single strand, negative sense RNA Viruses Elliot J. Lefkowitz
Feb 23, 2016
single strand, negative sense RNA Viruses
Elliot J. Lefkowitz
•[email protected]•Web Site
•http://www.genome.uab.edu•Office
•BBRB 277A
•Phone•934-1946
Contact Information: Elliot Lefkowitz, Ph.D.
Associate Professor, Microbiology
Objectives
•To understand the fundamental common and distinguishing properties of (-) ssRNA viruses
•To understand the basic replication strategies of (-) ssRNA viruses
•To be able to identify human pathogens that belong to (-) ssRNA virus families, and some of their biological and pathogenic properties
Reading
•Medical Microbiology, Murray et al. 6th Edition•General classification
•Chapter 4•RNA virus properties and replication
•Chapters 58, 59, 60, 63•Pathogenesis
•Chapters 48, 67
Slide References
•Fields Virology, 5th Edition•Viruses and Human Disease
•Strauss and Strauss•University of Leicester - Virology Online
•http://www-micro.msb.le.ac.uk/3035/index.html
•International Committee on Taxonomy of Viruses•The 9th ICTV Report
•Primary literature
Virus classification
The Virus World
The (-) RNA Virus World
RNA Virus Genome Structure
•Number of strands•Single or double stranded
•Strand polarity•Positive, negative, or ambisense (both +
and -)•Positive (Plus) sense denotes the coding
(mRNA) strand•Number of segments
•Single or multi-segmented
single strand RNA virus genome polarity
virion RNA (+) sense
virus mRNA (+) sense translation
3’5’
translationtranscriptionvirion RNA (-) sense
virus mRNA (+) sense 3’5’5’3’
(+) sense RNA virus
(-) sense RNA virus
Negative/Ambisense ssRNA Viruses
Properties of (-) sense ssRNA Viruses
• Enveloped virion• Helical nucleocapsid• Negative-sense, linear, single segment RNA genome
• Bornaviruses, Filoviruses, Rhabdoviruses, Paramyxoviruses
• Negative and Ambisense, linear, multi segment RNA genomes• Arenaviruses, Bunyaviruses, Orthomyxoviruses
• Cytoplasmic replication• Exception: Bornaviruses, Orthomyxoviruses
• Genomes are non-infectious• An initial round of transcription is required for
genome replication• Virion must contain proteins required for transcription
• Bornaviridae• Bornavirus
• Filoviridae• Marburg virus• Ebola virus
• Paramyxoviridae• Paramyxovirinae
• Henipavirus• Morbillivirus• Respirovirus• Rubulavirus
• Pneumovirinae• Pneumovirus• Metapneumovirus
• Rhabdoviridae• Vesiculovirus• Lyssavirus
Order: Mononegavirales:Single segment, (-) sense, ssRNA
Multi-Segment, (-) sense ssRNA viruses
•Orthomyxoviridae•Influenzavirus A
•8 genome segments•Influenzavirus B
•8 genome segments•Influenzavirus C
•7 genome segments•Isavirus
•8 genome segments•Thogotavirus
•6 genome segments
Multi-Segment, Negative and Ambisense ssRNA viruses
•Arenaviridae•Two ambisense RNA segments
•Bunyaviridae•Three RNA segments•Both negative-sense and ambisense
segments•Depends on genus
The Virus
Virion, Genome, Proteins
Viral Proteins•Attachment/entry
•G – Membrane glycoprotein•F – Fusion protein•H – Hemagglutinin•N – Neuraminidase
•Structural/Assembly•M – Matrix
•Underlies lipid bylayer•Replication
•N – nucleocapsid protein•P – Phosphoprotein•L – RNA dependent RNA polymerase
Rhabdovirus Virion
Virus replication Machinery•Proteins
•RNA-dependent RNA-polymerase (RdRp)•Transcription•Replication
•Nucleocapsidprotein (N)•Encapsidates RNA•Forms helical nucleocapsid
•P protein•Phosphoprotein - polymerase cofactor•Forms complexes with N and L•Binds to RNA termini
•RNA Genome
Genome Organization Mononegavirales
Filoviridae
Paramyxoviridae
Rhabdoviridae
Genome OrganizationArenaviridae
Bunyaviridae
Influenza A Genome Structure
Virus Coding Strategies•Individual ORFs
•Multiple transcripts with transcription attenuation
•Polyprotein processing•Single transcript to Large polyprotein:
Proteolytic processing•RNA Editing
•Insertion/deletion of additional residues (at a specified site) altering the reading frame
•Multiple ribosomal initiation sites•Stop codon read-through
Virus Replication
RNA-dependent RNA Polymerase(RdRp – L Protein)
•Catalytic subunit of the polymerase complex•Polymerization of nucleotides
•Transcription of mRNA•Capping•Methylation•Polyadenylation
•Genome Replication•Most conserved protein between the
mononegavirales virus families
Source of the RNA-dependent RNA Polymerase
•Host cells do not have a suitable one •Therefore the virus must provide its own•RNA viruses use 2 different strategies to
provide the RdRp:•Synthesized immediately upon entry
and unpackaging of the virion into the cell (positive-sense viruses)•Therefore protein synthesis is the first
step in the replication process•Packaged within the virion (negative-
sense viruses)•Therefore mRNA transcription is the
first step in the replication process
VSV Transcription & Replication
(-) sense ssRNA virus Human Pathogens
Major Viral Target Tissues
Arenaviruses/Bunyaviruses
Arenavirus and Bunyavirus Disease
• Arenaviruses• Mostly rodent viruses
• Human zoonoses• Junin virus
• Argentine hemorrhagic fever• Lassa Fever
• Bunyaviruses• Large group of arthropod-borne viruses
• Human pathogens – hemorrhagic fever• Hantaviruses
• Rodent-borne• Pulmonary Syndrome/Hemorrhagic fever
• Rift Valley Fever virus• Mosquito-borne virus
Filoviruses
Filovirus Disease
Rhabdoviruses
Rhabdoviruses
Rabies virus Pathogenesis
Paramyxoviruses
Paramyxoviruses
Human Respiratory Syncytial virus
•Major cause of lower respiratory tract infections•Rarely life-threatening• Individuals get repeat infections
•Highly infectious•Spread is by exchange of respiratory secretions• Infection confined to respiratory tract
•Globally: 100,000,000 infections/year•200,000 deaths/year
• In USA: All infants by age of 4 years are infected•100,000 hospitalizations/year•Estimated cost of $300,000,000/year (1985) •25-50% of hospital staff infected during
outbreaks
Measles virus•Extremely infectious
•Spreads through contact with respiratory secretions
•Victims are infectious before symptoms are evident
•Develops systemic infection•Globally: 45,000,000 infections/year
•1,000,000 deaths/year• In USA: Infections are rare•Occasional epidemic in unvaccinated
populations•MMR (Measles, mumps, and rubella) vaccine
highly effective (2 shots)
Acute Disseminated EncephalomyelitisMeasles Inclusion Body EncephalitisSubacute Sclerosing Panencephalitis
Neurologic Complications of Measles
Orthomyxoviruses
Orthomyxoviruses
• Influenza•A: Mild to severe disease involving upper and
especially lower respiratory tract•B: Similar spectrum of illness to A but generally
more mild•C: Sporadic upper respiratory illness in humans
•96% of human adults have antibodies•Thogotovirus
•Natural host: Ticks•Also infects: Humans, cattle, goats, waterfowl,
etc.• Isavirus
• Infectious salmon anemia virus
G Neumann et al. Nature 000, 1-9 (2009) doi:10.1038/nature08157
Schematic diagram of influenza A viruses
• Involved in virion uncoating
•Highly conserved
•Target for amantadine
M2 Ion Channel
Hemagglutinin
•Virion release from cell membrane
•Cleavage of sialic acid from cell membrane thus preventing binding by HA
•Target for Oseltamavir (Tamavir) and Zanamivir (Relenza)
Neuraminidase
Influenza virus
Variation and evolution
Influenza Virus Variation
•Antigenic drift•Amino acid changes
•Antigenic shift•Reassortment/exchange of genome
segments between strains•Recombination
•Detected but rare
Reassortment
G Neumann et al. Nature 000, 1-9 (2009) doi:10.1038/nature08157
Genesis of swine-origin H1N1 influenza viruses
Why Pigs?
•Susceptible to infection by influenza virus
•Express both human- and avian-like influenza virus receptors on their tracheal epithelial cells
•Swine may therefore be acting as a “mixing vessel” for the production, replication, and transmission of novel influenza virus reassortments
US Influenza Surveillance 2004-2008
US Influenza Surveillance 2008-2009
US Influenza Surveillance 2010-2011
Fighting back•Antiviral drugs
•Neuraminidase inhibitors•Oseltamavir (Tamavir) and Zanamivir
(Relenza)•Active against influenza A and B
• Ion channel blockers•Amantidine and rimantidine•Prevent release and subsequent transport
of the virus RNP•Active only against Influenza A
•Vaccines• Inactivated•Live attenuated
Antiviral Resistance
Antiviral Resistance 2010 - 2011
Antiviral Resistance 2008 - 2009
Vaccine Development•Inactivated vaccine (TIV)
•Produced from seed stocks in eggs•Live-attenuated vaccine (LAIV)
•Administered as a nasal spray•Vaccines contain three viruses
•H3N2; H1N1; B•Exact strains used change each year
•Strain choice determined by data collected by WHO on currently circulating strains
•Decision on composition made in February and September
Vaccine Strains for the2009-2010 and 2010-2011
Seasons• 2009 – 2010 Seasonal Vaccine
• A components unchanged from 2008-2009• B component changed toB/Brisbane/60/2008
• Related to B/Victoria• 2009 Supplementary Vaccine
• A/California/7/2009 (H1N1)• 2009 pandemic influenza A (H1N1) virus
• 2010 – 2011 AND 2011 – 2012 influenza A (H1N1) virus• A/California/7/2009 (H1N1)-like virus (99.8%
of 2010-2011 viruses match)• A/Perth/16/2009 (H3N2)-like (96.8% of 2010-
2011 viruses match)• B/Brisbane/60/2008 (94% of 2010-2011
viruses match)
And finally, how is influenza spread
between humans and pigs?