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Friday, November 6, 2020

Coronavirus and other “mutants”

Marvel Comics, horror movies, punk rock, or Ninja Turtles –popular culture teems with mutants, usually not good ones (except perhaps for those turtles). So when you see in the news that the virus is mutating, it sounds ominous. Even when you search on the word “mutant,” coronavirus comes up with everything else.

The most recent articles report a novel coronavirus mutation that enabled it to infect mink and headlines report that mink farms in Europe may have to kill thousands of them. This is sad but not surprising. The coronavirus is an RNA virus, which means it mutates constantly and sometimes adapts to a new host animal. After all, it found us. With that in mind, I’d like to back up and put the mink mutations in context.

It won’t be easy, because there is an enormous amount of research being done worldwide on the coronavirus genome. Mapping the genome and how it changes has significant implications for vaccine research, contagion, and mapping how the virus spreads. To give an idea of the scope of genomic research, I did a search on “covid mutation chart” and turned up this–just one of many pages displayed on my phone:

Clearly I can only skim the surface, so let’s look at three things: first, how does the virus mutate; second, who’s keeping track; third, what about those minks.

First, mutation: Do you remember the DNA double helix in your biology textbook? A virus is essentially a package of reproductive code. There are RNA viruses and DNA viruses. The novel coronavirus, the one that causes COVID-19, is an RNA virus, meaning that its genetic code is housed on a single molecular strand. When a DNA virus replicates, its double-helix structure and replication enzymes work together to identify and repair mistakes. The RNA virus has one strand which carries a sequence of 29,903 nucleotides. When the virus enters a cell, it sets about making tens of thousands of copies which it releases in virions to infect other cells. But its work ethic is fast and sloppy, so it makes mistakes as it copies.

Some copying mistakes result in nonviable code sequences which go nowhere. Some changes don’t really matter to us or the virus. A few help the virus to enter a new host. That’s not likely, but it’s like the old adage about an infinite number of monkeys using an infinite number of typewriters. Sooner or later something makes sense.

Covid virus does not mutate as fast as flu or HIV. But over time changes occur and over 12,000 mutations have been catalogued. See: “The coronavirus is mutating—does it matter?” Nature, Sept. 8, 2020. https://www.nature.com/articles/d41586-020-02544-6

Second, who is keeping track? The good news is that research is being done all over the world and this vital information is being shared. One site is GISAID (Global Initiative on Sharing All Influenza Data) founded in 2007. See: https://www.gisaid.org/ . The U. S. participates in this international nonprofit center of genetic epidemiology through the CDC.

The NIH provides a “Comprehensive List of Open-access Data Sites and Computational Resources to Address Covid-19 at https://datascience.nih.gov/covid-19-open-access-resources . Links to thirty-five resources are listed today. Here are a few examples: CAS COVID-19 Antiviral Candidate Compounds Dataset which includes nearly 50,000 chemical substances structurally similar to known antivirals; COVID Digital Pathology Resources provides slide images of tissue samples relevant to COVID-19; GenBank Nucleotide Sequences, European Bioinformatics Institute COVID-19 Data Portal; Nextstrain COVID-19 enetic epidemiology provides open-source genome data and analytic and visualization tools. The point is, there is a variety of research approaches supported by open-source data sharing which allow researchers to make progress faster.

Some of these resources began with the influenza or HIV pandemics of recent decades and they will help equip us to meet the next pandemic. Because viruses are not going away.

For a simple and informative PowerPoint presentation on mutations and the coronavirus, I recommend: “Discovering the new coronavirus
and bioinformatics…” from the Swiss Institute on Bioinformatics found at: http://education.expasy.org/bioinformatique/pdfs/Bioinfo_corona_vs11_EN.pdf

  Danish Mink and Other Way Mutations Are Used:

  1. The D614G Mutation. This mutation changed the spike protein’s 614th amino acid position from D to G. The G version became more common in Europe in March and now predominates worldwide. It’s sometimes called a new “strain,” but this is not a very specific term. The G version may be more more transmissible or it may have spread more for other reasons. It’s under investigation.
  2. Finding “Patient Zero:” See article link below. Painstaking genetic mapping of COVID through thousands of samples has enabled researchers to trace back to the original virus genome. It also enables tracking of how the virus currently spreads throughout the world.
  3. Can you catch COVID twice? A large-scale study in Qatar went through a database of 130,000 positive cases to identify reinfections. A reinfection was defined as a second case with a different genome, since the virus from a true second infection would show some mutation changes. They found four cases of reinfection.
  4. Evaluating treatments and vaccines: The antiviral Remdesivir actually targets a viral enzyme and it may be a location that mutates. Antibody therapies given as a cocktail are less likely to be foiled by a mutation. Vaccines elicit multiple antibodies, so they can be effective even if a mutation affecting one of their targets has taken place. Researchers understand mutations that might interfere and find ways to get around them.
  5. And those minks: A mutated form of COVID-19 was able to infect minks on mink farms and has spread to at least 12 humans in Denmark, where it appears to have a resistance to antibodies. So people who were exposed have been tested and quarantined and the plan is to destroy all the farmed minks. This is reminiscent of 1997 when the H5N1 bird flu spread to 18 humans in Hong Kong with a fatality rate of 33 per cent. When the flu virus was found in poultry markets in Hong Kong it was decided to cull all domestic poultry in Hong Kong and 1.5 million chickens were destroyed.

H5N1 still exists in poultry around the world. The WHO The World Health Organization) tracks it and helps countries detect and manage it when it is found in humans. See https://www.who.int/news-room/q-a-detail/influenza-h5n1. So far this “flu” does not spread from human to human. Let’s hope it stays that way.

Today’s Notable Headlines

“Denmark plans to cull up to 17 million mink to stop mutated coronavirus,” CNN, Nov. 5, 2020. https://www.cnn.com/2020/11/05/europe/denmark-mink-cull-coronavirus-intl-hnk-scli/index.html

“Mutation Could Allow SARS-CoV-2 to Develop Resistance to Gilead’s Remdesivir, Suggests New Research,” Hospimedica.com, Oct. 9, 2020. https://www.hospimedica.com/covid-19/articles/294784948/mutation-could-allow-sars-cov-2-to-develop-resistance-to-gileads-remdesivir-suggests-new-research.html

“COVID-19 Patient Zero: Data Analysis Identifies the “Mother” of All SARS-CoV-2 Genomes,” SciTechDaily, Nov. 7, 2020. https://scitechdaily.com/covid-19-patient-zero-data-analysis-identifies-the-mother-of-all-sars-cov-2-genomes/

“Qatar confirms 4 coronavirus reinfections in largest study to date,” BNO News, Sept. 29, 2020. https://bnonews.com/index.php/2020/09/qatar-confirms-4-coronavirus-reinfection-cases-in-largest-study-to-date/

“Is the coronavirus mutating? Yes. But here’s why you don’t need to panic,” ScienceNews, May 26, 2020. https://www.sciencenews.org/article/coronavirus-covid19-mutations-strains-variants

And thanks to:

Spillover: Animal Infections and the Next Human Pandemic, David Quammen, WW Norton, New York, 2012. pages 268-69 and 508-08.

Why am I doing this?

The coronavirus pandemic will be indelibly written on our memories just as the Great Depression or the Battle of Britain left their mark on past generations. It is my intention to journal the pandemic experience from three perspectives: as a retired medical technologist, a historian (Ph.D., 2014), and an ordinary person living through an extraordinary crisis.

You are on History’s Edge.

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