Phylogenetic (molecular) epidemiology. When the source and age of an epidemic needs to be estimated, phylogenetic analysis of the pathogen can be very informative. This includes forensic analysis where the genetic evidence continues to evolve after the alleged event. Recent examples of this include:

Both HCF and HIV-1 have been shown through phylogenetic analysis to be transmitted from an orthopedic surgeon or dentist to more than one of their patients in the United States, events that have happened during the recent decade.

During 1998, a Louisiana physician was sentenced to 50 years in prison for injecting his girl friend with HIV-1 (an event that occurred during 1994 and ostensibly involved a vitamin injection).

During 1998, five Bulgarian nurses and one Palestinian doctor were accused of infecting 418 children with HIV-1 and HCV at Al-Fateh Hospital in Benghazi, Libya (these six where held in a Libyan prison until early 2008). Phylogenetic evidence published in a 2006 issue of Nature in part exonerated the six medical workers and led to their release from the Libyan prison.

HIV-1 was thought to have been introduced into the human population from chimpanzee kidneys utilized for the culture media of polio virus in the country of Democratic Republic of Congo (formerly Belgian Congo and Zaire) during the 1950’s by the Wistar Company based out of Philadelphia, Pennsylvania. An alternative hypothesis was that HIV-1 was introduced into the human population via the bush-meat trade (wild slaughter of chimp and other animal species and the urban marketing of the rendered meats), which has occurred most prominently to the west of the Democratic Republic of Congo, across the Zaire River, in countries such as the Republic of Congo, Gabon, and Cameroon. Notably, the Zaire River serves as a boundary for two chimp subspecies that are each monophyletic (Pan troglodytes schweinfurthii, the eastern chimp, to the east, and Pan troglodytes troglodytes, the central chimp, to the west of the Zaire River).

Phylogenetic analysis has show that the origin of virulent strains of human influenza virus has been the result of recombination among human, bird, and swine influenza viruses such that human influenza can occasionally pick up novel coat proteins that escape detection of the human immune system (text pages 532-537).

See chapter 1, pages 25-27, figures 1.21a and 1.21b, The Origin of HIV, and related text questions, pages 30-31, #1 (At least 60 years ago, the first strain of SIV was transmitted to human populations from the chimpanzee. Molecular phylogenies reveal a HIV1 founder event with a SIV source from the chimpanzee.) and #12 (If SIV was derived from HIV, then a phylogeny would have to be resolved in which the earliest ancestral nodes were optimized as HIV). See also chapter 14, pages 532-537, figures 14.7 – 14.10, Flu virus evolution, and related text questions, page 570, #10 & Figure 14.33 (the source of the North American West Nile encephalitis virus was NOT from resident strains of this virus but rather from an immigrant strain).

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