How Scientists Were Prepared for an Emerging Disease Pandemic

by Janice Nigro

If you didn’t know what molecular biologists did before SARS-CoV-2, you might now know that what they do matters. While the rest of us are locked down in our basements, molecular biologists have come out of theirs, forcing people to bone up on their basic biology. “What is a virus?” or What is RNA?” you might want to know.

The pandemic unlike any other disease in our time has become their stage. Governments might not have been prepared for an emerging disease pandemic, but molecular biologists were. Decades of feeding their curiosities of natural phenomena and the characteristics of weird and wacky creatures has created a fertile ground for the imagination, innovation and business. Molecular biology, which has creeped into the daily lives of Americans over the last decade and a half, has found its poster child in SARS-CoV-2.

Molecular biologists have a tough job in the spotlight though. What they do can’t be seen directly. Charts and graphs and models on paper can’t compare to the awe inspiring launch of a rocket ship. But while their science might be just entering our conscience, for molecular biologists worldwide, adaptation to Covid-19 is a small detour from their average day. The disease is unique, but today’s technology to isolate it, test for it and develop vaccines or treatments against it is universal.

Discovery of SARS-CoV-2 with state-of-the-art molecular biology

Scientists began their detective work on a possible new disease achieving almost Amazon Prime-like delivery of the identification of the infecting pathogen. Within weeks of the original cluster of 41 symptomatic patients appearing in hospitals as early as 1 December 2019 (published in the journal The Lancet 24 January 2020), Chinese scientists had identified SARS-CoV-2 as the pathogen causing the acute respiratory distress symptom (published online 11 January 2020 and officially in the journal Nature 03 February 2020).

Evidence of the culprit was fished out of the millions of bits of data generated from genetic material captured in the bronchoalveolar lavage fluid of a symptomatic patient. In comparison, the search for the pathogen HIV causing AIDS took from 1982 to 1984 requiring some educated guesses and hard core experiments at the lab bench along the way.

The method used to find coronavirus, Next Generation Sequencing, is a way to determine the order of nucleotides (or bases), the As, Cs, Gs, and Ts/Us in DNA or RNA, representing all the genes present from humans and possible pathogens in the fluid. The whole mix of genetic information, like a grab bag, is sorted out afterwards with computer analysis.

Next Generation Sequencing is the go-to method today to study disease. The method has become so routine that sequencing the coronavirus from thousands of patients has helped to define the path of infection across the United States and the world. In less than six months, a single technique has provided the basic information necessary for the more critical steps, the design of tests, vaccines, and treatments. In another time, it might have taken years to do what now takes just a few weeks.

Breakthrough strategies, such as Next Generation Sequencing, have long been in development in the United States. American scientists even won Nobel Prizes for some of these methods, including the revolutionary Polymerase Chain Reaction which is the basis for today’s diagnostic testing. With this history and technological capability, the United States still lagged behind in testing and tracking of infected individuals. Ouch.

The gold standard for testing

A postmortem in real time of the testing for SARS-CoV-2 in the United States has already helped move the country from behind in the number of tests administered.

According to scientists, it takes only a couple of hours to design a test to detect SARS-CoV-2 once the complete RNA genome of the virus, which is the virus equivalent of our chromosomes, was available. Scientists worldwide were on top of it when the RNA genome was published online on 11 January 2020.

The current gold standard for diagnostic testing of the virus is based on the Polymerase Chain Reaction. The Polymerase Chain Reaction generates copies of genetic material, DNA or RNA, in a test tube when there isn’t very much of it. Like a Xerox copier, the test tube becomes a mini-manufacturing plant producing DNA.

The method takes advantage of the double stranded nature of DNA. Each strand on its own contains the information, the sequence of the nucleotides, to reproduce its unique partner strand.

The Polymerase Chain Reaction can be adapted for any organism or pathogen if the genome or some genes are known. Smaller chains of nucleotides, the primers, are designed to bind to specific genes of a target organism. They guide the polymerase, the enzyme that makes the DNA, to the starting point. While the basic components of the reaction are universal, the primers make the test unique. A couple of genes from coronavirus can be selectively copied while swimming in a sea of DNA and RNA from the human and pathogens in a patient sample.

The genome of some pathogens, such as the SARS-CoV-2, are made up of RNA, requiring the extra step of conversion into DNA first.

Discoveries across biology have led to improvements in the assay over decades. DNA polymerases isolated from diverse creatures often collected from extreme habitats, including hot springs, tolerate the rigors of the reaction conditions better. The DNA made is detected with fluorescence, which is an idea stolen from marine life, such as the jelly fish or coral. An instrument with lasers stimulates and detects fluorescence, and within a couple hours the results are ready to be analyzed.

A basic property of all of nature, DNA and RNA, has become the foundation for a simple assay used to identify any organism or pathogen on the planet.

Pitfalls of designing a test for a new pathogen

But SARS-CoV-2 is new. Although the technology exists, the test had to be designed to detect a virus which was unlike any previously known virus.

A scientist familiar with the technology might have one or two of their designs out of three or four that will work. In the best case scenario, a new test run using standard PCR might be ready for use within three weeks of the design. Samples can be split for analysis among reference and novel tests to speed up the validation process in labs around the country during an emerging disease crisis.

The frustration with the testing early on in the United States was with the flatfooted, bureaucratic response of the CDC and FDA. The established path in an emergency situation is for the CDC to design an assay for a concerning pathogen and for the FDA to authorize use of the test in labs around the country. When the CDC and FDA realized they had a problem with the negative control in the CDC’s original test, the FDA relented, allowing scientists in industry and academia to apply for Emergency Use Authorization (EUA) of their own test designs.

Shifting into the manufacturing phase came with new complications. Reagents needed to be scaled up for the millions of tests necessary to screen Americans across the country. Small companies, for example, have the technology, but not the cash to produce their products to meet the demands of a market expanding in real time. The government responded by providing funding through the Rapid Acceleration of Diagnostics (RADx) program born out of The Paycheck Protection Program and Health Care Enhancement Act from 24 April 2020.

The ease of designing the diagnostic test for SARS-CoV-2 can also be viewed as a potential liability. Companies or labs around the world might try to sell tests in an area in which they have no experience.

Labs must also be certified to run the tests. Although the CDC and FDA failed initially, the goal was to provide a high accuracy test that would work consistently across the country.

One final problem for countries in the West is the issue of health privacy. With policies such as the Health Insurance Portability and Accountability Act (HIPAA) in the USA, tracking infected individuals and notifying contacts of their status might be bordering on infringing on rights to privacy.

American ingenuity to the rescue

There’s never been a time in US history when existing technology was so poised to meet the demands of an emerging infectious disease. In retrospect, depending on a single source for testing is an outdated strategy, especially in a research environment so rich in many options.

Testing is only the beginning, and a negative test one day does not mean you won’t test positive another day. So with the knowledge of the virus genome, scientists have dived into the bigger goals, development of vaccines and treatments. Despite the bureaucratic pitfalls during this pandemic, molecular biologists in academia and private industry were not deterred. I for one am excited to see what they do next.

 

©Janice Marie Nigro/janikiInk.com

Looking for a scientific editor or writer? Contact Janice Nigro at Janice Nigro Ink. I have published in Cell, Science, and Nature, and articles I have edited have appeared in Cancer Research, Clinical Cancer Research, PLoSONE, the Journal of Surgical Oncology, and Oncotarget.