��Looking Beyond the Pandemic
Depending on one’s views, the final ACT of the COVID-19 pandemic — post vaccines — reverberates with either haunting refrain or sighs of relief. Thankfully, for many, vaccines are saturating the landscape. The Delta variant, however, remains a concern of the watchful.
In virology, a variant is a subtype, a microorganism spawned from its progenitor strain. Like most offspring, variants quickly develop a personality of their own; some more aggressive than others, though all on a singular mission to infect. SARS-CoV-2 spawned a great number of variants, prominent among them strains originating in the UK, South Africa, Brazil, and India — the origin to perhaps the worst of the lot, the highly-infectious Delta variant, which arrived nearly a year into the pandemic. By early summer, COVID-19, led by Delta, had once again strained healthcare systems around the globe, primarily in areas with low vaccination rates.
Globally, the pandemic continues to take a toll.
By mid-September, worldwide cases had reached 225 million with more than 4.6 million deaths. Friends, families and loved ones remain staggered but standing. The U.S. alone has seen nearly 42 million cases and almost 676,000 deaths.
When COVID arrived in January of 2020, the World Health Organization (WHO) announcement labelled it “a mysterious coronavirus-related pneumonia coming out of Wuhan, China.” The WHO would elevate it to pandemic status two months later, but not before the onset of global air travel restrictions, cruise ship disasters and a CDC warning of how the U.S. — along with the rest of the world — seemed headed pell-mell toward a brewing health crisis. These developments and a rising death toll quickly embedded COVID-19 deep within humanities collective consciousness.
It’s no wonder then that questions persist. When will it end? What have we learned? And … Can it happen again?
According to David Engelthaler, Ph.D., director of TGen’s Pathogen and Microbiome Division in Flagstaff, Arizona (more commonly known as TGen North) the answers are much like the virus itself, best delivered with nuance rather than a hard and fast yes or no.
“These past 20 months in many respects truly have felt like 20 years,” says Dr. Engelthaler. “While there is no doubt that given the global devastation, COVID is a medical and virological phenomenon, the public health scientist in me finds relief in the knowledge we’ve acquired in terms of understanding the biology behind the virus and the epidemiology
behind the disease at a much deeper level than any previous disease outbreak. What’s most heartening are the technological advances that drove much of the discovery and have led to our path out of the pandemic: vaccines.”
“Short term, I can honestly say we are nearing the tail end of the pandemic; in the U.S. at least,” adds Engelthaler. “It doesn’t feel like it, with Delta spreading seemingly unabated, but the vaccines have absolutely changed the nature of the pandemic and are getting us to a point we can — and have to — live with. Globally, I don’t see COVID going away as quickly.”
Engelthaler attributes the continuing global pandemic to the lack of vaccine access in other countries and the mid-summer spike in the Delta variant. And while a COVID ending may not be a true ending — as in a complete eradication — he does believe any lingering aftereffects fall under the heading of endemic rather than pandemic.
“COVID is not going away, there is no ’COVID-Zero’. Our scientific understanding of COVID-19 suggests that the virus will stay with us, regardless of vaccination rates. We’ve seen first-hand how adept Delta is at finding the next susceptible person, even in communities with high vaccination rates. I expect that we all will be immunized within the next 6-12 months, either by vaccine or infection … or both.”
Despite the Delta surges around the world, Engelthaler takes many positives away from the past 20 months.
The collective scientific and technological energy that went into the moon walk of 1969 netted numerous societal benefits, including fire proof material, solar panels and improved medical devices. Space shuttle technology gifted society the artificial heart, advanced prosthetics and improved cancer treatments. Engelthaler sees similar scientific and societal gains emerging post pandemic.
He says, “The whole idea of a moon shot stimulates and drives our intellectual capacity and resources focused on a singular goal. That happened in several distinct ways during this pandemic.”
The most important involved vaccines. The speed at which teams developed the novel COVID vaccines had a great deal to do with the technical advances of the past decade or so and the vast amount of scientific data generated post Human Genome Project. The fact that the U.S. led the way in terms of funding and de-risking (this allowed for rapid and parallel vaccine production) also paved the way for expedited distribution across America.
“Overall, the vaccines work remarkably well. Yes, there are relatively rare breakthrough cases and we’re monitoring the variants should mutations occur that render the vaccine less effective or ineffective, but to date they have significantly and essentially diminished the deadly part of the pandemic in the U.S. We will likely need a booster at some point in response to a new variant or to maintain a high level of personal immunity, similar to how we protect ourselves from influenza,” says Engelthaler. “The FDA is already paving the way for boosters to get to those that need it most, but make no mistake – the vaccine is what turns this monster virus into a bad cold, at worst, for almost everybody going forward.”
Digitizing the Natural World
Another major advance occurred with genomic sequencing – the digital decoding of the virus’ genetic blueprint. Given the need to sequence as many samples as possible to track the virus and its variants, we are seeing a moonshot effect on the cost, speed and accuracy of viral genomic sequencing.
“Sequencing reveals the secrets of the virus – where it comes from, how it is changing and even if it will evade some treatments. It allows us to move beyond simply counting cases and generate actionable intelligence,” says Engelthaler. "This in-depth information may one day allow hospitals and public health providers to jump ahead of outbreaks and treat patients based on the actual infection they have, not just on the type of infection they have, as we do now.”
Today, the cost of sequencing a pathogen genome comes in at around $100. The goal is less than $25 per genome.
This, according to Engelthaler, would place it on par with many routine hospital tests and revolutionize the adoption of public health measures into the clinical care stream. Engelthaler refers to this as ’democratizing sequencing’ and he hopes to make it the standard of care for response to all critical pathogens.
TGen’s sequencing advances also gave rise to the Arizona COVID-19 Sequencing Dashboard, a web-based portal built by TGen for the state of Arizona.
“The portal provides a visual display of what’s occurring in near real time across Arizona such as when did the first U.K. variant show up? How prevalent is the Delta variant in various regions?” says Engelthaler. “It helps health departments and health officials understand what variant exists and at what level (there are three levels: variants of interest, concern and high consequence) at any given point in time and provides insight into what communities are experiencing.”
To date, TGen North faculty and staff have uploaded data from more than 36,000 genome sequences.
By generating such vast amounts of data — what Engelthaler calls ’pathogen intelligence’ — scientists are digitizing the natural world, with variants tracked, data analyzed, risks carefully weighed and shared on a global scale. And not only for COVID. TGen North scientists are also busy applying this technology and approach on other viruses and bacteria that plague our world, particularly in healthcare settings, a direction Engelthaler views as a boon for advancing the state of both clinical medicine and public health.
Which begs the question, what’s next?
“Undoubtedly, there will be a next,” says Engelthaler. “COVID wasn’t our first major outbreak and it won’t be our last. We saw SARS-CoV-1 in 2003; Pandemic Swine Flu in 2009; MERS-CoV in 2012; and Ebola in 2014, and many others on a lesser scale that plague our communities and hospitals every day.”
Engelthaler is quick to point out that Mother Nature is an inventor, and she is developing new strains, new variants and even new pathogens all the time. As we push into the world's natural habitats, we expose ourselves to new bugs that in turn give rise to new infectious diseases, which now can spread around the world at the speed of
Yogi Berra famously said, “It’s tough to make predictions, especially about the future.” And while it’s doubtful Yogi had a pandemic in mind, the sentiment could easily apply to the next pathogen outbreak. The when, where and how remain anyone’s guess, says Engelthaler, but he has no doubt that somewhere out there a new virus awaits a host.
“And that,” he adds, “is why pathogen intelligence is critical. Understanding nature at the molecular level allows us to understand what is happing right now and hopefully prepare and be ready for the next one.”