Ricki Lewis

The components of certain things are meant to remain mysterious. The ingredients of sausage. A burger's slimy secret sauce. The recipe for Coke or Kentucky Fried Chicken.

Researchers from Stanford University are tackling the make-up of another entity, something rather new to our world: the stuff retrieved from swabs shoved up nostrils to sample genetic material from SARS-CoV-2, the virus behind COVID-19. A swab actually samples much more than the virus's RNA, required for diagnosis.

Super Swabs

John Gorzynski and colleagues describe the "multi-omic data repositories" from deployed swabs in a preprint (not yet peer-reviewed) and at the recent virtual annual meeting of The American Society of Human Genetics.

"A single nasopharyngeal swab can reveal substantial host and viral genomic information in a high-throughput manner that will facilitate public health pandemic tracking and research into the mechanisms underlying virus-host interactions," they write.

That's a mouthful. I'll just call them super swabs.

Amplifying Viral Sequences

Extracting clues from the stuff on the swabs is a little like collecting evidence at a crime scene. Several things happen.

To continue reading, please go to my blog DNA Science at Public Library of Science, where this post first appeared.

Antibodies are supposed to be the good guys. The proteins, built of distinctive Y-shaped pieces, enter the bloodstream early in infection, pouring out from plasma cells. They then latch onto molecules festooning pathogens and alert natural killer cells, which release a torrent of cytokines and complement, which are the biochemical weapons of an immune response.

Fighting infection is a complex business.

In a mysterious phenomenon called "antibody-dependent enhancement," the proteins actually make matters worse, intensifying symptoms. When a vaccine elicits the errant antibodies, the backfiring is called "vaccine enhancement of disease." We know these reactions exist, but still do not completely understand them.

The turncoat antibodies can be coaxed to appear in test tube experiments, but are elusive in a patient who is getting sicker. That is, there's no clinical way to distinguish antibody-dependent enhancement from just a severe case of an infectious disease. And that can complicate analysis of a candidate vaccine. "Vaccine enhancement of disease" would show up in a clinical trial as more people receiving a vaccine getting sick than the participants getting placebo.

Reportedly that hasn't happened for the candidate COVID-19 vaccines, but the data won't be published until the phase 3 trials are completed.

To continue reading, please go to my blog DNA Science at Public Library of Science. 

To those who've never thought about volunteering to be intentionally infected to test a vaccine, the idea may at first seem a bit bonkers. But such "challenge" studies not only have a rich history, but nearly 40,000 people have already checked the box "I am interested in being exposed to the coronavirus to speed up vaccine development" at 1daysooner, a website and non-profit organization that launched in April.

Challenge studies go by other names: "controlled human infection models," "human viral challenge," and "purposeful infection." Dripping virus-tainted saltwater into a volunteer's nostrils enables researchers to track infection, and the immune system's response to it, right from the start. The approach complements phase 3 clinical "field" trials of efficacy that await natural infection in the community.

To continue reading, go to Genetic Literacy Project, where this post first appeared.

Times have been strange for us all, weird indeed for science journalists.

The initial manageable flow of news alerts to the media back in January quickly became an unceasing torrent. Every day now I receive dozens of news releases and heads-ups from science and medical journals. Many papers are preprints (not yet peer-reviewed) or embargoed, meaning we agree to not report findings until a certain date and time.

This is COVID article #42 for me. Today's post covers 5 news releases that seemed intriguing. Cats first!

Cats Get COVID From Owners

When four-year-old Negrito's human died of COVID-19, relatives took in the bereft European/Persian mix, who lived in Barcelona. Then Negrito developed difficulty breathing, so the new owners, who also had COVID, took him to the vet. Negrito's shortness of breath was due to an enlarged heart from a pre-existing condition, and he humanely crossed the rainbow bridge. But his bloodwork revealed a low viral load of SARS-CoV-2, although the cat had no other symptoms of COVID-19.

To continue reading go to DNA Science, where this post first appeared.

Early in this unforgettable year, a wet market in Wuhan, China, emerged as a possible step along the way, if not the place of origin, of the outbreak that would seed the pandemic of COVID-19. Prescient researchers have reached back to meat samples collected in 2013 and 2014 and used genetic testing to trace what might have happened again more recently: the magnification of viral infection from wild or farmed meat to large markets to restaurants. The report appears in PLoS ONE.

"This study shows the wildlife supply chain generates a one-two punch when it comes to spillover risk. It is known to increase contact rates between wildlife and people and here we show how it greatly amplifies the number of infected animals along the way," write Amanda E. Fine from the Wildlife Conservation Society, Viet Nam Country Program in Ha Noi and the Wildlife Conservation Society, Health Program, Bronx, New York, and colleagues.

COVID-19 was not a surprise to anyone familiar with the ways of viruses. A lot of folks weren't paying attention, even when repeatedly warned.

Collecting Rats

To continue reading, go to DNA Science, where this post first appeared. 

As the days unfold with a seeming sameness in this odd summer of the pandemic, news of vaccine clinical trials begins to trickle in, and another buzzword from epidemiology is entering the everyday lexicon: durability.

To be successful, a vaccine's protection must last or booster shots periodically restore it. Some vaccines lose efficacy over time, including those for yellow fever, pertussis, and of course influenza.

For some vaccines, antibodies and the B cells that make them persist and protect for a long time. For other infectious diseases, like TB and malaria, T cells are needed in vaccines too. B and T cells (lymphocytes) are types of white blood cells, which are part of the immune system.

Antibody response may be ephemeral

"Give a man a fish and you feed him for a day. Teach him how to fish and you feed him for a lifetime," said Chinese philosopher Lao Tzu, founder of Taoism.

Tzu might have been referring metaphorically to the immune system's response to viral infection: an initial rush of antibodies that fades as a longer-lasting cell-based memory builds that primes the body to rapidly release antibodies upon a future encounter with the pathogen.

To continue reading, go to Genetic Literacy Project, where this post first appeared.

New York City has become a curious mosaic of crowds and barrenness, people packed into hospitals and homes, yet familiar favorite spaces eerily empty. The haunted cityscapes that accompany this article will fill again once we have a vaccine.

If all goes extremely well — with global cooperation, advances and insights to come, overlapping clinical trial phases, and a lot of luck — a year from now a vaccine or even vaccines against the novel coronavirus may exist. But that's a best-case scenario. Experts tend to be conservative.

"It's hard for me to see that we'd have a vaccine on this side of January. The process is designed to be slow, reflective, peer-reviewed and evidence-based. It takes a long time, not the science part nor to build the vaccine, but to conduct safety testing in enough people across enough time," said Gregory A. Poland, MD, director of the Mayo Clinic's Vaccine Research Group and editor-in-chief of the journal Vaccine.

To continue reading please go to Genetic Literacy Project, where this post first appeared.