Literature Concepts Flashcards
Buruli Ulcerans
This paper investigated the link between Buruli cases and man made environmental changes, especially dams. Many environmental samples collected and observation of cases, which occurred mostly along rivers. Comparision of cases in the region of interest with cases from all over Africa. Case distribution very focal. Dating-> about 10 years after damming.
Leprosy
Investigation of possible animal reservoir for leprosy. Comparision of strains in Armadillos and patients with molecular markers (NOT WGS). Had to sequence a few patients and Armadillos to find which markers they could use. Little diversity between strains, genome degradation, no horizontal gene transfer.
Malaria
Investigation into drug resistant parasites in cambodia, how it spreads and why it seems to always arise there. WGS. Combining WGS and cluster analysis with geography? The origins matter bc. you can adjust policies.
Here they had to discard many samples: must ask yourself if you can still answer the research question!
Plague
Working with ancient DNA to find out if outbreak in the past was caused by Yersinia pestis or not. Comparision of ancient sequences with contemporary ones. For microevolutionary changes: comparision of plague victim sequences with one another.
DNA capture: select medival DNA only by ligating complementary sequences onto solid surface-> hybridization.
Tuberculosis
Showing host-parasite adaptations by showing that people from certain ethnic origin are infected mostly with strain from their “home” region. Phylogeography. Genomic deletions as marker (no horizontal gene transfer).
HIV
Finding the origins of HIV by comparing ancient samples with each other-> genetic distance-> dating via the molecular clock. Chose conserved genes as molecular markers.
COVID
Combining sequencing data with mobility data to show transmission of COVID lineages.
