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Genetic Linkage

How Viral Variants Arise

The public has had a crash course in virology. But sometimes media coverage spews jargon so fast, often without definitions or descriptions, that I wonder to what degree readers or viewers know what terms like antibody, cytokine, or mRNA actually mean.

 

"Variant" is especially problematical, when coming after "viral," because it has a plain language meaning too – variation on a theme, something just a little bit different from what we're used to. But during an epidemic, a small genetic change can have sweeping consequences, fueling a pandemic.

 

Mutations Build Variants

Variants of SARS-CoV-2 – the COVID virus – are sets of mutations. A mutation is a specific change in a specific gene.

 

Different variants have some mutations in common, so it can get confusing. For example, three variants circulating in India each has 6 or 7 mutations, three in common. The first and second variants that were discovered each has a unique mutation, but the third variant is a subset of parts of the first two. Got that?

 

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

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Expand Rapid Testing to Help Counter COVID Variant Spread, Says Harvard Epidemiologist Michael Mina

I just returned from an enlightening trip to CVS, to photograph Abbott Lab's at-home rapid antigen test for COVID, BinaxNOW. It became available at three major drugstore chains on April 19.

 

"Do you have the rapid COVID test? The at-home one?" I asked the woman behind the pharmacy counter.

Deer-in-the-headlights.

 

Fortunately, the pharmacist behind her overheard. "Not only don't we have it, but we don't know when we'll be getting it." I wasn't too surprised; I live in a small town.

 

So I got on line to buy some vitamin gummies, appropriately socially distanced, and saw to my immediate left a prominent display of items that everyone should have to prevent COVID: wipes, hand sanitizer, gloves, masks. They provided a backdrop to a stack of 6 boxes of – BinaxNOW!

 

Of course, a detection test to see if you've been infected is not at all the same thing as a preventive measure. So I circled back to the pharmacy, and within seconds of notifying the pharmacist that the tests were indeed available, an angry summons for the manager bellowed out over the loudspeaker.

 

Oops.

 

 

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

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Would you agree to be infected with COVID for science? Intentional 'challenge' studies underway as researchers explore new vaccines and treatments

(hVIVO)

Lauren Thomas, who just turned 26, is trying to get into a clinical trial at the University of Oxford, where the American is in a master's program in data science. She's seeking to be intentionally reinfected with SARS-CoV-2, the virus that caused her bout with COVID-19 back in October.

 

Thomas had a mild case – just a fever. So now she's volunteering to help researchers understand the aftermath of infection, waiting to hear whether she'll get into the clinical trial. In the meantime, she's an organizer for 1daysooner, a non-profit advocacy group for people wishing to participate in research and launched in April 2020. A major focus has been joining clinical trials for COVID vaccines.

 

Why would anyone sign up for a second encounter with the virus that has shattered the world?

 

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

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3 Possible Origins of COVID: Lab Escapee, Evolution, or Mutator Genes?

B.1.1.7 variant (NIAID)

"Virus outbreak: research says COVID-19 likely synthetic," shouted the headline in the Taipei Times on February 23, 2020. The idea that the novel coronavirus SARS-CoV-2 arose in a virology lab in China – by accident or as a bioweapon – has sparked an undulation of accusation and explanation ever since.

 

The latest chapter: An "open letter" in the April 7, 2021 New York Times, calling for "a full investigation into the origins of COVID-19." The two dozen scientists who signed the letter cite the continuing absence of a "robust process" to examine critical records and biological samples. Their argument responds to the WHO's March 20 press event that barely considered an origin other than from a natural spillover.

 

But two types of new information may counter the lab escapee hypothesis: filling-in-the-blanks of mammals that may have served as "missing links" in the evolution of disease transmission, and the rapid rise of viral variants reflecting a tendency to mutate that may underlie SARS-CoV-2 seemingly bursting from out of nowhere.

 

So here is my view, as a geneticist, of three possible origins of SARS-CoV-2:

 

1. Bioweapon – an engineered pathogen or escape of a natural candidate

 

2. Gradual evolutionary change through intermediate animal hosts, mutating along the way and becoming more virulent

 

3. "Mutator" genes that trigger mutations in other genes, speeding evolution

 

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

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‘Challenge studies’: Should we be testing COVID vaccines by intentionally infecting volunteers?

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.

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