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CDC Revises SARS-CoV-2 Assay Protocol; Surveillance Testing on Track to Start Next Week

NEW YORK – The US Centers for Disease Control and Prevention said Friday that it has validated a new protocol for its assay to detect SARS-CoV-2, the virus that causes the novel coronavirus disease COVID-19. Local labs that have the test kits already can use them with a modified protocol, and the agency will also ship new kits.

With the new modifications, state and local public health labs will be able to test possible cases more locally. Meanwhile, the surveillance testing that has been previously described will likely be up and running at six initial sites by next week.

Problems with a reagent in the real-time reverse transcriptase (RT-PCR) test developed by CDC have limited rollout of the test to US public health labs. On Tuesday this week, the Association of Public Health Labs had asked FDA to grant an exception so that labs could develop their own tests, but the request was declined on Wednesday. Nevertheless, the American Association of Clinical Chemistry sent a letter to the FDA Friday supporting APHL's request, and further requesting that the FDA also exempt national and regional clinical laboratories separate from the public health system but that also have the expertise and capacity to develop and perform coronavirus tests.

On a call with the media, Nancy Messonier, the director of the National Center for Immunization and Respiratory Diseases, said that containment strategies have been largely successful to date, and as a result, the US has seen very few cases of COVID-19 and the risk to the general public remains low.

Still, Messonier reiterated that CDC's role is to get all state and local public health labs the capacity to test for the virus, and acknowledged, "this has not gone as smoothly as we would have liked."

The agency has been working on two possible solutions to a problem with the N3 reagent in its emergency use-authorized test initially reported on February 12th. The reagent is intended for the universal detection of SARS-like coronaviruses, while two other reagents in the assay are specifically for detection of SARS-CoV-2.

"Right now, labs can start testing with existing CDC test kits," Messonier said.

States that were able to validate kits from the get-go, and did not see the spurious results during quality control evaluations, should continue to use them, while states that were only able to validate the two components specific to the novel coronavirus can test using only those two components only, following revised instructions developed at CDC.

The agency has established that the third test component, which was the cause of inconclusive results, can be excluded from testing without affecting accuracy, Messonier said. She emphasized that CDC developed its test from the published genetic sequence, before there were cases in the US, but now that there have been patients here, "it has become clear that with two of the three reactions, we actually are appropriately sensitive and specific in identifying cases," she said.

Furthermore, the agency has been working with the US Food and Drug Administration, "and they agree with our approach," she said.

CDC is currently in the process of amending the existing EUA it was granted on Feb. 4, but Messonier says it has discretionary authority from FDA to proceed using the modified test protocol. The new protocol will now "increase testing capacity at state and local health departments," but all results will continue to be confirmed by CDC for some time.

"Our goal is to have every state and local health department online and doing their own testing by the end of next week, and we are doing everything we can to try to ensure that," Messonier said.

Additionally, CDC has manufactured brand new test kits that will only include the two components that are specific to the novel coronavirus, she said. Those test kits are now available through the International Reagent Resource.

Although the agency is working quickly to get CDC test kits to state and local public health authorities, Messonier also noted that "during any infectious disease response there is a great need for test manufacturers to rapidly make testing available in clinics, in hospitals, and at the bedside," adding, "This is part of a huge effort within the US government led by Health and Human Services."

In addition to diagnostic testing for people who meet the CDC's testing criteria, community-level surveillance testing is also increasingly important, Messonier said.

"We expect the first six [surveillance] sites to be doing testing by next week and hope to be able to rapidly move from six to all 50 states," she said. The overall approach is layered, with well-established influenza and respiratory disease surveillance programs being modified to also test for SARS-CoV-2.

Because there have been so few cases in the US so far, the agency has also been able to be very aggressive in contact tracing of infected people, Messonier said. Other than two cases and a recent case in California, all cases in the US had a history of travel to areas where the disease was spreading. Two cases were spouses of travelers who had close physical contact.

Regarding the patient in California who is suspected of being the first instance of community spread, Messonier reviewed the timeline of that case.

CDC's officials first heard from public health colleagues in California about this patient last Sunday, Feb. 23rd, she said. "California reported a severely ill person who had not recently traveled abroad or had contact with a known case of COVID-19. CDC recommended testing for COVID-19 that day. We received samples on Feb. 25th and confirmed the results with public health officials in California the day they were finalized, on Feb. 26th."

Messonier also said the agency has also sent a team to support the local public health department to do a thorough contact tracing for that patient.

"There has been some confusion about whether this person met CDC's criteria for testing for COVID-19," Messonier said. She explained that the agency has a broad definition of a "patient under investigation," or PUI, but focuses on travelers and close contacts of infected people.

"We have been looking for people with fever, cough, or trouble breathing. Fever and cough are pretty broad parameters, especially during flu season, so we had to rule out many people who had other respiratory illnesses," she said.

However, the agency's criteria also allows for clinical discretion. "As public health professionals, we know that there is no substitute for the astute clinician on the front lines of patient care," Messonier said. "Our clinical team, working with state and local health departments to assess PUIs, has not said no to any request for testing," she insisted.

Although reports in the media have suggested that clinicians in California requested testing for the patient on Feb. 19th, Messonier said that according to CDC records, the first call the agency received about this patient was Sunday, Feb. 23rd, "Period."

The CDC's updated PUI criteria now includes symptomatic people with known exposure to a lab-confirmed case, severely ill people with no other known cause of illness, and people who have traveled to areas with sustained community transmission within two weeks of symptom onset. According to CDC's website, these areas currently include China, Iran, Italy, Japan, and South Korea.

Messonier also addressed questions from the media about whether there may be a low case count in the US because there has not been enough testing, and why the US has run only a few thousand diagnostic tests while China and Korea have run tens of thousands of tests.

"The epidemiological situation in China and other countries is really different than the US," Messonier said. The US has been able to focus testing on people at the highest risk, she said, and because of an aggressive strategy at the borders, there have not been as many of these cases. "That is why the number of PUI's has been smaller than other countries."

In terms of testing volume, Messonier reiterated that CDC's role was to rapidly develop a diagnostic and focus on the front line, getting it out to public health labs. But, "It has been always very clear that is only part of the solution, and a larger part of the response in any such infectious disease emergency is getting test kits out more broadly, not just to public health labs but to hospitals, and to the bedside ... That is part of a US government strategy that is a huge priority with HHS leadership right now," Messonier said.