Table 1.
Overview of viral fitness study systems reported in the literature from January 2009 to April 2012
| Host | Virusesa (No. refs/98)b | Host systems | Topics addressed |
|---|---|---|---|
| Human | HIV-1 (27), influenza (10), HCV (6), HBV (2), SARS (1) |
cultured cell lines, ex vivo PBMC, other ex vivo tissue explants, in vivo nonhuman primates, mice, waterfowl, guinea pig, ferrets, field sample surveys | drug resistance, immune escape, vaccine escape, epistasis, role of quasispecies, virulence evolution |
| Animal and insect (Arboviruses) | DENV (5), VSV (5), WNV (4), CHIKV (2) |
cultured cell lines, mosquitoes, chickens, mice, nonhuman primates, field sample surveys | host specificity, alternating host cycles, generalist vs. specialist, drug resistance, virulence determinants, virulence evolution, replication fidelity, role of quasispecies, single cell infection, environmental change, field displacements |
| Vertebrate animals (nonhuman) | SHIV (1), SIV (2), FMDV (1), CPV (1), EIAV (1), IHNV (3), Friend virus complex (1) |
cultured cell lines, ex vivo PBMC, other ex vivo tissue explants, mice, fish, nonhuman primates | immune escape, superinfection, virulence evolution, host specificity, host switching, virus infection cycle, viral load variation, field displacements, MHC evolution |
| Invertebrate animals | baculovirus (1), entomopoxvirus (1), WSSV (1) | insects, shrimp, crab | genetic modifications, genetic diversity, insect biocontrol, virulence |
| Plants | PVY (4), TEV (2), tobamovirus (1), MSV (1), CMVsat (1) |
pepper, tobacco, potato, maize, melon, aphids, leafhoppers | virulence evolution, host specificity, host adaptation, host resistance, mutation effects, mutation interactions, recombination, transmission fitness, transmission tradeoffs |
| Bacteriophage | Qβ (2), ΦX174 (2), F1 (2), Φ6 (2), MS2 (1), SP (1), SP6 (1), G4 (1), Φ2 (1), cyanophage (1) | E. coli, Pseudomonas, Salmonella, cyanobacteria databases (in silico) | mutation effects, host shifts, host range expansion, abiotic environment, antiviral resistance, in silico viral fitness model |
Virus abbreviations: HIV-1, human immunodeficiency virus-1; HCV, hepatitis C virus; HBV, hepatitis B virus; SARS, severe acute respiratory syndrome virus; DENV, dengue virus; VSV, vesicular stomatitis virus; WNV, West Nile virus; CHIKV, chikungunya virus; SHIV, simian/human immunodeficiency virus; SIV, simian immunodeficiency virus; FMDV, foot and mouth disease virus; CPV, canine parvovirus; EIAV, equine infectious anemia virus; IHNV, infectious hematopoietic necrosis virus; Friend complex virus, mixed infection with Friend murine leukemia virus and spleen focus forming virus (defective); WSSV, white spot shrimp virus; PYV, potato Y virus; TEV, tobacco etch virus; MSV, maize streak virus; CMVsat, cucumber mosaic virus satellite RNA.
Number of fitness-related papers published in scientific journals during 2009–2012 using each viral study system, from a total set of 98 viral fitness papers selected to represent breadth of activity in the field. Due to space limitations several papers counted for this Table are not cited in the text, but the full list is available from the authors upon request.