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— Research

“We must all get on the same page”

A Q&A with David Pride, MD, PhD, associate professor of pathology at UC San Diego School of Medicine and director of the Clinical Molecular Microbiology Laboratory at UC San Diego Health


  • Question

    In the beginning of the pandemic, there was much concern and angst regarding COVID-19 testing in terms of accuracy of results, capacity and timing. You were deeply involved in developing and advancing testing throughout the pandemic. How would you describe that experience, the highs and lows?

    Answer:It was very difficult for clinical laboratories like ours early in the pandemic. We are accustomed to evaluating tests much more deeply than we were able to do before we started offering some of the tests we did earlier in the pandemic. It was also very problematic not to be able to give physicians definitive answers when they asked about the sensitivity and specificity of our tests. They simply hadn’t been studied well enough for us to have those answers. It was also quite problematic for laboratories like ours to have so many different tests simultaneously that all checked for the same virus. In general, we evaluate all the available tests and choose the one that works best or that best suits our institutional needs. Because there was such a limited supply of testing available, we often had to choose tests, even before we were able to evaluate how well they worked. This was, in essence, a lab director’s worst nightmare. In retrospect, we are relieved that most of the tests we chose work really well, and most importantly, are still available on the market because of their superior performances.

  • Question

    There is talk of an almost instantaneous breath test for COVID-19. Do you think that might happen, maybe before the next pandemic?

    Answer:It will be difficult for a COVID-19 breath test to rival the sensitivity/specificity that we have with our assays based on quantitative PCR. We find for many of the more rapid antigen assays the sensitivity would likely be too low to have a performance that would give us confidence in telling people they are not infected.

  • Question

    One observation you’ve made is that, even if a person isn’t infected by SARS-CoV-2, they are not virus-free. Quite the contrary: Bacteria residing in and on each of us outnumber human cells, and viruses outnumber bacteria — we each carry an estimated 380 trillion viruses. Your point is that most of these viruses are not dangerous, but simply part of the human virome. What is a virome and what’s currently known about it?

    Answer:Regardless of whether we are healthy or sick, we’ve all got viromes, which essentially are just collections of viruses that inhabit the human body. Many of these viruses infect the many bacteria that also live in the human body, and thus, we probably need to think about ourselves slightly differently than we probably do. That is, that we are collections of microbes that vastly outnumber our own cells, and that our bodies are fertile hunting grounds for viruses to attack their bacterial hosts. All of this goes on pretty much every second of every day, and we have very little insight into the fact that this is happening. We know that most, if not all human body surfaces, are inhabited by viruses. This competition for space and resources in the human body probably plays a role in our homeostasis, but this hasn’t been borne out so well by studies yet. We know that these viruses can change the bacterial communities and that these viruses can be readily shared with our close contacts. We believe that, because our bacterial microbiomes can be involved in helping determine healthy and disease phenotypes among us, the fact that viruses can attack these bacteria suggests that they may be involved in this process as well.

  • Question

    You’ve said the development of COVID-19 vaccines, and the underlying research, was the top scientific breakthrough of 2020. Why?

    Answer:Simply put, science doesn’t typically move at the speed that was observed earlier in the COVID-19 pandemic. Not only were vaccines developed in record time using existing technologies, but they were also tested in thousands of people to ensure they were safe and effective prior to being rolled out to millions across the world. This will go down as one of the top scientific breakthroughs, perhaps of all time, and we have to thank the scientists who developed the vaccines, the people who were willing to participate in these clinical trials without having foreknowledge of the potential beneficial or deleterious outcomes, and the regulatory agencies that worked closely with scientists to make all this happen. I don’t think the average person realizes how much everyone involved had to set aside their own personal biases, difficult working relationships, and even political disagreements to work together to do the most beneficial thing that they could to benefit the health of everyone.

  • Question

    Like many of your colleagues, you have cautioned about the dangers of antibiotic resistance, which you say is here to stay. But you also argue that there is much that can be done to mitigate antibiotic resistant bacteria, a public health challenge that the World Health Organization predicts might kill 10 million people annually by 2050. Antibiotics don’t work against viruses, which have different structures and methods of replication compared to bacteria. Apart from developing vaccines to prevent viral infections or reduce transmission, what is the remedy?

    Answer:Unfortunately, bacteria respond to what we do to them by developing resistance to antibiotics. It’s remarkable how bacteria will develop resistance specifically to antibiotics that are used in a particular hospital, but not some of those antibiotics that are used in other hospital systems. This reveals a key feature of bacteria: that they continually evolve to solve the problems that they are faced with, such as antibiotics. It is interesting to see that this is exactly what we are observing in the current virus pandemic. We responded by rapidly developing vaccines that had the potential to significantly reduce, if not eradicate, SARS-CoV-2. Instead of simply going away, the virus has evolved specific means to respond to what we have done. The virus has chosen to infect largely those who are unvaccinated and has even mutated to become clever enough to infect some who are vaccinated. This persistence despite our best efforts is real-time proof that this virus will continue to try to respond to what we do to eliminate it. It also strongly suggests that we must all get on the same page and have a coordinated response if we expect to eliminate it. If we do anything less, SARS-CoV-2 has proven that it will seek out refuge, mutate, and then potentially come roaring back