Day 2: Liveblogging the Molecular Evolution/Infectious Diseases Keystone Conference

Day 2
Morning Session: DNA viruses
Elliot Lefkowitz gave the opening session today. He spoke about gene acquisition and loss as driving factors in speciation of poxviruses. He focused on the orthopoxviridae (the group containing vaccinia, variola, monkeypox, and other pathogens). They have developed computational tools to do gene prediction and annotation across all known poxvirus genomes. This has allowed them to get around problems with inconsistency in annotation among deposited sequences. Gene acquisition in the core region appears to play much less of a role in orthopoxvirus speciation. These techniques have also enabled them to look at the process of gene fragmentation and loss over the evolutionary history of these viruses. They have begun to test these predictions, especially with regard to promoters. Some of this work is in a recent PNAS paper:
Assarsson, E., Greenbaum, J.A., Sundstrom, M., Schaffer, L., Hammond, J.A., Pasquetto, V., Oseroff, C., Hendrickson, R.C., Lefkowitz, E.J., Tscharke, D.C., Sidney, J., Grey, H.M., Head, S.R., Peters, B., Sette, A. (2008). Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proceedings of the National Academy of Sciences, 105(6), 2140-2145. DOI: 10.1073/pnas.0711573105

The parvovirus family was the subject of the next talk, by Colin Parrish from Cornell. His title was “How to change your host range in a few easy steps: canine and feline parvoviruses.” In the 1970s, there was a host range shift within a feline parvovirus (FPV) that allowed it to infect dogs rather than cats. Within a year or two, this (now) canine parvovirus (CPV-2) spread through a wide geographic area and shifted again to allow efficient spread to both cats and dogs. All of the canine parvoviruses today appear to be descendants of this virus, and most are in the CPV-2a group. Nearly whole genome analysis has allowed description of geographically distinct clades within the CPV-2a group. Certain residues on the threefold spike of the capsid protein appear to control host range. The host receptor is the transferrin receptor, and binding to it triggers chathrin-mediated uptake.

Thomas Schultz talked about diversity within the rhadinoviruses (RV, which are gamma-2-herpesviruses, including KSHV – the causative agent of Kaposi’s sarcoma). There are two major branches within the RV lineage, and these are distant relatives of Epstein-Barr virus (EBV). Within KSHV, there was an early split into a number of geographically distinct lineages. More recently, there has been significant recombination among these lineages as well as introduction of sequences at the ends of the genome. KSHV protein K1, which contains hypervariable regions and has oncogenic properties, is located at one end of the genome at a position analogous to LMP-1 in EBV. KSHV protein K15, which activates host cell proinflammatory signaling, is at the other end. Homologues of K15 appear in other related viruses and seem to have distinct signaling profiles.

Mary Odom from the Lefkowitz lab gave a short talk about gene acquisition by poxviruses via horizontal transfer. She has developed bioinformatic techniques to look for putative transfer events. By looking at multiple databases (viral vs. eukaryotic or viral vs. bacterial), they can generate 2D plots of best BLASTP scores to generate leads.

Edgar Sevilla-Reyes gave a short talk about the dynamic gene content of human cytomegalovirus (CMV). Gene disrupting mutations occur after only a few passages in vitro. After more passages, larger deletions predominate, especially at the ends of the UL sequence. They studied genetic integrity at the ends of UL for 22 CMV isolates and found striking clustering of the sites of mutations. These same sites were also found to be mutated in a subset of non-passaged clinical CMV isolates, raising the question of what the selective pressures on these sites might be.


Workshop
short talk session

Nels Elde described an evolutionary arms race between poxviruses and their hosts. Protein kinase R (PKR) is a host factor with antiviral effects. In its dimeric (active) form, PKR phosphorylates eIF2alpha, which leads to a global transcriptional arrest. This blocks viral protein synthesis and can aid in host defense. As evidence of the importance of this strategy, several pathogenic viruses encode substrate mimics to block PKR. These mimics (K3L is the poxvirus example used here) are structurally similar to eIF2aplha and can block the PKR/eIF2alpha interaction. Analysis of the dN/dS ratio suggested that PKR was under positive selection but eIF2alpha was subject to purifying selection (i.e. PKR is undergoing adaptive evolution, while changes in eIF2alpha are generally selected against). By mapping specific sites in all three of the involved proteins (PKR, eIF2alpha, and K3L), the picture of a rapidly evolving selective race appears.

Willem van Ballegooijen talked about surveillance of hepatitis B virus (HBV) sequences following targeted vaccination of risk groups (not global vaccination!) in the Netherlands, starting in 1998. He used coalescent-based analysis of HBV DNA sequence and Bayesian analysis to provide statistical support for a decreasing incidence of infection, starting in about 2000.

Intrahost diversity and evolutionary dynamics of influenza were the topics of
Elodie Ghedin’s talk. Because of evidence of reassortment among cocirculating clades of influenza during a single season (see yesterday’s talks), she hypothesized that coinfection of individuals must occur. Using samples from human isolates, she examined diversity among influenza sequences. She found convincing evidence for double and even triple infections with influenza subtypes (which is something that we see clinically as well) and hypothesizes that this may be a source for flu reassortment and diversity during the active season.

Ma Luo from the University of Mannitoba discussed evolutionary interactions between HLA alleles and HIV-1 infection within an East African sex worker population. She studied women from the Pumwani sexworker cohort (high prevalence) and a mother-child cohort (low prevalence). They examined linkage of HLA class I alleles to the risk of seroconversion during the study and grouped these into “protective” and “susceptible” alleles. Over time (1985-1992 vs. 1993-2001) there was a decrease in the susceptible allele prevalence and an increase in the protective allele prevalence in the high-risk cohort.

Molly OhAinle talked about the evolution of the APOBEC3 locus of anti-retroviral elements in hominids. She presented evidence that the anti-retroelement of APOBEC3H, which is a broadly active member of the family, has undergone very recent changes. Macaque APOBEC3H efficiently inhibits HIV infectivity, which human APOBEC3H does not. The loss of this activity of APOBEC3H appears to have occurred independently at least twice in recent human evolution. Human APOBEC3H is considerably less stable than that of other primates, which accounts for its lack of activity. Ancestral sequence reconstitution suggests that recent human ancestors had stable (effective) APOBEC3H. Is there selection for non-functional APOBEC3H alleles in the human population?

Bouke de Jong (NYU) examined the phylogeography of the Mycobacterium tuberculosis complex, specifically the appearance of M. africanum in West Africa. By looking at genotypes of organisms from smear-positive tuberculosis (TB) cases and their contacts. A significant portion of TB in the Gambia appears to be caused by M. africanum. There are differences in risk of progression but not transmission or severity when comparing M. africanum with M. tuberculosis.

Joel Wertheim used Bayesian dating strategies to calibrate a molecular clock for SIV evolution. They used envelope and polymerase sequences to develop their model, which allowed specific estimation of dates for divergence of SIV clades as well as HIV-2.

Tsan Yuk Lam discussed transmission dynamics of natural reassortant H5N1 influenza in Indonesia. His analysis is consistent with a single clade arising from a single H5N1 introduction from China. There has been intralineage reassortment within Indonesia over a short time.

Evening Session: Retroviruses

Beatrice Hahn (UAB): Origins of HIV-1 and adaptation to its human host
John Moran (U. Michigan): Studies of a human transposable element (LINE elements)
Nathan Wolfe (UCLA): Cross-species transmission and establishment of novel human retroviruses.
Christine Clouser (U. Minnesota): Short talk: Exploiting the mutation rate of HIV