Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates

Importance Restriction factors are host proteins that block viral infection and replication. Many viruses, like HIV-1 and related retroviruses, evolved accessory proteins to counteract these restriction factors. The importance of these interactions is evidenced by the intense adaptive selection pressures that dominates the evolutionary histories of both the host and viral genes involved in this so-called arms race. The dynamics of these arms races can point to mechanisms by which these viral infections can be prevented. Two human genes were recently identified as targets of an HIV-1 accessory protein important for viral infectivity: SERINC3 and SERINC5. Unexpectedly, we found that these SERINC genes, unlike other host restriction factors, show no evidence of a recent evolutionary arms race with viral pathogens.
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Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome

Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Abstract

"The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin."

 

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Viral genome remnants indicate that the mysterious Denisovans, not humans, are Neanderthals' closest cousins

Viral genome remnants indicate that the mysterious Denisovans, not humans, are Neanderthals' closest cousins | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Humans and Neanderthals are close cousins. So close, in fact, that some researchers argue the two hominids might actually be members of the same species. But a few years ago, anthropologists discovered a mysterious new type of hominid that shook up the family tree. Known only from a finger fragment, a molar tooth and the DNA derived from both, the Denisovans lived in Asia and were contemporaries of Neanderthals and modern humans. And they might have been Neanderthals’ closest relatives. A recent study of virus “fossils” provides new evidence of this relationship.

 

Hidden inside each, embedded in our DNA, are the genetic remnants of viral infections that afflicted our ancestors thousands, even millions of years ago. Most known virus fossils are retroviruses, the group that includes HIV. Consisting of a single strand of RNA, a retrovirus can’t reproduce on its own. After the retrovirus invades a host cell, an enzyme reads the RNA and builds a corresponding strand of DNA. The virus-derived DNA then implants itself into the host cell’s DNA. By modifying the host’s genetic blueprints, the virus tricks the host into making new copies of the retrovirus. These virus fossils have distinct genetic patterns that scientists can identify during DNA analyses. After the Human Genome Project was finished in 2003, researchers estimated that about 8 percent of human DNA is made up of virus DNA.

 


Via Dr. Stefan Gruenwald
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PLoS Pathogens: A Single Nucleotide Polymorphism in Tetherin Promotes Retrovirus Restriction In Vivo

PLoS Pathogens: A Single Nucleotide Polymorphism in Tetherin Promotes Retrovirus Restriction In Vivo | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Tetherin is a membrane protein of unusual topology expressed from rodents to humans that accumulates enveloped virus particles on the surface of infected cells.

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Retrovirology | Abstract | Host-pathogen interactome mapping for HTLV-1 and 2 retroviruses

Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes.
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Scientists uncover history of ancient viruses as far back as 30 million years ago

Researchers from Boston College, US, have revealed the global spread of an ancient group of retroviruses that affected about 28 of 50 modern mammals' ancestors some 15 to 30 million years ago.
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We know what retroviruses were up to 407 million years million years ago - MicrobiologyBytes

We know what retroviruses were up to 407 million years million years ago - MicrobiologyBytes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The tale of the coelacanth and the retrovirus - close friends for 407 million years.

The deep history of retroviruses is still obscure. Retroviruses can leave integrated copies within their hosts’ genomes, providing a fossil record for studying their long-term evolution. Endogenous forms of foamy viruses, complex retroviruses known to infect only mammalian species, appear to be extremely rare, so far found only in sloths and the aye-aye.

This paper reports the discovery of endogenous foamy virus-like insertions within the genome of a so-called ‘living fossil’, the (Latimeria chalumnae). It provides evidence suggesting that foamy viruses and their hosts share a coevolutionary history of more than 407 million years, and that foamy viruses accompanied their vertebrate hosts on the evolutionary transition from water to land. These findings indicate that the retroviruses originated in the primeval ocean millions of years ago.

 

Thanks @AJCann!


Via Ed Rybicki
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The impact of endogenous retroviruses on antiviral immunity

The impact of endogenous retroviruses on antiviral immunity | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

NIMR virologists and immunologists have shown that endogenous retroviruses can enhance antiviral immunity. The research is published in PLoS Pathogens.

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Discovery of Retroviral Homologs in Bats: Implications for the Origin of Mammalian Gammaretroviruses

Gammaretroviruses infect a wide range of vertebrate species where they are associated with leukemias, neurological diseases and immunodeficiencies. However, the origin of these infectious agents is unknown.

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