This Week in Virology

TWiV gives an update on poliovirus in wastewater, and reveals a vast world of viroids that infect a wide range of host species in diverse ecosystems. Hosts: Vincent Racaniello, Alan Dove, Rich Condit, and Kathy Spindler Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode •Research assistant position at FDA (pdf) •Register for ASV 2023 •MicrobeTV Discord Server •Nick Muzyczka passes •CDC planning wastewater testing for polio (CDC) •Wastewater testing for poliovirus (MMWR) •NY state poliovirus wastewater surveillance (NYSDOH) •CDC wastewater poliovirus surveillance in select communities (CDC) •Vast world of viroid-like RNAs (Cell) •Timestamps by Jolene. Thanks! Weekly Picks Kathy – 3B new Milky Way objects, Green comet Rich – Virology under the Microscope—a Call for Rational Discourse Alan – Indie story-driven games series #3: Valiant Hearts: The Great War Vincent – Vaccines and Related Biological Products Advisory Committee Meeting January 26, 2023 – pdf Listener Picks Florencia – An elegant way to stop deadly Hendra virus spillovers from bats to horses … to us (Nature article) Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv

In his weekly clinical update Dr. Griffin discusses co-detections of other respiratory viruses among children hospitalized with COVID-19, preprint review should form part of PhD programs and postdoc training, early and increased Influenza activity among children, COVID-19 vaccines versus pediatric hospitalization, SARS-CoV-2 variant-related abnormalities detected by prenatal MRI, protective effectiveness of previous SARS-CoV-2 infection and hybrid immunity against the Omicron variant and severe disease, protective effectiveness of previous SARS-CoV-2 infection and hybrid immunity against the omicron variant and severe disease, persistent COVID-19 Symptoms at 6 months after onset and the role of vaccination before or after SARS-COV-2 infection, effect of Dexamethasone use on viral clearance among patients with COVID-19, and the impact of vaccination on post-acute sequelae of SARS CoV-2 infection in patients with rheumatic diseases. Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Codetections of other respiratory viruses among children with COVID-19 (Pediatrics)  Preprint review should form part of PhD programmes and postdoc training (Nature) Early and increased Influenza activity among children (CDC) COVID-19 vaccines versus pediatric hospitalization (Cell)  SARS-CoV-2 variant abnormalities detected by prenatal MRI (The Lancet)  Protective effectiveness of previous SARS-CoV-2 infection and hybrid immunity (The Lancet)  Persistent COVID-19 symptoms at 6 months and role of vaccination (JAMA) Effects of Dexamethasone use among patients with COVID-19 (IJID) Impact of vaccination on sequelae of SARS CoV-2 in patients with rheumatic diseases (BMJ) Contribute to our MicrobeTV fundraiser at PWB Dr. Griffin’s treatment guide (pdf) Letters read on TWiV 978 Don’t crush Paxlovid (pdf) Timestamps by Jolene. Thanks! Intro music is by Ronald Jenkees Send your questions for Dr. Griffin to daniel@microbe.tv

TWiV covers a study of SARS-CoV-2 persistence at multiple sites in the human body, and the role of endogenous retroviruses in ageing and senescence. Hosts: Vincent Racaniello, Dickson Despommier, Alan Dove, Brianne Barker, and Angela Mingarelli Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode •Research assistant position at FDA (pdf) •Register for ASV 2023 •MicrobeTV Discord Server •Persistence of SARS-CoV-2 (Nature) •Endogenous retroviruses and senescence (Cell) •Timestamps by Jolene. Thanks! Weekly Picks Dickson – Baritone Saxophone: Gerry Mulligan. No one else comes close Signature song: Bernie’s Tune Angela – World’s Longest Animal Brianne – Green Comet to Pass By Earth for first time in 50,000 years Alan – Indie games series: Golf Club Wasteland Vincent – Bivalent Covid-19 Vaccines — A Cautionary Tale Listener Picks Lisa – The River and the Wall Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv

In his weekly clinical update Dr. Griffin discusses China reporting almost 60,000 Covid-related deaths after abrupt shift in policy, detection of SARS-CoV-2 IgA and IgG in human milk and breastfeeding infant stool 6 months after maternal COVID-19 vaccination, effect of Fluvoxamine vs placebo on time to sustained recovery in outpatients with mild to moderate COVID-19, hyperimmune globulin for severely immunocompromised patients hospitalized with COVID-19, long COVID outcomes at one year after mild SARS-CoV-2 infection, long COVID: major findings, mechanisms and recommendations, a systematic review of trials currently investigating therapeutic modalities for post-acute COVID-19 syndrome and registered on World Health Organization international clinical trials platform, and the effect of using a structured pacing protocol on post-exertional symptom exacerbation and health status in a longitudinal cohort with the post-COVID-19 syndrome. Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode China records almost 60,000 COVID-related deaths (SCMP) Detection of SARS-CoV-2 IgA and IgG in human milk and breastfeeding infant stool (Nature) Effect of Fluvoxamine vs placebo in outpatients with COVID-19 (JAMA) Hyperimmune Globulin for immunocompromised patients with COVID-19 (JID) Long COVID outcomes at one year after mild infection (BMJ)  Major findings, mechanisms and recommendations for Long COVID (Nature) Review of trials investigating therapeutic modalities for post-acute COVID-19 (CMI) Effect of using a structured pacing protocol (JMV) Contribute to our MicrobeTV fundraiser at PWB Dr. Griffin’s treatment guide (pdf) Letters read on TWiV 976 Don’t crush Paxlovid (pdf) Timestamps by Jolene. Thanks! Intro music is by Ronald Jenkees Send your questions for Dr. Griffin to daniel@microbe.tv

Daniela joins TWiV to discuss her career and her research on T cells, their role in infection with SARS-CoV-2, T cell epitopes and why a variant that evades T cell immunity is not likely to emerge. Hosts: Vincent Racaniello, Alan Dove, and Brianne Barker Guest: Daniela Weiskopf Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode •Research assistant position at FDA (pdf) •Register for ASV 2023 •Cross reactive T cells to SARS-CoV-2 (Science) •SARS-CoV-2 exposure history and T cell response (Cell Rep Med) •Spike T cells cross- recognize Omicron (Nature) •Ancestral SARS-CoV-2 T cells recognize Omicron (Nature) •NVX-CoV2373 induces T cell responses (J Clin Inves) •Letters read on TWiV 975 •Timestamps by Jolene. Thanks! Weekly Picks Brianne – Video of viral attachment (based on this article) Alan – Starting a series of innovative indie video games. First up: The Longing. Vincent – The Amy Papers and Calendar for live events Listener Picks Judy – Innate immune evasion strategies of SARS-CoV-2 Charles – Who’s Talking to Chris Wallace? Season 1, epitope 30: Dr. Anthony Fauci on HBO Max Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv

In his weekly clinical update Dr. Griffin discusses poliovirus returns to New York wastewater, COVID-19 is more widespread in animals than we thought, increasing ventilation reduces SARS-CoV-2 airborne transmission in schools, the use of carbon dioxide monitoring to assess ventilation at a national infectious diseases conference, effectiveness of the bivalent mRNA vaccine in preventing severe COVID-19 outcomes, 7-month duration of SARS-CoV-2 mucosal immunoglobulin-A responses and protection, and long COVID outcomes at one year after mild SARS-CoV-2 infection. Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode COVID-19 more widespread in animals than thought (Nat Geo) Increasing ventilation reduces airborne transmission in schools (Frontiers) Carbon dioxide monitoring to assess ventilation at a NID conference (CID) Paxlovid patient eligbiliity screening checklist (FDA) Effectiveness of bivalent mRNA vaccine in preventing severe COVID-19 (Lancet) Duration of SARS-CoV-2 mucosal immunoglobulin-A responses and protection (Lancet) Long COVID outcomes at one year after mild SARS-CoV-2 infection (BMJ) Contribute to our MicrobeTV fundraiser at PWB Dr. Griffin’s treatment guide (pdf) Letters read on TWiV 974 Timestamps by Jolene. Thanks! Intro music is by Ronald Jenkees Send your questions for Dr. Griffin to daniel@microbe.tv

Felicia joins TWiV to discuss her career and her research on human cytomegalovirus, which infects most of us for our entire lives yet mainly causes disease in the immunosuppressed. Hosts: Vincent Racaniello, Alan Dove, and Brianne Barker Guest: Felicia Goodrum Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode •Research assistant position at FDA (pdf) •The loss of binary (Curr Clin Micro Rep) •Virology in Peril (mBio) •Letters read on TWiV 973 •Timestamps by Jolene. Thanks! Weekly Picks Brianne – “Leukocyte” immunology video parody Alan – West Point Removing Confederate Monuments, and Ty Seidule’s book on that subject Vincent – The works of Haruki Murakami – South of the Border, West of the Sun; also short stories (First Person Singular, particularly Confessions of a Shinagawa Monkey; and Men Without Women, particularly Drive My Car) Listener Picks Karen – On All Fours: Transient Laborers, the Threat of Movement, and the Aftermath of Disease Kevin – James Hoffmann and Bald and Bankrupt Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv

In his weekly clinical update Dr. Griffin discusses the infectiousness of SARS-CoV-2 breakthrough infections and reinfections during the Omicron wave, virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants, antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants, comparative effectiveness of third doses of mRNA-based COVID-19 vaccines in US veterans, time to negative PCR conversion among high-risk patients with mild-to-moderate Omicron BA.1 and BA.2 COVID-19 treated by Sotrovimab or Nirmatrelvir, COVID drug Paxlovid was hailed as a game-changer, what happened?, the Fc-effector function of COVID-19 convalescent plasma contributes to SARS-CoV-2 treatment efficacy in mice, SARS-CoV-2 infection and persistence in the human body and brain at autopsy, long-term cardiovascular outcomes of COVID-19, and how heart-disease risk soars after COVID — even with a mild case. Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Infectiousness of breakthrough infections & reinfections during Omicron wave (Nature) Virological characteristics of the SARS-CoV-2 XBB variant (bioRxiv) Antibody evasion properties of BQ and XBB subvariants (Cell) Comparative effectiveness of third doses of mRNA vaccines in US veterans (Nature) Time to negative PCR conversion among high-risk patients treated by Sotrovimab or Nirmatrelvir (CMI) Paxlovid patient eligbiliity screening checklist (FDA) COVID drug Paxlovid was hailed as a game-changer. What happened? (Nature) Fc-effector function of COVID-19 convalescent plasma contributes to treatment efficacy (Cell) SARS-CoV-2 infection and persistence in the human body and brain at autopsy (Nature) Long-term cardiovascular outcomes of COVID-19 (Nature) Heart-disease risk soars after COVID (Nature) Contribute to our MicrobeTV fundraiser at PWB Dr. Griffin’s treatment guide (pdf) Letters read on TWiV 972 Timestamps by Jolene. Thanks! Intro music is by Ronald Jenkees Send your questions for Dr. Griffin to daniel@microbe.tv

In the first epitope of 2023, TWiV reviews our coverage of virology in 2022, including favorite story arcs, episodes, show titles, and much more. Hosts: Vincent Racaniello, Dickson Despommier, Rich Condit, Kathy Spindler, and Brianne Barker Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Our favorite 2022 virology stories: •Vincent: Paul Offit on bivalent boosters (TWiV 917, 942, Special) •Dickson: Interviews with Paul Offit and Andy Slavitt •Rich: TWiV 948: Breathless with David Quammen •Kathy: TWiV 915: Mouse mouth to mouse mom •Brianne: Spillovers (TWiV 923 and 876) •Vincent: Giant viruses (TWiV 873, 906, 968) •Dickson: TWiV 960 – Getting Funky with Dan Wilson •Rich: TWiV 927: Merchlinsky vs monkeypox •Kathy: TWiV 958: Pass the RNA and have some venison pi •Brianne: TWiV 869: Epstein-Barr virus and MS, a perfect storm •Twiverse •Letters read on TWiV 968 •Timestamps by Jolene. Thanks! Weekly Picks Dickson – Jazz Project: Tenor saxophone: John Coltrane/Dexter Gordon/Stan Getz: John Coltrane: Signature album: Giant Steps: Signature song: Blue Train; Dexter Gordon: Signature album: The Other Side Of Round Midnight. Signature song: Round Midnight; Stan Getz (with Charlie Byrd on guitar): Signature Album: Jazz Samba; Signature song: Desafinado Brianne – A Full Circle Rainbow over Norway Kathy – Frozen soap bubbles Rich – It’s Turtles All the Way Down in the Fossil Record by Asher Elbein Vincent – Vincent’s Top Ten Music Listener Picks Charles – Wayne Bergeron and Vince DiMartino MacArthur Park Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv

In his weekly clinical update Dr. Griffin discusses modelling the adjustment of COVID-19 response and exit from dynamic zero-COVID in China, canine real-time detection of SARS-CoV-2 infections in the context of a mass screening event, two masks can be worse than one: N95 respirator failure caused by an overlying face mask, airflow patterns in double-occupancy patient rooms may contribute to roommate-to-roommate transmission of severe SARS-CoV-2, clinical validation of a novel T-Cell receptor sequencing assay for identification of recent or prior SARS-CoV-2 infection, antibody-dependent cellular cytotoxicity against SARS-CoV-2 Omicron sub-lineages is reduced in convalescent sera, regardless of the infecting variant, VV116 versus Nirmatrelvir–Ritonavir for oral treatment of Covid-19, Nirmatrelvir plus Ritonavir for early COVID-19 in a U.S. health system, Molnupiravir plus usual care versus usual care alone as early treatment for adults with COVID-19 at increased risk of adverse outcomes, higher dose corticosteroids in hospitalized COVID-19 patients with hypoxia but not requiring ventilatory support, FDA approves Roche’s Actemra (tocilizumab) for the treatment of COVID-19 in hospitalized adults, structural brain changes in post-acute COVID-19 patients with persistent olfactory dysfunction, persistent post–COVID-19 smell loss is associated with immune cell infiltration and altered gene expression in olfactory epithelium, epidemiology of long COVID in US adults, persistent symptoms and sequelae after SARS-CoV-2 infection not requiring hospitalization, and outpatient treatment of Covid-19 with metformin, ivermectin, and fluvoxamine and the development of Long Covid over 10-month follow-up. Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Modeling the adjustment of COVID-19 response and exit in China (Nature) Canine real-time detection of SARS-CoV-2 infections in mass screening events (BMJ) N95 respirator failure caused by an overlying face mask (ICHE) Airflow in patient rooms may contribute to transmission of severe SARS-CoV-2 (CID) Clinical validation of a T-Cell receptor for identification of recent or prior SARS-CoV-2 infection (CID) Antibody-dependent cellular cytotoxicity against SARS-CoV-2 Omicron sub-lineages (Cell) VV116 vs. Nirmatrelvir–Ritonavir for oral treatment of Covid-19 (NEJM) Nirmatrelvir plus Ritonavir for early COVID-19 in a U.S. health system (ACP) Molnupiravir as early treatment for adults with COVID-19 (The Lancet) Higher dose corticosteroids in hospitalized COVID-19 patients with hypoxia but not requiring ventilatory support (medRxiv) FDA approves Tocilizumab for the treatment of COVID-19 in hospitalized adults (Roche) Structural brain changes in post-acute COVID-19 patients with olfactory dysfunction (Annals) Paxlovid patient eligbiliity screening checklist (FDA) Persistent post–COVID-19 smell loss association (Science) Epidemiology of long COVID in US adults (CID) Persistent symptoms & sequelae after SARS-CoV-2 infection not requiring hospitalization (OFID) Outpatient treatment of COVID-19 with metformin, ivermectin, and fluvoxamine & the development of long COVID (medRxiv) Contribute to our MicrobeTV fundraiser at PWB Dr. Griffin’s treatment guide (pdf) Letters read on TWiV 970 Timestamps by Jolene. Thanks! Intro music is by Ronald Jenkees Send your questions for Dr. Griffin to daniel@microbe.tv

Carl Zimmer visits the Incubator to record a wide-ranging conversation about COVID-19, including origins, vaccines, public health responses, and impact on society. Host: Vincent Racaniello Guest: Carl Zimmer Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv

TWiV reviews eukaryotic viruses recovered from ancient permafrost, a mistake made by scientists on Omicron origins, and close relatives of MERS-CoV from bats that bind ACE2 for entry into cells. Hosts: Vincent Racaniello, Dickson Despommier, Alan Dove, Rich Condit, and Brianne Barker Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Support MicrobeTV with a Spike t-shirt (Vaccinated.us) with promo code MicrobeTV Positions with the Mosquito and Vector Control Division in Harris County Public Health (one and two) Ancient eukaryotic viruses from permafrost (bioRxiv) We made a mistake (Science) Bat MERS-like CoV bind ACE2 (Nature) Letters read on TWiV 968 Timestamps by Jolene. Thanks! Weekly Picks Dickson – Alto Saxophone: Paul Desmond/Cannonball Adderley/Charlie Parker/Randal Despommier: Paul Desmond: Signature album: Paul Desmond:The Complete RCA Victor Recordings (1961-1965). Signature song: Take Five (Dave Brubeck Quartet). Cannonball Adderley: Signature album: The Cannonball Adderley Quintet: Mercy, Mercy, Mercy. Signature song: Mercy, Mercy, Mercy. Charlie Parker (Bird): played in many groups: Signature album: Dizzy Gillespie and His Allstars. Signature song: A Night In Tunisia; Randal Despommier: Signature album: A Midsummer Odyssey. Signature song: I Hope It’s Spring For You. Brianne – How a See-Through Frog Hides its Red Blood from Predators (also covered in The Atlantic) Rich – Mindfulness in Plain English by Ven. Henepola Gunaratana Vincent – Unveiling skin macrophage dynamics explains both tattoo persistence and strenuous removal Listener Picks Rona – WKCR, FM 89.9 Columbia‘s radio station Alan – XKCD Proxy Variable Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv

In his weekly clinical update Dr. Griffin discusses how immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection, prevalence of SARS-CoV-2 and influenza coinfection and clinical characteristics among children and adolescents aged Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Immunological dysfunction persists for 8 months following SARS-CoV-2 infection (Nature) Prevalence of SARS-CoV-2 and Influenza coinfection and clinical characteristics (CDC) WHO estimates of excess mortality associated with the COVID-19 pandemic (Nature) Reconsideration of anti-nucleocapsid IgG antibody as a marker of SARS-CoV-2 infection (OFID) Impact of SARS-CoV-2 variants on inpatient clinical outcome (CID) Clinical features and burden of post-acute sequelae of SARS-CoV-2 infection (OFID) Similar SARS-CoV-2 Ct value distributions in samples from symptomatic children (JPIDS) Early estimates of bivalent mRNA vaccine effectiveness in preventing COVID-19 (CDC) Effect of Nirmatrelvir/Ritonavir vs placebo on COVID-19─Related hospitalizations (OFID) COVID-19 Convalescent Plasma outpatient therapy to prevent outpatient hospitalization (MedRxiv) Bacterial co-infection and empirical antibiotic therapy in patients with COVID-19 (OFID) Association of time to surgery after COVID-19 infection (JAMA) Demonstration of stable clusters of symptoms in long COVID (OFID) Paxlovid patient eligbiliity screening checklist (FDA) Longitudinal analysis of T cells in COVID-19 survivors with post-acute sequelae (OFID) Contribute to our MicrobeTV fundraiser at PWB Dr. Griffin’s treatment guide (pdf) Letters read on TWiV 967 Timestamps by Jolene. Thanks! Intro music is by Ronald Jenkees Send your questions for Dr. Griffin to daniel@microbe.tv

Vincent travels to the NIH campus to speak with Jeffery Taubenberger about his career, the 1918 influenza pandemic, deciphering the genome sequence of the virus from tissues of disease victims and using it to rescue infectious virus. Host: Vincent Racaniello Guest: Jeffery Taubenberger Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Support MicrobeTV with a Spike t-shirt (Vaccinated.us) with promo code MicrobeTV Influenza 1918 pandemic questions answered (Sci Transl Med) Reconstructed 1918 influenza virus (Science) Timestamps by Jolene. Thanks! Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv

Brazilian infectious diseases physician Esper Kallas returns to TWiV to discuss the state of viral diseases in his country, including those cause by Zika, dengue, and yellow fever viruses, MPOX, and SARS-CoV-2. Hosts: Vincent Racaniello and Alan Dove Guest: Esper Kallas Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode Support MicrobeTV with a Spike t-shirt (Vaccinated.us) with promo code MicrobeTV International Scientific Coordinator Position (agajewski at icsnicaragua.org for more info) Viral kinetics in sylvatic yellow fever (J Inf Dis) Safety and efficacy of Butanan-DV (Lancet Inf Dis) Immune responses to CoronaVac (Front Immunol) Timestamps by Jolene. Thanks! Weekly Picks Alan – A Voyage for Madmen Vincent – Some favorite holiday cookies: pignoli cookies and pfeffernusse Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv