Pathogen diversity
A pathogen is a disease-causing biological entity capable of replication within a host and transmission between hosts
Broad categories
- RNA viruses
- DNA viruses
- Bacteria
- 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, monkeypox
Bacterial cell
Bacterial diversity
Core vs pangenome
Divergent evolutionary histories between core chromosome and plasmids
Recombination is often rampant
Bacterial pathogens
- C. difficile
- Cholera
- Klebsiella
- Neisseria gonorrhoeae
- S. aureus (MRSA)
- Shigella
- Streptococcus pneumoniae
- Tuberculosis
- Typhoid
- Y. pestis
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
SARS-CoV-2
Genetic relationships of globally sampled SARS-CoV-2 to present
New variants rapidly replace existing diversity
S1 evolution remarkably fast relative to seasonal influenza
