Pathogen diversity

A pathogen is a disease-causing biological entity capable of replication within a host and transmission between hosts

Broad categories

  1. RNA viruses
  2. DNA viruses
  3. Bacteria
  4. Parasites and fungi

Mutation rate varies with genome size

Viroids are parasitic functionless RNA

Baltimore classification system describes virus groups

RNA virus lifecycle, internal vs surface proteins

Negative-sense RNA virus phylogeny

Negative-sense RNA virus phylogeny

Negative-sense RNA viruses

  • Influenza
  • Measles
  • Ebola
  • Rabies
  • Lassa
  • Hanta
  • Respiratory syncytial virus (RSV)

Positive-sense RNA viruses

  • Flaviviruses: Yellow fever, West Nile, Dengue, Zika, HCV
  • Coronaviruses, including SARS-CoV-2
  • Rhinovirus
  • Polio
  • Norovirus
  • Chikungunya

Retrovirus lifecycle

DNA virus genomes

Bigger genome allows for more functions

DNA viruses

  • Herpesviruses: HSV, Epstein–Barr virus (EBV), Varicella, Cytomegalovirus (CMV), Kaposi's sarcoma-associated herpesvirus (KSHV)
  • Papillomavirus (HPV)
  • Smallpox

Bacterial cell

Bacterial diversity

Core vs pangenome

Recombination is often rampant

Bacterial pathogens

  • Tuberculosis
  • C. difficile
  • Shigella
  • S. aureus (MRSA)
  • Cholera
  • Y. pestis
  • Typhoid
  • Klebsiella

Parasites

Parasite lifecycle

  • Malaria
  • Cryptosporidium
  • Trypanosomes
  • Giardia
  • Leishmaniasis

Influenza

Prototypical antigenically evolving pathogen

Influenza virion

Influenza life cycle

1918 "Spanish flu"

Flu pandemics caused by host switch events

Host switch events often occur through reassortment

Host switch events often occur through reassortment

Reassortment creates different histories

Influenza B does not have pandemic potential

Phylogenetic trees of different influenza lineages

Current circulation patterns of seasonal influenza virus