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Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
TLDR
It is shown that the new swine-origin influenza A (H1N1) virus emerged in Mexico and the United States was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak.
Phylogenetic evidence for recombination in dengue virus.
TLDR
The breakpoints were found to be in similar positions, within the fusion peptide of the envelope protein, demonstrating that a single recombination event occurred prior to the divergence of these two strains, the first report of recombination in natural populations of dengue virus.
The emergence of HIV/AIDS in the Americas and beyond
TLDR
Using HIV-1 gene sequences recovered from archival samples from some of the earliest known Haitian AIDS patients, it is found that subtype B likely moved from Africa to Haiti in or around 1966 and then spread there for some years before successfully dispersing elsewhere.
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960
TLDR
The recovery of viral gene sequences from decades-old paraffin-embedded tissues opens the door to a detailed palaeovirological investigation of the evolutionary history of HIV-1 that is not accessible by other methods.
Evolutionary aspects of recombination in RNA viruses.
TLDR
This work presents a meta-analyses of the immune system’s response to the presence of infectious disease in the context of organ transplants and its role in promoting wound healing.
The Isolation of Nucleic Acids from Fixed, Paraffin-Embedded Tissues–Which Methods Are Useful When?
TLDR
This study investigates the quality of nucleic acids recovered from a test panel of fixed specimens that have been manipulated following a number of the published protocols, and provides a quick reference table that can be used to determine appropriate protocols for particular aims.
Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities
Although bacteria are continually acquired over the lifetime of an individual, the phylogenetic relationships of great ape species is mirrored in the compositions of their gut microbial communities.
Potent protection against H5N1 and H7N9 influenza via childhood hemagglutinin imprinting
TLDR
Using data from all known human cases of these viruses, it is shown that an individual’s first IAV infection confers lifelong protection against severe disease from novel hemagglutinin (HA) subtypes in the same phylogenetic group, and statistical modeling shows that protective HA imprinting is the crucial explanatory factor.
Molecular Ecology and Natural History of Simian Foamy Virus Infection in Wild-Living Chimpanzees
TLDR
The first comprehensive survey of simian foamy viruses infection in free-ranging chimpanzees using newly developed, fecal-based assays indicates that SFVcpz is widely distributed among all chimpanzee subspecies and is transmitted predominantly by horizontal routes.
DNA Extraction from Dry Museum Beetles without Conferring External Morphological Damage
TLDR
This paper describes a method for the extraction of PCR-amplifiable mitochondrial and nuclear DNA from dry insects without causing external morphological damage and demonstrates the efficacy of this method on beetles collected up to 50 years ago.
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