15 papers on contemporary evolution in human viruses

29 May

In the fall semester of 2014 I taught a reading seminar for master students at SF State on contemporary evolution in human viruses. This blog post contains a list of the papers we read in the seminar.

I posted about this seminar previously here (about the seminar format) and here (no powerpoint allowed), and here (about being nervous for a talk).

The students’ work can be read and seen here (about H1N5), here (polio outbreak), here (Dengue), here (Ebola), here (HIV in court), here (doing my own homework), here (the origin of HIV), here (on bad small things) and here (Hep B).

These are the papers we read:

1. Fast evolution of drug resistance in HIV patient the 1980s


Resumption of HIV antigen production during continuous zidovudine treatment. Lancet. 1988 Feb 20;1(8582):421.
Reiss P, Lange JM, Boucher CA, Danner SA, Goudsmit J.

2. HIV: Doctor infects his ex-girlfriend, phylogenetic evidence in court


Metzker, Michael L., et al. “Molecular evidence of HIV-1 transmission in a criminal case.” Proceedings of the National Academy of Sciences 99.22 (2002): 14292-14297.

3. Very contemporary: the genomics of the West-African Ebola epidemic


Gire, Stephen K., et al. “Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.” Science 345.6202 (2014): 1369-1372.

4. Using phylogenetics to determine origin of Dengue-3 outbreak in Australia

An explosive epidemic of DENV-3 in Cairns, Australia. PLoS One. 2013 Jul 16;8(7):e68137. doi: 10.1371/journal.pone.0068137. Print 2013. Ritchie SA1, Pyke AT, Hall-Mendelin S, Day A, Mores CN, Christofferson RC, Gubler DJ, Bennett SN, van den Hurk AF.

5. Classic paper from Beatrice Hahn’s lab on origin of HIV-1


Gao, Feng, et al. “Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes.” Nature 397.6718 (1999): 436-441.

6. Timing the start of the HIV-1 pandemic


Korber, Bette, et al. “Timing the ancestor of the HIV-1 pandemic strains.”Science 288.5472 (2000): 1789-1796.

7. Where did the polio outbreak in Dominican Republic and Haiti come from?


Kew, Olen, et al. “Outbreak of poliomyelitis in Hispaniola associated with circulating type 1 vaccine-derived poliovirus.” Science 296.5566 (2002): 356-359.

8. Within-patient evolution of vaccine-derived polio virus


Martín, Javier, et al. “Evolution of the Sabin strain of type 3 poliovirus in an immunodeficient patient during the entire 637-day period of virus excretion.”Journal of Virology 74.7 (2000): 3001-3010.

 9. Hepatitis B within-patient evolution


Lim, Seng Gee, et al. “Viral quasi-species evolution during hepatitis Be antigen seroconversion.” Gastroenterology 133.3 (2007): 951-958.

10. Permissive mutations and the evolution of drug resistance in Influenza


Bloom JD, Gong LI, Baltimore D. Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance. Science (New York, NY). 2010;328(5983):1272-1275. doi:10.1126/science.1187816.

11. Controversial experiments on H5N1 Influenza


Airborne transmission of influenza A/H5N1 virus between ferrets. Science. 2012 Jun 22;336(6088):1534-41. doi: 10.1126/science.1213362.
Herfst S1, Schrauwen EJ, Linster M, Chutinimitkul S, de Wit E, Munster VJ, Sorrell EM, Bestebroer TM, Burke DF, Smith DJ, Rimmelzwaan GF, Osterhaus AD, Fouchier RA.

12. Influential study on treatment to prevent HIV


Grant, Robert M., et al. “Preexposure chemoprophylaxis for HIV prevention in men who have sex with men.” New England Journal of Medicine 363.27 (2010): 2587-2599.

 13. HIV drug resistance in women in Africa who were treated to prevent mother-to-child transmission


Eshleman, Susan H., et al. “Nevirapine (NVP) resistance in women with HIV-1 subtype C, compared with subtypes A and D, after the administration of single-dose NVP.” Journal of Infectious Diseases 192.1 (2005): 30-36.

 14. Evolution of Acyclovir resistance in Varicalla-Zoster Virus


Morfin, Florence, et al. “Phenotypic and genetic characterization of thymidine kinase from clinical strains of varicella-zoster virus resistant to acyclovir.”Antimicrobial agents and chemotherapy 43.10 (1999): 2412-2416.


15. Soft and hard sweeps during evolution of drug resistance in HIV

Loss and recovery of genetic diversity in adapting populations of HIV. PLoS Genet. 2014 Jan;10(1):e1004000. doi: 10.1371/journal.pgen.1004000. Epub 2014 Jan 23.
Pennings PS1, Kryazhimskiy S2, Wakeley J3.


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