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CDC Provides Test Protocol for Novel Coronavirus, Preps Kits for Local Use

NEW YORK – The US Centers for Disease Control and Prevention has publicly posted its assay for novel coronavirus 2019-nCoV and is now developing the test into kits, the agency announced Monday. It plans to distribute the test kits to state health departments and public health labs in the next few weeks.

In a call with the media, Nancy Messonnier, the director of the National Center for Immunization and Respiratory Diseases, said 110 people in 26 states are currently being investigated for 2019-nCoV infection.

"This is a cumulative number, and will only increase," she said, adding, "We still only have five confirmed positives, 32 that have tested negative, and no new confirmed cases overnight."

Messonnier provided an overall update on the laboratory side of the agency's work. All cases in the US are currently being tested at the CDC's lab, using a protocol the agency has developed.

Specifically, if a person is identified with a travel history or contact that could have led to exposure — and also has a fever and respiratory illness — typically a health department is alerted. Through discussion with CDC, it is determined whether diagnostics are merited, and a sample is sent to CDC.

"The time lag between the decision that a patient needs further laboratory testing and a [test] result is somewhere around a day, depending on geographically where that patient is being seen and how we can most efficiently ship" the sample, Messonnier said. The agency is currently prioritizing testing patients based the patients' risk of exposure.

The CDC diagnostic test is a reverse transcriptase real-time PCR (RT-PCR) assay developed for respiratory and blood serum samples. The protocol to make the assay was made publicly available on Friday, Messonnier said.

"This is essentially a blueprint to make the test," she said. "Currently we are refining the use of this test so we can provide optimal guidance to states and laboratorians on how to use it."  

The agency is also putting the test into a kit format. "We are working on a plan now so that priority states get these kits as soon as possible," Messonnier said, adding that in the coming one to two weeks the agency will share these kits with domestic and international partners so they can test for the virus themselves.

"We understand that for patients, clinicians, and health departments, it is preferable to have that kit as close as possible to the patient geographically, so that we can efficiently provide a result, but it is going to be another week or two" until the kits are available, she said.

CDC's longer-term plan is to share these tests through the agency's International Reagent Resource.

The agency has also uploaded the genome of the virus from the first and second reported US cases to GenBank.

The sequences are similar to the one posted by researchers in China earlier this month. "Based on CDC's analysis of the available data, it doesn't look like the virus has mutated," Messonnier said.

She also noted that the agency is growing the virus in cell culture and will provide it, once it is isolated, through the BEI Resources Repository.

In addition to the five cases confirmed positive in the US using the test, and 32 cases confirmed negative, there are also 73 cases pending, which the agency said on its website includes specimens received and awaiting testing, as well as specimens en route to CDC.

The protocol specifies primers and probes, provides guidance on sample preparation, and advises performing RT-PCR on the Thermo Fisher Scientific AB 7500 Fast DX thermal cycler. The agency's interim guidance for 2019-nCoV testing indicates biosafety precautions of using RNase Away or freshly prepared solution of 10 percent bleach for cleanup.

At this stage, CDC is still asking that clinical labs send samples to CDC for testing, however, to ensure that the results are as accurate as possible.

"As far as I know, every other country is doing centralized testing ... our most important priority is making sure that the test is accurate; speed is important, but accuracy is probably a priority," Messonnier said.

Will Weldon, team leader for the Population Immunity Lab at NCIRD, also said on the call that the agency's hope is that researchers can now take the protocol and adapt it in their own labs, "so they can have this important tool available at their disposal for testing samples from suspected patients."

The protocol is also now undergoing "rigorous evaluation" in the CDC labs, Weldon said, reaffirming that, "kits are being developed that will allow CDC to distribute [the assay] to state and international labs, so they will have the important reagents needed for the assay." For example, the protocol mentions a positive control, which could be something that CDC would need to distribute at this juncture.

Travel and screening insights

As of Monday morning, there have been 2,886 cases of 2019-nCoV globally, and 81 deaths, according to a tracker created by the Center for Systems Science and Engineering at Johns Hopkins University. Although 16 countries have been affected, the case numbers in all countries outside of mainland China are still in the single digits.

Direct flights to the US from Hubei province, including Wuhan — the area of China where the virus originated — have been halted, Messonnier said.

To date, the agency has screened 2,400 people at five selected US ports of entry. It is continuing to assess the public health situation as it evolves, she said, adding that CDC will likely be providing guidance on potential additional travel restrictions in the next few days.

"Right now, we are continuing to screen a few passengers from Wuhan at the five designated airports," Messonnier said. Testing also includes travelers with so-called "broken itineraries" who may have passed through Hubei but whose flight to the US was from a different location, she added.

Enhanced entry screening is meant to serve two purposes, she said. It detects illness and the proper authorities can respond to symptomatic people. Additionally, travelers can be educated about symptoms, so that they may present themselves for care should they become ill in the weeks following their arrival in the US.

"I expect that in the coming days our travel recommendations will change. I cannot provide details on this yet, but know that we are working on it," Messonnier said. "Given the aggressive public health response we are pursuing, there may be some disruptions experienced," she added. CDC is currently guiding travelers to avoid non-essential travel to Hubei province, and to use enhanced precautions for travel to all other parts of China.

Returning travelers with symptoms, and close contacts of people confirmed with 2019-nCoV "may be asked to take precautionary measures," she said, but did not specify what those might be.

She did note, however, that risk depends on exposure, and in the US at this time the virus is not spreading in the community.

"We continue to believe that the immediate health risk to the general American public is low at this time," she said. "This outbreak is unfolding rapidly, and we are rapidly looking at how that impacts our posture at the border — we are certainly considering a broadening of that screening," Messonnier said.

Importantly, this outbreak is also a rapidly changing situation, both here and abroad, she emphasized.

In terms of what is currently known about the virus, Messonnier provided some clarifications.

There has been no confirmed human-to-human transmission in the US.

The incubation time for the virus seems to be between two and 14 days, although it is unclear whether the virus is transmissible during this incubation period. Still, "we are being very aggressive and very cautious in tracking of close contacts," she said.

The infectivity of the virus, as characterized by its R0 value, is still being studied. The R0 is a measure of the number of infections that come from a single infected person, and at this point 2019-nCoV is modeled by different groups to have an R0 of 1.5 to 3. As a comparison, the R0 for measles is somewhere around 12 to 18, Messonnier said.

Sequencing analysis by research teams globally has also compared the virus' genome to other coronaviruses, including animal coronaviruses. "It does look like it may be somewhat similar to a bat coronavirus, but I think there is a lot more to be done in terms of both the genetic sequencing, as well as the knowledge of the epidemiological investigation before we're all going to be confident that we know how this started," Messonnier said.

She went on the say that the risk of contracting 2019-nCoV from imports shipped from China is low, based primarily on its similarity to SARS and MERS. "In general, because of the poor survivability of these coronaviruses on surfaces — in the range of hours — there is likely a very low, if any, risk of spread from products or packaging that is shipped over a period of days or weeks at ambient temperatures," she said.