How Viruses Shape Our World

David Quammen

National Geographic, February 2021

David Quammen (born February 24, 1948) is an American science, nature, and travel writer and the author of fifteen books. His articles have also appeared in National Geographic, Harper's, Rolling Stone, The New York Times Book Review, The New Yorker, and other periodicals. Yale University (B.A., 1970), University of Oxford (B.Litt., English, 1973). Quammen was drawn to the state of Montana in the early 1970s for the trout fishing. He still lives in Montana, while traveling widely for National Geographic and to research his books. During Autumn 2014, he was much involved, because of books and articles he has published, in the public discussion of the Ebola virus disease outbreak in West Africa and its spread beyond. From 2007 to 2009 he was the Wallace Stegner Professor of Western American Studies at Montana State University.

p46 What is a virus?

p46 Two lengths of DNA that originated from viruses, and now reside in the DNA of humans and other primates .. without which pregnancy would be impossible. Viral DNA helps package and store memories ...in tiny protein bubbles. Viruses contribute to the growth of the embryo, regulate immune systems, and resist cancer.

p48 A virus is a parasite, but sometimes work in mutual dependence between virus and host.

p48

• A virus is
  • Not a living cell
  • But from Forterre on p55: "A virus is alive when it's a virocell, even if its virions are inanimate."
• A virus is
  • A stretch of genetic instructions in DNA or RNA
  • packaged inside a protein capsule known as a capsid. Viral particles may be called virions. The total may be called a virocell.
  • some capsids are surrounded by membranous envelopes for protection and facilitation of interactions wit cells.
  • copies itself by entering cells and making use of cell's manufacturing capability (does that mean it uses the ribosomes of the cell?)
  • may back-engineer its little genome into the host's genome.
• SARS-CoV-2 manufactures components in epithelial cells of the human airway to the point of bursting the cells and leaving them as wreckage.
• Author takes the RNA world approach, presumes RNA as the first replicator.

p49 Are viruses alive? Most places I have read say no, but he equivocates. See Forterre section below.

• Origins of viruses?
  • Viruses first: Viruses came into existence before cells.
  • Escape: genes or stretches thereof "leaked out" of cells, became enclosed within protein capsids, and went rogue, finding a new niche as parasites.
  • Reduction: "cells downsized under competitive pressure".. "shedding genes until they were reduces to such minimalism that only by parasitizing cells could they survive."

p53 The giant viruses studied since 2003 have tipped expert opinion toward Reduction. Mimivirus found 2003 with 1.2x10⁶ letters genome compared to 13000 for influenza virus, 194,000 for smallpox. Genes for coding enzymes presumed to be uniquely cellular, but they were found in the giant viruses. Holdovers from a previous existence as cells? Other giant viruses soon discovered, some called pandoraviruses. They didn't replicate by fission.

p55 Patrick Forterre. The virocell concept focuses on this intracellular stage. "That's the delicate stage when the infected cell, like a zombie, is obeying the viral mandate, reading the viral genome and replicating it, but not always without skips, staggers, and mistakes. " Might be "cells taking genes from viruses."

p55 "An even more sweeping view...viruses are the preeminent font of genetic diversity." "one version of... horizontal gene transfer"

p62 Forterre et al have argued "The flow of viral genes into cellular genomes has been 'overwhelming' and may help explain some great evolutionary transitions, such as the origin of DNA, the origin of the cell nucleus in complex creatures, the origin of cell walls and maybe even the divergence of those three great limbs of the tree of life."

Thierry Hudmann - screened 33.1 billion letter human genome for stretches of DNA that looked like the kind of gene a virus would use to produce its envelope. Found about 20. Two were important because they had the capacity to perform functions essential to human pregnancy. Snyctin-1 and synctin-2 viral genes.

Human endogenous retroviruses - use RNA to make DNA and integrate it into the gnome of the infected cell. If they infect reproductive cells and insert their DNA into the heritable genome of the host - known as human endogenous retroviruses (HERVs), 8% of human genome consists of such viral DNA, Synctin-2 is among the more consequential of such substitutions. A viral gene was repurposed to generate a protein that helps cells fuse to create a special structure around what became the placenta, opening new possibilities in some animals: internal pregnancy. Synctin-2 is one of the two synctins in humans that helps fuse cells to form a placental layer next to the uterus. "That unique structure, mediating between mother and fetus, allows nutrients and oxygen in, carries waste products and carbon dioxide out, and probably protects the fetus from being attacked by the mother's immune system. It's a near miracle of efficient design, in which evolution shaped a viral component into a human component."

p63 Jason Shepherd, Univ of Utah. ARC gene acts in brain to package information embodied as RNA into little protein sacks that carry it from one neuron to another.

p63 Joanna Wysocka at Stanford: HERV-K in human embryos protects from infection, helping fetal development. Points to a transposon present 697 places, seem to help turn on almost 300 human genes. "our history of past retroviral infections is continuing to shape our evolution as a species."

p67 Some types of viruses are more likely to cause pandemics than others. Near the top of the list of the most worrisome candidates are coronaviruses, because of the nature of their genomes, their capacity to change and evolve, and their history of causing serious human disease. So when the phrase 'novel coronavirus' began to be used to describe the new thing causing clusters of illness in Wuhan, China, those two words were enough to make disease scientists around the world shudder."