Novel Coronavirus Lab Protocols and Responses: Next Steps

Feb. 3, 2020

Update: The previous nomenclature of 2019-nCoV has been replaced with the official name of the virus, SARS-CoV-2, and the disease that the virus causes, COVID-19.

The sensational nature of an infectious disease outbreak combined with the ease of spreading information leads to rumors and misinformation, and this has certainly been true with the 2019 novel coronavirus (now named SARS-CoV-2, which causes the disease COVID-19). There are many reports of what the case fatality rate (CFR) is of COVID-19 during this outbreak. However, we really don’t know what the overall CFR will be because it requires more data (confirmed cases based on trusted medical laboratory tests) and time.

The Chinese government and their healthcare/public health system has made the containment of this virus the highest priority in China, as it should be. They must work together with the public to identify people/patients with symptoms (early case definition is people presenting with fever, respiratory illness and a travel history in the region), rapidly test patients with the approved medical laboratory test, isolate patients if required (hospital or homes) and provide supportive medical care while keeping front-line responders (doctors, nurses, etc.) protected.

Is there a reason the scientific community working with a new pathogen, SARS-CoV-2, may be in the dark on precautions or methodology for understanding this agent? Fortunately, the answer is no. The scientific and healthcare community learned a great deal about coronavirus biology and behavior via the relatedness to previous outbreaks: severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV).

Previous coronavirus outbreaks have allowed guidelines for the current outbreak to be quickly generated and distributed for healthcare worker safety.

Previous coronavirus outbreaks have allowed guidelines for the current outbreak to be quickly generated and distributed for healthcare worker safety. An early report demonstrates that patients infected with SARS-CoV-2 might develop acute respiratory distress syndrome (ARDS), have a high likelihood of admission to intensive care, and may die. Initial COVID-19 cases suggest the most severe cases are associated with the elderly and/or patients with significant comorbidities. More efforts should and will be made to understand the whole spectrum and pathophysiology of the new disease.

ASM Coronavirus Resource Page.

Coronavirus Laboratory Guidelines

The Centers for Disease Control and Prevention (CDC) has published the Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Patients Under Investigation (PUIs) for 2019 Novel Coronavirus (2019-nCoV). Currently, in the United States, diagnostic testing for COVID-19 can be conducted only at the CDC. Likewise, the Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with 2019 Novel Coronavirus (2019-nCoV) has also been published. These 2 documents should be consulted for appropriate measures in handling and processing of suspect PUIs specimens unless further instruction is provided.

Clinical laboratories performing routine hematology, urinalysis and clinical chemistry studies—and microbiology laboratories performing diagnostic tests on serum, blood or urine specimens—should follow standard laboratory practices, including Standard Precautions when handling potential COVID-19 specimens. For additional information, see Biosafety in Microbiological and Biomedical Laboratories (BMBL),Fifth Edition (page 225).

Within a month of initial COVID-19 reports, the CDC had developed a real time Reverse Transcription-Polymerase Chain Reaction (rRT-PCR) test that can diagnose COVID-19. As time progresses, CDC will share these tests with domestic and international partners through the agency’s International Reagent Resource. It has been interesting and exciting to see how quickly the global community came together to analyze genetic data on the SARS-CoV-2 to create a rapid and accurate medical laboratory confirmatory test to be used in the outbreak.

The CDC has shared instructions for the use of real-time RT PCR (rT-PCR) assays for the in vitro qualitative detection of SARS-CoV-2 in respiratory specimens and sera. The SARS-CoV-2 primer and probe sets are designed for the universal detection of SARS-like coronaviruses and for specific detection of SARS-CoV-2. Limitations of the shared protocols are non-validated for platforms or chemistries other than those described by the CDC.

A lesson learned from past outbreak events is the need for personal protective equipment (PPE) for front-line responders and other critical personnel (vaccine developers, family members caring for isolated patients, etc.). Infection control and prevention efforts, including any new and developed PPE, must be distributed for their safety. Hospitals, including emergency rooms/departments, must have proven training and education plans for implementation of said efforts as almost all major outbreaks (Ebola, SARS, flu, etc.) have shown how critical this need is for protecting critical personnel (think specialists, intensivists, others) that may not be easily replaced.

The NETEC has developed an instructional video for donning and doffing PPE when working with the 2019 novel coronavirus. Source:

MTM Podcast Episode: 20 Years of the Lab Response Network with Julie Villanueva.

A Plan for Global Public Health Response

The global scientific and healthcare communities will need urgent development and support for any possible antivirals or other antimicrobials/treatments that show promise in efforts against reduction of viral loads and/or eradication of the virus completely.

What will a global plan look like? A global plan should focus on a number of important features with the flexibility to adapt to new circumstances of the outbreak:

  1. Vaccine development as the highest priority unless experts have reasoning to make other priority first (e.g. proven antimicrobials, isolation possible, etc.).
  2. Public and private efforts should be supported in vaccine development, including cooperation among all involved to eliminate an/or reduce hurdles for the safest vaccine possible.
  3. Vaccine production and distribution will require cooperative efforts and creative methods (may be multiple sites of vaccine production and stockpiling) in the face of regulatory hurdles.

There should be attention to other ongoing and critical public health and healthcare concerns. For example, healthcare officials may need to pay special attention to secondary infections from antibiotic resistant infections surrounding COVID-19 (or other outbreak agents) such as MRSA pneumonia.

Importantly, the global community must work with countries and regions that will not have the resources, economy, scientific training and personnel to handle the outbreak.

All involved parties must work to plan for these types of open and accurate communication efforts if we are going to succeed in not only the current COVID-19 outbreak, but in all future and coming outbreaks and global emergencies. Experience has shown that it is prudent to be proactive versus reactive in not only microbial outbreaks, but in all public health measures.

Lessons from Past Outbreaks

My 25-year career has allowed me to witness, experience, and work through some of the newsworthy microbial public health events in recent history. While at the Texas Department of State Health Services (DSHS), Bureau of Laboratories and Zoonosis Control Division, I participated in the inaugural and international Oral Rabies Vaccine Program. These efforts led to the elimination of canine rabies in Texas. As a DSHS employee, which included 2 stints of Visiting Scientist in training at the CDC, I have been involved with the response to the induction of WNV into the United States, the 2001 anthrax scare, SARS, influenza, dengue and other arboviruses and many other agents and outbreaks. Through it all, I’ve always been surrounded by amazing colleagues, many of whom are global experts in public health, health security, healthcare and wonderful dedicated public servants.

Lessons from the SARS-CoV outbreak have helped guide protocols for front-line workers in the 2019-nCoV outbreak. Both SARS-CoV and 2019-nCoV are coronaviruses, which have a "crown" appearance of spikes. Shown here: SARS-CoV electron micrograph.
Lessons from the SARS-CoV outbreak have helped guide protocols for front-line workers in the 2019-nCoV outbreak. Both SARS-CoV and 2019-nCoV are coronaviruses, which have a "crown" appearance of spikes. Shown here: SARS-CoV electron micrograph.

There are predictions that we might eventually see hundreds of thousands of COVID-19 cases. However, many predicted millions of cases of Ebola in West Africa, which did not happen. Remember Zika? Remember avian flu? Public health efforts continue to address these disease threats while keeping the public informed about best practices. Vigilance is important with outbreak diseases, but it is equally important with agents like measles and seasonal influenza, for which we already have effective vaccines. In the end, we need to monitor COVID-19 and apply the same proper precautions and perspective that other agents have warranted.

Every year in this country and elsewhere, influenza kills thousands, but we have not set up airport screening or banned transportation. Keep in mind that every time you travel, you may be sitting next to someone with the flu, a common cold, or even another coronavirus. Don’t panic. Proper medical and public health precautions along with perspective and understanding of risk is critical to the global response.

Microbes don’t care about your geographical location, politics, economic status, culture or ethnicity. Microbes only care about reproduction, spreading and finding the next host. They don’t read our textbooks, public health plans or listen to experts. Therefore, the global community must work together to reduce and defeat these outbreaks. We’ve done it before with the elimination of smallpox; we can do it again. Have we learned enough from past lessons to stop SARS-CoV-2 or the next disease outbreak? Make no mistake, there will be another outbreak. The experiences from this one will be humbly studied by all involved; only by continuing to learn from each disease outbreak can we become a better prepared global health community.

ASM Coronavirus Resource Page.

The above represent the views of the author and does not necessarily reflect the opinion of the American Society for Microbiology.

Author: Rodney Rohde, Ph.D., SM(ASCP), SVCM, MBCM, FACSc

Rodney Rohde, Ph.D., SM(ASCP), SVCM, MBCM, FACSc
Dr. Rodney Rohde is the Associate Director of the Translational Health Research Initiative at Texas State University.