icon caret-left icon caret-right instagram pinterest linkedin facebook twitter goodreads question-circle facebook circle twitter circle linkedin circle instagram circle goodreads circle pinterest circle

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.

Be the first to comment

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.

Be the first to comment

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.

Be the first to comment

Science Writing in the Age of COVID-19

It's been a strange and busy 15 months for science journalists.

 

Each day, throughout the day, our inboxes overflow with the latest from the technical medical and science journals – tables-of-contents, abstracts, news releases, and the never-ending stream of article preprints. We jumpstart the journals by going straight to medRxiv and bioRxiv, aka "med-archive" and "bio-archive," where investigators post articles before peer review.

 

Where We Get Information

 

It's a deluge, an unrelenting barrage of new reports from the Science and Nature family of journals; the medical journals like JAMA, the Lancet group, and the NEJM; and publications that cover more basic science, like Cell and the journals from Public Library of Science, which has sponsored this blog since 2012. The journals send wrap-ups on the weekends, in case we've missed anything.

 

The clearinghouse for news releases for journalists, Eurekalert, provides information from a wide range of publications, government agencies, academic institutions, research centers, nonprofits, and companies, with quotes from experts and images and videos we can use. Eurekalert added a COVID tab to the topics menu early in the pandemic. Much appreciated!

 

As we try to stay ahead of our inboxes, we're invited to webinars, zooms, and podcasts, all wonderfully helpful in crafting our stories.

 

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

Be the first to comment

On the Anniversary of the Pandemic, Considering the Bioweapon Hypothesis

A year ago, the Director General of the World Health Organization, Tedros Adhanom Ghebreyesus, delivered the message that would divide time:

 

"WHO has been assessing this outbreak around the clock and we are deeply concerned both by the alarming levels of spread and severity, and by the alarming levels of inaction. We have therefore made the assessment that COVID-19 can be characterized as a pandemic."

 

What followed was a call to action to all. "We have rung the alarm bell loud and clear." And instantly, the redundant "global pandemic" ricocheted across the media, reverberating still.

 

The name of the enemy had changed quickly as 2020 began, from the "Wuhan coronavirus" to "2019 novel coronavirus" shortened to "2019-nCoV," and finally to SARS-CoV-2, acknowledging similarity to SARS, circa 2003-2004.

 

Whatever it's name, did SARS-CoV-2 have an older guise, perhaps in a lab?

 

The Bioweapon Hypothesis

 

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

Be the first to comment

Is COVID Optimism Finally Overtaking Pessimism? Harvard Experts Weigh In

Glimmers of hope are beginning to shine through the gloom of the past year. That was evident in a recent webinar that the Massachusetts Consortium on Pathogen Readiness (MassCPR) held to "demystify" the new viral variants. Each consists of several mutations.

 

Will the variants fuel "a novel stage of contagion, COVID 2.0?" opened George Daley, MD, PhD, dean of Harvard Medical School. "What has been unsettling is how many times mutations have cropped up independently in infected patients across the globe and in petri dishes. This is a consequence of Darwinian evolution by natural selection in real time," he added. The fact that the virus, SARS-CoV-2, has mutated in the same ways at different times and places suggests that the changes benefit the virus.

 

Also disturbing is that once variants appear, they proliferate. "That suggests the virus is more contagious, or replicates faster, so that it takes over the outbreak," said Jeremy Luban, MD, from the University of Massachusetts Medical School. Most mutations are neutral; we need to worry when they combine into "variants of concern," aka VOC. "They could permit the virus to escape immune control that's been established in a person from prior infection or from a vaccine," Luban added.

 

The "big three" variants of most concern now have hard-to-remember numerical names, which avoid stigmatizing a place: B.1.3.5.1 variant (South Africa), B.1.1.7 (UK), and P.1 (Brazil). The last one may be the worst to arise, so far. It first came to attention in Manaus, Amazonia. "Up to 70% of the population had been infected and they had developed what we'd consider herd immunity that would prevent new infection," Luban explained. The explosion of hospitalizations and deaths in December, a second wave, coincided with the appearance of the P.1 variant. "Many mutations in it raise concerns about whether the virus is resistant to the immune response against the first virus," he added.

 

Tackling variants requires asking three questions, Luban said:
• Do they enhance transmission?
• Do they permit reinfection?
• Do they decrease vaccine efficacy?

 

Fortunately, the vaccines so far are doing their job. Here are 6 pieces of good news.

 

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

Be the first to comment

Are We Hurtling or Hurdling Towards Herd Immunity for COVID-19?

Vaccines against COVID-19 were developed in record-smashing time, and now that the rollout has begun, attention is returning to herd immunity, in a real rather than hypothetical sense.

 

Herd immunity refers to the protection against an infectious disease that arises when a critical mass of individuals in a population becomes immune. The pathogen can't find welcoming bodies, and the epidemic dies out. Once herd immunity is attained, mitigation measures can be relaxed. But if society opens too soon, a second and even third wave of disease can ensue – as we've seen.

 

A vaccine, engineered to evoke a strong and diverse antibody response, is more likely to build herd immunity than is natural infection.

 

Establishing herd immunity against COVID-19 requires that a whole bunch of ducks align. The variables include:

 

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

Be the first to comment

A dangerous stage in the evolution of the novel coronavirus is upon us with the discovery of “escape mutations.” Artificial intelligence may be our best response

Real life with COVID-19 is now scarier than anything a sci-fi writer could envision. So-called "escape mutations" that can turn the virus into an out-of-control shape-shifter that hides from the immune system are now a frightening reality. And they can't be totally stopped with masks or social distancing, lockdowns or travel restrictions. Even if we could keep all viruses out, the ones already here are mutating in a direction that keeps them infectious and deadly. The battle between us and this often-lethal virus has just jumped to a new level. 

 

While it may take awhile to see whether these escape mutations will evade the vaccines approved or in the pipeline, Tyler Starr from the Fred Hutchinson Cancer Research Center and colleagues report in a new study in Science an effect on two already available treatments — monoclonal antibodies. They've identified an escape mutation with a single glitch that enables the virus to evade Regeneron's double-antibody REGN-COV2 "cocktail" (which Trump took) and a third antibody in Eli Lilly's LY-CoV016. The researchers found the escapee using a new lab mapping technique that displays viruses contorted with mutation, and then they found it in a patient who was still testing positive, 145 days after the first test.

 

What does this mean? The discovery of escape mutations derailing antibody treatments means that the companies' initial tests hadn't caught them all. And the escape mutations — the new mapping revealed three others — are already in circulation.

 

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

Be the first to comment

Mutants Come to Saratoga: COVID New Variants Explained

When a new variant of the COVID-19 virus appeared in the UK as 2020 drew to a close, I didn't think it would show up a half hour's drive from my home soon after. The first cases were near Denver and in San Diego, and then traced to a jewelry store on Broadway in Saratoga Springs. We've felt rather insulated and isolated here, hours from New York City.

 

The Legacy of Caffe Lena

This week began with an email from Sarah Craig, executive director of Caffe Lena, the oldest coffeehouse in the US. Don McLean debuted "American Pie" there, Arlo Guthrie first tried out "Alice's Restaurant," and Bob Dylan and many others have commanded the iconic tiny stage in the small, homey establishment that opened in 1960.

 

The café is now in "Safe Mode," with even the fabulous online events it has held throughout the pandemic too risky to record. The one-month shutdown follows the death January 12 from COVID of Matt McCabe, owner of Saratoga Guitar and frequent performer at the coffeehouse. The opening image captures his final show, in December.

 

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

Be the first to comment

Why Do Males Fare Worse With COVID-19? A Clue From Calico Cats

Early on in the pandemic, a worse clinical scenario for the male of the species emerged. A study published mid-May from Italian researchers offered early statistics from the WHO and Chinese scientists: a death rate of 1.7% for women and 2.8% for men. Then Hong Kong hospitals reported that 15% of females and 32% of males with COVID-19 needed intensive care or had died.

 

In July a Perspective published in Nature Reviews Immunology from researchers at Johns Hopkins University and the University of Montreal noted a similar "male bias" for other viral infections, including SARS and MERS. By then, the wide community testing in South Korea and data from the U.S. indicated 1.5-fold higher mortality for men for COVID-19. The pattern repeated in 38 countries, for patients of all ages.

 

Now a new study published in Nature Communications expands the increased risk for those who have only one X chromosome

 

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

Be the first to comment