This Week In Evolution

Nels and Vincent discuss the identification of novel bat coronaviruses that shed light on the evolution of SARS-CoV-2, dating the first cases of COVID-19 to mid-November 2019, and recovery of deleted genome sequences from early in the Wuhan outbreak. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Identification of novel bat coronaviruses (Cell) Dating first cases of COVID-19 (PLoS Path) Recovery of deleted SARS-CoV-2 sequences (bioRxiv) Time stamps by Jolene. Thanks! Science Picks Nels – The Last—And Only—Foreign Scientist in the Wuhan Lab Speaks Out Vincent – Human Behavior During the Pandemic Is More Important Than Any Covid Variant Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent explain a new method for calculating the most recent common ancestor of SARS-CoV-2, which concludes that the ancestral virus was circulating in October/November 2019, before its first detection in China. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Evolutionary portrait of SARS-CoV-2 (Mol Biol Evolution) Letters read on TWiEVO 68 Time stamps by Jolene. Thanks! Science Picks Nels – Ed Yong pandemic trauma and We’re Not Ready for the Next Pandemic Vincent – Furin cleavage site is not a smoking gun Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent review evidence for recombinant SARS-CoV-2 genomes arising in the B.1.1.7 lineage within the United Kingdom. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Recombination in B.1.1.7 lineage (Virological) CoVariants Letters read on TWiEVO 67 Time stamps by Jolene. Thanks! Science Picks Nels – Mars rover helicopter flight! Vincent – TWiN 17: Worms see the light with Michael Nitabach Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent review a preprint demonstrating that changes in the genomes of the SARS-CoV-2 variants B1.351 and P.1 allow the viruses to reproduce in mouse cells in culture and in laboratory mice. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Tony Schountz on TWiV 668 SARS-CoV-2 variants infect mice (bioRxiv) CoVariants Letters read on TWiEVO 66 Time stamps by Jolene. Thanks! Science Picks Nels – Billion years of plate tectonics Vincent – Sapiens a Graphic History by Yuval Noah Harari Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent review evidence that a single amino acid change in the SARS-CoV-2 spike protein has driven adaptation to humans, followed by an update on the status of variants of concern. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Selective sweep drove SARS-CoV-2 adaptation (bioRxiv) Novel coronavirus haplotypes Letters read on TWiEVO 65 Time stamps by Jolene. Thanks! Science Picks Nels – Radio Garden Vincent – Our World in Data – Coronavirus Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent consider evolution of antibody immunity to SARS-CoV-2, and update the situation on novel virus variants of concern with potentially altered fitness and reactivity with antibodies. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Evolution of SARS-CoV-2 antibodies (Nature) mRNA vaccine-elicited antibodies to variants (bioRxiv) Scott Hensley thread (Twitter) Analysis of B.1.17 lineage (virological) Trevor Bedford thread (Twitter) Andrew Rambaut on variant naming (Twitter) Letters read on TWiEVO 64 Time stamps by Jolene. Thanks! Science Picks Nels – Biden Administration PCAST and The Hill We Climb Vincent – Four inaugural quotations – Lincoln, Roosevelt, Kennedy, Biden Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent wrap up 2020 with a discussion of novel variants of SARS-CoV-2 that have emerged in the United Kingdom and South Africa, how to interpret the rapidly emerging genome sequence data and what to look for in the coming weeks as these variants spread across the globe. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Preliminary genomic characterization of UK variant (virological) Clinical outcomes of infection with Orf8 variants (Lancet) Global Report Investigating Novel Coronavirus Haplotypes (GRINCH) South African SARS-CoV-2 lineage (medRxiv) Time stamps by Jolene. Thanks! Science Picks Nels – Katalin Karikos’ career and mRNA vaccines Vincent – Reverse Engineering of mRNA vaccine Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Daniel joins Nels and Vincent to discuss his new book on army ants, the wickedest insects ever to roam the planet, and his research on them and clonal raider ants. Hosts: Nels Elde and Vincent Racaniello Guest: Daniel Kronauer Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode This Week in Ants (TWiEVO 13) Raiders of the Lost Orco (TWiEVO 18) Army Ants by Daniel Kronauer Time stamps by Jolene. Thanks! Science Picks Daniel – Desert Navigator by Rüdiger Wehner and Insects of Suriname by Maria Sibylla Merian Nels – NPR Scicommers Vincent – The Vintage Beauty Of Soviet Control Rooms Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Nels and Vincent discuss an opinion piece on 12 evolutionary insights into how the COVID-19 pandemic is shaping human nature, and prolonged SARS-CoV-2 reproduction in an immunosuppressed patient. Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Microbe.TV on instagram Pandemic exposes human nature (PNAS) Carl Bergstrom calls BS (Twitter) Prolonged SARS-CoV-2 reproduction in patient (J Inf Dis) Letters read on TWiEVO 61 Time stamps by Jolene. Thanks! Science Picks Nels – Scott Edwards bikes across US; support diversity in evolution Vincent – 30 computers sculpture project Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

On the fifth anniversary of TWiEVO, Nels and Vincent invite 12 evolutionary biologists to describe exciting future directions for the field and their laboratory in the next five years. Hosts: Nels Elde and Vincent Racaniello Guests: Lillian Fritz Laylin, Talia Karasov, Andrew Kern, Sarah Tishkoff, Dmitri Petrov, Nancy Chen, Amanda Larracuente, John McCutcheon, Ambika Kamath, Chip Aquadro, Rebekah Rogers, Yaniv Braindvain, and Harmit Malik Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Science Picks Nels - Science Mill Virtual Tour and Benefit Vincent - Das Coronavirus summaries Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv  

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO 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 Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO 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! Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO 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 Send your evolution questions and comments to twievo@microbe.tv

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO 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! Science Picks Nels - The Cell in Evolution Vincent - Visual Science Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO 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! Science Picks Nels - In Memoriam: Gordon Lark Vincent - John Oliver Discussion of Antibody Tests Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO 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! Science Picks Nels - EvoEco seminars Vincent - Coronavirus book for children Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO 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! Science Picks Nels - Science Mill Explorer Zone Vincent - COVID-19 treatment and therapy tracker Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO 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! Science Picks Nels - Alejandro Sanchez TED Talk Vincent - WHO SARS-CoV-2 Sitrep Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Primordial emergence of a nucleic acid binding protein (bioRxiv) Tawfik laboratory Image credit Letters read on TWiEVO 51 Time stamps by Jolene. Thanks! Science Picks Nels - Universal principled review Vincent - Hostile Planet by National Geographic Listener Pick Courtney - Nightwish Endless Forms Most Beautiful and Shudder Before The Beautiful Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

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 Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiEVO Assembly of a young vertebrate Y chromosome (bioRxiv) Image credit Letters read on TWiEVO 50 Time stamps by Jolene. Thanks! Science Picks Nels - Genome from a 5,700-Year-Old Wad of Chewed Gum Vincent - NJ Sea-Level Rise Reports Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv