Question

In 2002, Trask et al. published a study showing that a high frequency of HIV transmissions in Lusaka, Zambia occurred between marriage partners. Specifically, they studied a cohort of married couples where, at the beginning of the study, one partner was infected and the other was not. Later, the uninfected partner became infected. If you were doing this study, how could you use phylogenetic methods to determine whether the newly infected individual was likely infected by his/her partner? Briefly describe your study design and results that would support and results that would refute (you can use drawings if you wish) the partner-partner transmission scenario.

Answer 1

The phylogenetic method can be used for finding out the likely of the uninfected partner to be infected by the disease. The phylogenetic tree is the heart of the evolution process and that is how it is going to find how the virus infected. It can be done by aligning a group of sequences followed by comparing the position of the nucleotides and it helps in establishing how genetically distant or far the strains are. The construction of the evolutionary tree speaks for the underlying principle and gives coherent information about how the infectious virus is genetically similar. There are a lot of assumptions that can be made out of this which helps in stating that changes at one nucleotide position might be independent of other positions.

There are many interferences that can be made from the evolutionary trees are its complete construction. In the tree each pattern of the evolution leaves something unique. There might be lineages that might survive due to natural selection and there might be lineages which can survive upon getting a certain condition. When it comes to HIV, the lineage tree is mostly dense.

Phylogenetic analysis helps in identifying how closely two related sample of HIV are that are taken from both the partners. If the samples are not closely related, it might be possible that the person might not have got it from their partner. Phylogenetic analysis helps in better understanding of a species and hence helps in establishing a connection.