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Early Days of Testing for COVID19

On January 3, 2020, Zhang Yongzhen, a professor at the Shanghai Public Health Center and School of Public Health, received a sample of the virus from Wuhan. His research team immediately started sequencing the viral genome

On January 5 at 2:00 a.m., Zhang Yongzhen’s laboratory completed sequencing the virus received from Wuhan and realized it was closely related to SARS. He shared the viral genome sequence with members of his consortium, which included Australian scientist Eddie Holmes.

On Jan. 11, Eddie Holmes asked Zhang Yongzhen for permission to publish the viral genetic sequence on the website Holmes uploaded the sequence and tweeted, “All, an initial genome sequence of the coronavirus associated with the Wuhan outbreak is now available at

On January 12, three Chinese government laboratories published their genetic sequence on GISAID.

On January 13, multiple European groups led by Dr. Chrisian Drosten, released a protocol for a quantitative reverse transcription polymerase chain reaction (RT-PCR) to detect the novel coronavirus. Their E gene primer and probe set was adopted by the WHO and incorporated into many commercial assays. The same day, WHO published the RT-PCR protocol.

On January 16, the first batch of novel coronavirus 2019 (2019-nCoV) PCR tests were delivered to Wuhan from Beijing.

On February 1, CDC issued Patients Under Investigation criteria for diagnosing people with the novel coronavirus. Despite the need for widespread testing made apparent by reports of asymptomatic spread, CDC’s criteria limited testing to people with fever, cough, and shortness of breath who had traveled to Hubei province or had close contact with a confirmed patient. Hospitalized patients with those symptoms who had traveled to China within the last 14 days could also be tested. Specimens had to be transported to CDC in Atlanta, Georgia for testing.

On February 2, WHO shipped the first dispatch of RT-PCR lab diagnostic kits to its  regional offices around the world.

By February 3, hospitals throughout China reported shortages of test kits, causing a large reduction in diagnosis and reporting of cases.  

On February 4, the U.S. secretary of health and human services (HHS) declared that emergency use of diagnostics for the novel coronavirus was justified. This action allowed FDA to grant emergency use authorization (EUA) for a device if it reasonably believed the test was effective. EUA allowed molecular diagnostic tests to be developed, validated, and deployed within weeks rather than months to years. FDA permitted test performance to be validated by demonstrating detection of publicly available novel coronavirus RNA sequences that were added to human specimens, rather than testing actual patient specimens.  

On Feb 5, CDC began shipping its SARS-CoV-2 PCR kits to 100 state and local public health laboratories, but they produced unreliable results and were deemed unusable. CDC refused to employ the WHO test kit, which had proven to be reliable and forbade hospital and private laboratories from producing their own PCR assays.

On February 5, Chief Scientist Denise Hinton announced that FDA had sent the template for similar novel coronavirus test authorizations to 35 other test developers.

On February 7, Scott Becker, executive director of the Association of Public Health Laboratories (APHL), alerted CDC and FDA that CDC’s test was not working accurately. More than 50 days passed before CDC was able to develop an alternative PCR test. Even after kits become available, testing was further hampered by a shortage of RNA extraction reagents and nasopharyngeal swabs.

On February 9, the Association of Public Health Laboratories sent a message to its member labs in all 50 states, notifying them that they’d had problems verifying CDC’s test.

On February 14, Dr. Messonnier admitted there were problems with CDC ‘s test.

On February 23, an FDA official inspected the CDC’s Respiratory Virus Diagnostic Lab, which was assembling test kit reagents, and found the laboratory was contaminated. The investigation noted that CDC skipped quality control testing of the kits before shipping them to public health labs.

On February 25, the Association of Public Health Laboratories requested that the FDA allow its laboratories to make their own tests.

On February 29, Food and Drug Administration (FDA) issued new guidance giving permission to public health laboratories, starting with New York state, to be able to develop their own COVID19 molecular diagnostics tests and begin use prior to obtaining Emergency Use Authorization (EUA). FDA put labs developing their own COVID19 tests on the honor system and prioritized early access over independent confirmation of accuracy. Laboratories had to apply for FDA EUA approval within 15 business days of clinical use.

Clinical laboratories could purchase primers and probes for the CDC assay from Integrated DNA Technologies (IDT), but other reagents had to be procured elsewhere. To remain in FDA compliance, laboratories had to follow the exact specifications under which the EUA was granted. If laboratories ran the IDT kit on an alternative platform, this was a deviation from EUA clearance that required new EUA approval. This ordeal was too onerous for most hospital clinical laboratories.

On March 3 when asked about CDC’s limitation on testing, Dr. Messonnier responded that “CDC’s criteria for patients under investigation has always started with the importance of astute clinicians who are making judgments about what their patients are likely to have. So we’ve always allowed those patients to be part of the testing criteria.”

On March 8, CDC revised their guidelines for COVID19 laboratory testing to:

  • Hospitalized patients with signs and symptoms compatible with COVID19.
  • Other symptomatic individuals such as, older adults (age ≥ 65 years) and individuals with chronic medical conditions and/or an immunocompromised state.
  • Any persons including healthcare personnel, who within 14 days of symptom onset had close contact with a suspect or laboratory-confirmed4 COVID-19 patient, or who have a history of travel from affected geographic areas within 14 days of their symptom onset.

On March 12, FDA approved the first private SARS-CoV-2 test under emergency authorization (EUA).  Enough tests were not available in the United States until the end of April.  

Several commercial reference labs began testing during the second week of March. Major IVD vendors (Abbott, Roche, Diasorin, GenMark, Cepheid, Luminex, and BioFire) eventually received EUA for their assays. These assays provided the best option for most hospital clinical laboratories. Validations for these assays was accomplished using synthetic RNA sequences spiked into respiratory samples. Data documenting the clinical diagnostic performance of these assays was limited.

On March 13, 2020, AMA announced a new CPT code, 87635, to report COVID19 test results for Medicare and private insurers. CMS also created two billing codes to be used by laboratories when testing for the virus. Laboratories could bill HCPCS code U0001 if they were performing the CDC test for SARS-CoV-2 and HCPCS code U0002 for non-CDC laboratory tests for SARS-CoV-2. Medicare’s initial payment was $36.00 for the CDC test and $52.00 for non-CDC tests. To encourage more clinical laboratories to offer testing, CMS increased reimbursement on April 14, 2020, to $51 and $100, respectively.

On March 29 during a Coronavirus Task Force press briefing, President Trump announced the FDA had authorized Abbott’s ID-NOW COVID19 rapid molecular test after only four weeks of review.

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