Virus Variation and Evolution; Antiviral Drugs PDF

Virus Variation and Evolution; Antiviral Drugs Block IV, Vet Med 5400. Colin Parrish, Ph.D. [email protected]  Learning Objectives 1. Describe key features of virus sequences variation and how they arise. 2. Explain the evolution o...

Virus Variation and Evolution; Antiviral Drugs Block IV, Vet Med 5400. Colin Parrish, Ph.D. [email protected]  Learning Objectives 1. Describe key features of virus sequences variation and how they arise. 2. Explain the evolution of viruses and the relationships between virus types. 3. Define and describe the steps of viral genome recombination and reassortment. 4. Explain how phylogenetic analysis of viral sequences is used to characterize outbreaks and epidemics. 5. Describe the basic mechanisms of action for Amantadine, Rimantidine, Tamiflu, Famciclovir and Valacyclovir, and how resistance to these drugs can arise. *Note: Learning objectives generally describe the minimum knowledge needed to pass the course.  Outline Viral Evolution and Variation – Mechanisms of variation. – Mutations, recombination, reassortment. – Fitness and selection. – Epidemiological analysis. Antiviral Drugs. – Background. – Nucleoside analogs. – Amatadine and Neuraminidase Inhibitors.  Virus Variation and Evolution Many viruses vary extensively. Allows new strains and variants to arise. Antigenic variation allows escape from immunity. Varying host or tissue tropism –different diseases. Persistence, latency and/or prolonged shedding – give extended opportunities for variation and spread. Human influenza evolution: 2006-2017 Nature Medicine volume 25, pages212–220 (2019)  Mechanisms of variation Sources of Variation: Error rate of replication, tolerance for variation, large population sizes, and recombination of genome RNA or DNA. RNA viruses: More error prone, generally no proof reading (coronaviruses do proof read via exonuclease). Retroviruses: reverse transcription RNA to DNA is low fidelity. dsDNA viruses: Less error prone; lower levels of variation. Important impacts on veterinary viruses: Examples: Influenza serotypes and virulence. Canine parvovirus host range. Feline coronavirus - FIPV variants. High pathogenicity feline calicivirus strains. Infectious bronchitis virus strain variation.  Recombination and Reassortment. Recombination and Reassortment: Common most viruses (not -ve strand RNA viruses). Reassortment = viruses with segmented genomes. Both: Need co-infection of a cell with two viruses, mostly homologous recombination. Some viruses acquire genes from the host mRNAs – Bovine viral diarrhea virus (BVDV) cytopathic variants (see below). Recombination between strains; sometimes with vaccine strains - infectious bronchitis virus (IBV), and feline caliciviruses.  Recombination between viruses Creation of viral lineage with new properties. Alphavirus: Western equine encephalitis virus = recombinant between Eastern equine encephalitis/ Venezuelan-like virus and a Sindbis-like virus. Dominant virus in Western USA.  Recombination with host RNAs Example of viral variation from recombination: Bovine Viral Diarrhea Virus (BVDV) cytopathic variants: may acquire RNA from host = insertions into the NS3 gene. Increases protein cleavage gives cytopathic virus that is recognized by host responses = mucosal disease.  Reassortment of Segmented Viruses A special case of recombination. Only segmented genomed viruses: Orthomyxo (8 segments) or reoviruses and rotaviruses (10 or 11). Bunyaviruses (3 segments) Arenaviruses (2 segments). Creates new genetic and antigenic combinations = variants with different properties.  Fitness and selection. What is Viral Fitness? Relative ability to replicate and cause disease. Ability to transmit more readily (various mechanisms) Narrow fitness peak - little variation tolerated by these viruses. Broad fitness peak – viruses more variable in sequence and functions. μ = mutation rate  Sequence variation and separation Viruses vary over time = accumulation of mutations. Most of the changes are genetic drift (i.e. neutral evolution - not being selected). Viral sequences diverge when separated from each other (space or over time). Comparing sequences can explain viral spread and epidemiology - particularly during outbreaks. However - some changes selected. Selections may include antibody selection (antigenic variation), or host range differences.  Epidemiological analysis Phylogenetic analysis – sequence comparisons show viral endemic circulation or spread. e.g. Feline Calicivirus – virus in each colony genetically distinct and from a single introduction. Virus persisted and evolved within each colony. Any newly introduced or transferred virus would be obvious.  Sequence variation over time - Epidemiology Evolution of H3N8 Equine Influenza Viruses. Rapid evolution of virus – antigenic drift. Viruses in different parts of world - some distinct, also international transfers. North America Asia – China – Japan South America Journal of Virology Jun 2019, 93 (13) e00116-19; DOI: Europe 10.1128/JVI.00116-19  Epidemiological analysis – Foot and mouth disease virus in the UK Example of outbreak: FMDV - UK outbreak of 2001 – shows routes of transfer in the early stages of the epidemic. Early long- distance transfers enhanced outbreak. SARS CoV-2 Zoonotic virus – origin in bats; spread in humans. Emerged ~December 2019 – first seen in China. Spread world- wide January – March 2020. The analysis of the early virus sequences shows the global spread. doi: 10.1038/s41467-020-18877-9 Analysis of SARS CoV-2 in whitetail deer in Ohio. Using phylogenetic analysis to identify the viral strains. SARS CoV-2 – infects and spreads between mink, deer, (occasionally cats and other animals). Example – white tail deer in Ohio (and elsewhere) virus spread from humans on multiple occasions, and then epidemic spread among deer. Hale VL,, Madden C, et al., Bowman AS. 2022. SARS-CoV-2 infection in free-ranging white-tailed deer. Nature. 602(7897):481-486. doi: 10.1038/s41586-021-04353-x. PMID: 34942632; PMCID: PMC8857059. Take Home #1 - Virus Variation and Evolution Viruses vary through mutation, recombination (and reassortment). Variation derives from errors in replication – rates vary between viral types. May lead to evasion of immunity, or variation in biological properties – host range, tissue tropism, virulence. Sequencing used to track viruses as they spread in outbreaks – understanding epidemiology allows improved control measures. For veterinary medicine shows connections between human and animal – spillovers and outbreaks.  Antiviral Drugs Introduction and Overview: Few compounds in veterinary medicine. Expensive, relatively poorly effective or toxic. May show rapid resistance development. Dosing often based on weight of animal (when not topical) – expensive in large animals. Best drugs specific for conserved structures in the viral protein, but not altering cellular functions.  Amantadine and Rimantidine Influenza A viruses. Target M2 protein - H+ ion channel in viral envelope or cell membranes. Block ion channel – controls pH inside virus. Viral protein (HA) structure affected by low pH.  Amantadine and Rimantidine Give within 24-48 hrs of infection (or prior to infection). Amantidine differs from Rimantidine - is methylated so cannot cross blood-brain barrier. Resistance to high concentrations of drug = mutations result in HA changing to infectious form at higher pH.  Nucleoside Analogs Widely used and often effective in human medicine. Target viral DNA or RNA replication, or reverse transcription of RNA to DNA. Antiviral but non-toxic = more efficient at inhibiting viral replication than cellular DNA/RNA replication. May be activated (e.g. phosphorylated) by a viral enzyme for activity – occurs in infected cells.  Acyclovir Antiviral – mostly against herpesviruses. Guanine analog - viral thymidine kinase (TK) = kinases. Diphosphate and triphosphate by cellular kinases. Acyclovir- triphosphate has higher affinity for herpesvirus DNA polymerase.  Cidofovir Similar to acycolvir, but already phosphorylated. For ophthalmic treatment of cats with feline herpes conjunctivitis and keratitis. Twice daily administration, short treatment.  Famciclovir and Valacyclovir Famvir and Valtrex – improved oral bioavalability. Pro-prodrugs, cleaved within cell to penciclovir or acyclovir (which are then kinased). Incorporated into DNA chains, terminate synthesis, poor substrate for 3’-exonuclease. Pharmacological reviews 63(3):750-71  Azidothymidine (AZT) AZT Thymidine analog – targets reverse transcriptase of retroviruses. 3’ OH group replaced by azido (N3) group. AZT-5’-triphosphate 100x greater affinity for RT than cellular polymerases. Can inhibit FeLV and FIV in cats.  Neuraminidase Inhibitors Neuraminidase inhibitors - against influenza A infections. Neuraminidases (= sialidases) cleave sialic acid from oligosaccharides. Zanamivir = Relenza - inhibits Sialic acid influenza A NA – binds in active site. Spray application. Oseltamivir = Tamiflu – same activity, but better bioavailability, can be taken Oseltamivir orally.  Neuraminidase Inhibitors Virus released from infected Normal virus release cells are stuck together, or become trapped in mucus. Veterinary uses - generally impractical to use against animal influenza viruses. Exceptional circumstances. Viral aggregates Protects veterinarians and animal handlers. DOI:https://doi.org/10.1016/S0140- 6736(99)11433-8 Treatments - Feline Coronavirus Antiviral drugs are informally being used to treat feline infectious peritonitis caused by feline coronavirus. Since June 2024 may be used in the USA as approved therapies. Information widely shared on social media. GS-441524. The main plasma metabolite of the antiviral prodrug remdesivir. The most commonly used antiviral to treat FIP. Now legally available in US. Treatments - Feline Coronavirus Remdesivir/GS-5734 is the pro-drug of GS-441524. Prodrug allows intracellular delivery of GS-441524 monophosphate - kinased into GS-441524 triphosphate. Inhibitor of viral RNA polymerase. Appears to be an effective treatment for FIP, similar to GS-441524. Not specifically approved for veterinary applications; has been approved or authorized for emergency use to treat COVID-19 in humans in many countries, making it legal for off- label prescription use, although not always easily obtainable. Unlicensed Treatments - Feline Coronavirus GC376 is a 3CL protease inhibitor and is effective at treating FIP. Being developed for the veterinary market by Anivive Lifesciences, likely still a few years away from FDA approval.  Take Home #2 - Antiviral Drugs Antiviral drugs mainly developed for humans, quite expensive and sometimes toxic. Target different steps in viral replication – entry, DNA replication; release and shedding. Still few common applications in veterinary medicine - ocular herpesviruses, sometimes systemic application for herpes viruses or retroviruses. Recently available drugs for feline infectious peritonitis. Additional therapeutics for feline coronaviruses likely. Therapeutic antibodies also in development and deployment.