Nels and Vincent answer listener questions and discuss a newly discovered virus of amoeba with a nearly complete ORFan genome: none of the proteins encoded in the viral genome look like any other proteins.

Hosts: Nels Elde and Vincent Racaniello

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Links for this episode

• Yaravirus (PNAS)
• Letters read on TWiEVO 59
• Time stamps by Jolene. Thanks!

Science Picks

Nels - Blog by Ambika Kamath Vincent - TWiVerse

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Simon and Heather join TWiEVO to discuss their analysis of the evolutionary history of ACE2 usage by coronaviruses in the Sarbecovirus genus.

Hosts: Nels Elde and Vincent Racaniello

Guests: Simon Anthony and Heather Wells

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Links for this episode

• Evolutionary history of sarbecovirus ACE2 binding (bioRxiv)
• Bombali virus in bats (Nat Micro)
• Herpesviruses in Puerto Rican bats (bioRxiv)
• Adenovirus and herpesvirus in great apes (PLoS One)
• Time stamps by Jolene. Thanks!

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Jessie, Allie and Tyler join Nels and Vincent to describe their work on deep mutational scanning of the SARS-CoV-2 receptor binding domain.

Hosts: Nels Elde and Vincent Racaniello

Guests: Jesse Bloom, Allie Greaney, and Tyler Starr

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Links for this episode

• Bloom Laboratory
• Deep mutational scanning of SARS-CoV-2 RBD (bioRxiv)
• Time stamps by Jolene. Thanks!

Music on TWiEVO is performed by Trampled by Turtles

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Nels and Vincent continue their discussion of SARS-CoV-2 evolution, including understanding recurrent mutations in the viral genome, and the potential for re-emergence of the virus from an animal reservoir.

Hosts: Nels Elde and Vincent Racaniello

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• SARS-CoV-2 genomic diversity (Inf, Genet, Evol)
• Re-emergence of SARS-CoV-2 (bioRxiv)
• Tackling SARS-CoV-2 rumors (virological.org)
• Letters read on TWiEVO 56
• Image credit
• Time stamps by Jolene. Thanks!

Nels - The Cell in Evolution Vincent - Visual Science

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Nels and Vincent continue their discussion of SARS-CoV-2 evolution, with a report that the coronavirus proofreading enzyme stimulates RNA recombination, and debunking the conclusion that a change in the viral spike glycoprotein is associated with increased human to human transmission.

Hosts: Nels Elde and Vincent Racaniello

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• CoV proofreading enzyme stimulates recombination (bioRxiv)
• CoV spike mutation pipeline (bioRxiv)
• Issues with CoV sequencing data (virological.org)
• Bill Hanage on selection vs bottleneck (threader.app)
• Image credit
• Time stamps by Jolene. Thanks!

Nels - In Memoriam: Gordon Lark Vincent - John Oliver Discussion of Antibody Tests

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Nels and Vincent continue their discussion of SARS-CoV-2 from an evolutionary viewpoint, including function of the furin cleavage site, whether Vervet cells are an informative system, another bat isolate, and a nomenclature to assist genomic epidemiology.

Hosts: Nels Elde and Vincent Racaniello

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• SARS-CoV-2 in Vero cells (bioRxiv)
• More related SARSr virus from bat (bioRxiv)
• Patient isolates in Vero cells (medRxiv)
• Nomenclature for genomic epidemiology (bioRxiv)
• Time stamps by Jolene. Thanks!

Nels - EvoEco seminars Vincent - Coronavirus book for children

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Nels and Vincent continue their discussion of SARS-CoV-2 from an evolutionary viewpoint, focusing on what the genome sequences tell us about the virus.

Hosts: Nels Elde and Vincent Racaniello

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• Clement Chow with COVID-19 (Salt Lake Trib)
• Scientists exposed to coronavirus (Nature)
• CoV by Britt Glaunsinger (YouTube)
• Genetic epidemiology of novel coronavirus (nextstrain.org)
• Time stamps by Jolene. Thanks!

Nels - Science Mill Explorer Zone Vincent - COVID-19 treatment and therapy tracker

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Nels and Vincent examine SARS-CoV-2 from an evolutionary viewpoint, examining what the spike glycoprotein sequence informs us about the origin of the virus.

Hosts: Nels Elde and Vincent Racaniello

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• Distinct CoV name needed (Lancet)
• Proximal origin of SARS-COV-2 (virological)
• CoV spillovers not rare (Goats and Soda)
• SARS-CoV-2 phylodynamics analysis (virological)
• Bat CoV surveillance in China (PLoS Path)
• Image credit
• Time stamps by Jolene. Thanks!

Nels - Alejandro Sanchez TED Talk Vincent - WHO SARS-CoV-2 Sitrep

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Nels and Vincent dive deep into evolution and consider how new proteins emerged billions of years ago, when there were no other proteins to serve as starting material.

Hosts: Nels Elde and Vincent Racaniello

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• Primordial emergence of a nucleic acid binding protein (bioRxiv)
• Tawfik laboratory
• Image credit
• Letters read on TWiEVO 51
• Time stamps by Jolene. Thanks!

Nels - Universal principled review Vincent - Hostile Planet by National Geographic

Courtney - Nightwish Endless Forms Most Beautiful and Shudder Before The Beautiful

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Nels and Vincent discuss signatures of sex chromosome evolution revealed by assembly of a young vertebrate Y chromosome from 3-spined stickleback fish.

Hosts: Nels Elde and Vincent Racaniello

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• Assembly of a young vertebrate Y chromosome (bioRxiv)
• Image credit
• Letters read on TWiEVO 50
• Time stamps by Jolene. Thanks!

Nels - Genome from a 5,700-Year-Old Wad of Chewed Gum Vincent - NJ Sea-Level Rise Reports

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