Photograph of a researcher handling patient samples prior to performing a diagnostic PCR test.
PCR tests for diagnosis and surveillance of infection have applications beyond COVID-19 detection to respiratory testing, HIV surveillance, and analyzing urinary tract microbiota.
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Humans versus Pathogens: COVID-19 and Beyond

Advances in COVID-19 detection can also give us a fighting chance against other pathogens

Photo portrait of Zahraa Chorghay
Zahraa Chorghay, PhD
May 31, 2022 | 5 min read

Pathogens have been waging war on living things through time immemorial. While vaccinations and medications are effective in helping defeat pathogens like COVID-19 and preventing their spread, a public health strategy must be more comprehensive. This is where testing comes in. By allowing us to have a degree of certainty regarding infection, testing allows us to make better health care decisions on an individual and population level.

According to Manoj Gandhi, MD, PhD, senior medical director at Thermo Fisher Scientific, the widespread and easy use of tests?—the “democratization of molecular diagnostics”—is the small silver lining of the recent COVID-19 pandemic, with applications far beyond this virus to other pathogens and infections

Endemicity and pathogen assaults throughout the ages

Harmful pathogens like viruses extol a significant fitness cost from their host by diverting the host’s resources away from vital functions and toward replication of the pathogen genome. In response, host populations evolve survival strategies to reduce the severity of infection and transmissibility, in turn placing a selective pressure on the pathogen to further evolve and evade host defense mechanisms. It is an intense arms race between pathogen and host, with survival as the end goal.

Over the last two years, viruses gained immense public attention during the COVID-19 pandemic, but pandemics are not new to our world. As the human population rapidly increased over time, it became increasingly easier for pathogens to jump from domesticated animals to humans. Influenza, malaria, measles, polio, smallpox, bird flu, HIV, and now COVID-19, are just a few of the many viral diseases throughout history that forever altered the lives of the people they affected.

Photograph of two masked workers bumping elbows to prevent viral spread from handshakes and hugs during the COVID-19 pandemic.
Like other infectious diseases, it is thought that COVID-19 will become endemic.
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With proper public health measures in place, many pathogens were eradicated while others are now considered endemic. An example is influenza, where its outbreak in 1918 was estimated to have infected a third of the global population and resulted in 50 million deaths. Today, it is known as “the common flu.” COVID-19 will likely face the same fate of endemicity over time.

While acknowledging that the precise definition of “endemic” can vary depending on whom you ask, Gandhi says, “Endemicity means a couple of things in my book. First, that there is some sort of predictability—when can you expect to see the emergence of infections for the virus and to prepare for it, for example, in the flu season? The second part of the equation is learning to live with a virus through social behavioral changes.”

Molecular diagnostics pinpoint the culprit

Different kinds of tests are currently available for the public, each with their own advantages and disadvantages. Antigen tests offer a quick and convenient way to detect viral antigen, while polymerase chain reaction (PCR) tests take more time but detect viral genetic material and are therefore considered to be much more accurate. PCR tests for diagnosis and surveillance of infection must be able to detect the specific pathogen as well as reliably distinguish it from related pathogens. “From an efficiency standpoint, there is no need to run separate tests for different pathogens that have the same clinical presentation,” Gandhi explains.

"Routine multiplex technology for simultaneous testing of respiratory infections allows for tracking the spread of these pathogens, making timely treatment decisions, minimizing isolation times for individuals, and reducing transmission rates."

With advances in SARS-CoV-2 detection, respiratory testing has already seen a major shift. Shared symptoms among respiratory infections, including fever and chills, cough, runny nose and congestion, and shortness of breath, make it challenging to diagnose based on symptoms alone. However, routine multiplex technology for simultaneous testing of respiratory infections allows for tracking the spread of these pathogens, making timely treatment decisions, minimizing isolation times for individuals, and reducing transmission rates. Gandhi concludes, “Multiplex testing is necessary not only to efficiently differentiate between pathogens, but also to detect occasional cases where coinfections occur.”

Lessons from COVID-19 about variant detection

Since pathogens evolve, molecular diagnostics tests must not only identify the presence of the virus but also track the emergence of new variants. SARS-CoV-2 RNA encodes several proteins. The S gene encoding the spike protein is needed for the virus to bind to the ACE2 receptor on human cells and infect them. Most RNA vaccines, medications, and diagnostic tests often target the spike protein. As the spike protein evolves, variants emerge that better evade S gene targeting. Thus, if a PCR test relies entirely on S gene detection, it may not reliably detect new variants.

Instead, assays like The Applied Biosystems TaqPath COVID-19 diagnostics test* are designed with built-in redundancy to compensate for mutations by targeting three SARS-CoV-2 viral genes, including the ORF1ab, S, and N regions. The redundancy facilitates detection of the virus—as long as any two of the three targets are present, the test will yield a positive result.

World map with emerging COVID-19 variants.
Having PCR tests with multiple gene targets enabled detection of emerging COVID-19 variants.
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An important lesson here is that even the failure to detect a gene can provide valuable information. With the emergence of Alpha, which was one of the first SARS-CoV-2 variants to be identified, researchers at Thermo Fisher initially wondered if there was an issue with their test because the S gene became undetectable. Instead, it turns out that the failure to detect the S gene was a reflection of mutations in the Alpha variant. Months later, the S gene could again be detected as the Delta variant emerged. Recently, researchers again observed S gene dropout with Omicron BA.1 but not with the newer BA.2 variant. Gandhi explains, “While the test was designed to simply test positive or negative for a virus, with multiple gene targets, the TaqPath test also indirectly gives information on the variant type.”

Beyond COVID-19

These lessons and advances in viral detection over the last two years will forever alter the molecular diagnostics landscape. Industry leaders like Thermo Fisher recognize this shift and are partnering with laboratories to design better assays for diagnostics applications far beyond COVID-19. For example, the new Applied Biosystems HIV-1 genotyping kit with integrase will enhance HIV-1 surveillance efforts and aid in mitigating the development of resistance to antiretroviral therapy, particularly in global regions with disproportionate disease burden. The kit is updated to analyze three HIV-1 genetic regions targeted by antiretroviral therapy and will be made available with access pricing by Thermo Fisher for adoption in low- and middle-income countries.

Other than respiratory and sexually transmitted infectious diseases, real-time PCR solutions for diagnostics can be used for a number of disease applications, such as detecting urogenital infections. The microbiota in the vagina and urinary tract can be analyzed more rapidly, with higher specificity and sensitivity, and with better scalability using a PCR-based test compared to current methods, including traditional culture-based methods.

Given that different pathogens vary in their transmissibility rate and route, as well as their susceptibility to certain vaccinations and medications, detecting the specific pathogen and variant underlying an individual’s infection is necessary for devising optimal public health and medical treatment strategies. Rather than relying on sheer trial and error, pathogen detection with high specificity leads to a better, targeted approach for defense against pathogen assaults. Through widespread and robust testing of viruses and other pathogens, humanity has a fighting chance to stay ahead of our biological foes.

*Original ComboKit and CE-IVD RT-PCR kit. Not applicable to version 2.0 kits.

For more information, please visit https://www.thermofisher.com/pathogendetection.