus is possible, only a few cases have been reported and verified.

If you want to participate in our saliva testing after testing positive for COVID, it is important to let your company HR or testing representative know.

What is a presumptive positive?

The UAlbany RNA Institute test refers to positives as "presumptive" because the test is a non-diagnostic PCR test due to the lab's level of certification.
A presumptive positive means that a detectable level of  Sars COV-2 RNA was identified in your sample.  We require a confirmatory diagnostic test for reporting to the Department of Health.  Very rarely, the confirmatory test may result in a negative result if the virus has cleared your system or you have an extremely low level of viral load.  In this case, the negative result means you are negative under Department of Health guidelines. Based on your situation (i.e. you have developed symptoms) we may encourage you to take a 2nd diagnostic / confirmatory test. We have encouraged these individuals to continue testing in the surveillance program. 

The background science of PCR testing

The UAlbany pooled saliva surveillance program utilizes an RT-PCR assay, which stands for Reverse Transcription – Polymerase Chain Reaction. It may see complicated at first but let’s break it down to the fundamentals.

Reverse Transcription (RT)

The SARS-CoV-2 virus is a single-stranded RNA virus, meaning that its genetic information is carried by RNA rather than DNA like most other organisms. RNA is similar to DNA, except it only contains a single strand rather than two strands or double-stranded like DNA. While RNA stores genetic information, it is easily degraded and difficult to work with and needs to be converted to DNA first, which is easy to work with and more stable. Reverse transcription refers to the process by which enzymes convert the RNA into DNA, or complementary DNA (cDNA). Most diagnostic tests that identify the SARS-CoV-2 virus utilizes reverse transcription to make cDNA, but it isn’t often mentioned in the media to keep things simple.

Polymerase Chain Reaction (PCR)

Polymerase chain reaction is the process by which a small segment of DNA is copied over and over again. The process uses two small segments of DNA that match a specific region of the DNA region of interest called primers, along with the individual DNA building blocks. When combined with an enzyme that makes DNA (DNA polymerase) and heat, an exact copy of the region of interest that reside between the two primers will be made. This cycle (heat and synthesis of DNA) is repeated over and over again so that the small region of interest is amplified making it easier to identify.

Ct value, viral load and viral RNA

To detect the SARS-CoV-2 virus in the saliva, we amplify a region of the SARS-CoV-2 nucleocapsid (N gene) RNA. We also amplify a small region from a human RNaseP (RP gene) RNA as a control to ensure the assay is working and that the sample contains human saliva and not water. During the amplification process, the testing instrument measures the amount of the amplified DNA region, during each cycle. The more viral RNA present, the quicker the amplified product will be detected. The cycle at which the amplified product can be detected over background threshold is called the cycle threshold or Ct value.

Ct values chart


A low Ct value typically occurs in samples with very high amount of viral RNA


A high Ct value typically occurs in samples with very low amount of viral RNA


PCR analysis is very sensitive so an upper limit or cut-off of the Ct value must be set. This number is the Ct value above which you can safely assume the signal is coming from background readings. For our program we utilize a conservative Ct cut-off of 40 cycles as recommended by the CDC, while some diagnostic tests utilize a lower Ct cut-off of 35 or 37. Depending upon the instrument, assay and sample in use, the background signal can be quite different. One approach isn’t better than another and most diagnostic tests don’t report Ct values so you shouldn’t worry if your COVID test doesn’t have an associated Ct value.

It is important to remember that we are detected the amount of viral RNA which is correlative with the amount of virus but does not detect the virus itself. Some individuals continue to have very low yet detectable levels of viral RNA (high Ct) long after they are infectious. This is important as with the cut-offs used in our program, it is possible that a presumptive positive individual identified by our program (Ct between 35 and 40) would show as negative in a diagnostic test (Ct cut-off of 35).

How does Ct value correlate with infectivity?

A little bit more about Ct value and infectivity

Ct value and infectivity chart

SARS-CoV-2 is a new virus and there are a number of ongoing studies on its infectivity. One study that touched upon how RT-PCR Ct values correlated with infectivity was recently published. In the above graph from the study, you can see that as the Ct value increases the ability of the lab to culture virus decreases. Obviously culturing virus in a lab is different from infection out in public but this data supports that RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus and likelihood of infectiousness.

Pooled Surveillance Testing Team

Dr. Andrew Berglund, Director of The RNA Institute

Testing Program Coordinators

John Cleary

Tammy Reid

Lab Technicians

Asmer Aliyeva

Chaz Blackwood

Lindsey Jones

Claudia Lennon

Amy Mascorro

Amber Rieger

Sharon Shaughnessy

Gordon Torrington

Morgan Williams

William Swift