Lagos Bat Virus, South Africa

Three more isolates of Lagos bat virus were recently recovered from fruit bats in South Africa after an apparent absence of this virus for 13 years. The sporadic occurrence of cases is likely due to inadequate surveillance programs for lyssavirus infections among bat populations in Africa

The Role of DNA Barcodes in Understanding and Conservation of Mammal Diversity in Southeast Asia

Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning.DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized.DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning

Histopathology rabies encephalitis due to Duvenhage virus.

<p>Rabies encephalitis (lyssavirus; genotype 4) brain pathology: cerebral cortex and anti-RNP Immunohistochemistry. (A) (HE staining): frontal cortex: extensive neuropil vacuolization and neuronal cell loss. (B) Few residual cortical neurons (arrows). (C) (HE staining): perivascular lymphocytic inflammatory infiltrates (arrows). (D and E) Anti-RNP immunoreactivity within the frontal cortex. Several neuronal cells show immunopositivity (arrows and insert in [E]) with multiple antigenic masses present in the neuronal cytoplasm, as well as in dendrites and axon. Scale bar: (A, B) 100 µm; (C, D) 60 µm; (E) 40 µm; insert in (E): 12 µm.</p

Immunofluorescence tests with antirabies nucleocapside conjugate.

<p>Immunofluorescence of murine neuroblastoma cells using antirabies nucleocapside conjugate (Bio-Rad). The arrow points to cells with positive green immunofluorescence. The right picture is a magnification of the left with the scale bar.</p

MRI brain on day 6 of admission.

<p>Axial T2-weighted images in a patient with rabies due to Duvenhage virus infection, at day 6 after admission; hyperintense signal in the posterior part of the medulla oblongata (arrow).</p

Lyssa virus phylogenetic tree with presented rabies case embedded.

<p>Phylogenetic tree of the presented rabies case (sequence arrowed) and representative <i>Lyssavirus</i> genomes. Mega 3.1 tree (neighbour joining, Kimura 2–parameter, 1,000 bootstrap values) based on a 367–base pair fragment in the nucleoprotein region. Bootstrap percentages higher than 75% are indicated. Genotype 1  =  rabies virus (RV); Genotype 2  =  Lagos bat virus (LBV); Genotype 3  =  Mokola virus (MV); Genotype 4  =  Duvenhage virus (DV); Genotype 5  =  European bat lyssavirus (EBLV) 1a and 1b; Genotype 6  =  European bat lyssavirus (EBVL) 2a and 2b; Genotype 7  =  Australian bat lyssavirus (ABLV). Present virus isolate in Genotype 4: DV E2007011420 (arrowed).</p

MRI brain on day 16 of admission (4 days before death).

<p>Axial T-2 weighted images in a patient with rabies due to Duvenhage virus infection, at day 17 after admission show increased signal in the posterior part of the medulla oblongata (arrow) and in the basal ganglia (arrows).</p

Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study

Age-mixing patterns are of key importance for understanding the dynamics of human immunodeficiency virus (HIV)-epidemics and target public health interventions. We use the densely sampled Swiss HIV Cohort Study (SHCS) resistance database to study the age difference at infection in HIV transmission pairs using phylogenetic methods. In addition, we investigate whether the mean age difference of pairs in the phylogenetic tree is influenced by sampling as well as by additional distance thresholds for including pairs. HIV-1 pol-sequences of 11,922 SHCS patients and approximately 240,000 Los Alamos background sequences were used to build a phylogenetic tree. Using this tree, 100 per cent down to 1 per cent of the tips were sampled repeatedly to generate pruned trees (N = 500 for each sample proportion), of which pairs of SHCS patients were extracted. The mean of the absolute age differences of the pairs, measured as the absolute difference of the birth years, was analyzed with respect to this sample proportion and a distance criterion for inclusion of the pairs. In addition, the transmission groups men having sex with men (MSM), intravenous drug users (IDU), and heterosexuals (HET) were analyzed separately. Considering the tree with all 11,922 SHCS patients, 2,991 pairs could be extracted, with 954 (31.9 per cent) MSM-pairs, 635 (21.2 per cent) HET-pairs, 414 (13.8 per cent) IDU-pairs, and 352 (11.8 per cent) HET/IDU-pairs. For all transmission groups, the age difference at infection was significantly (P < 0.001) smaller for pairs in the tree compared with randomly assigned pairs, meaning that patients of similar age are more likely to be pairs. The mean age difference in the phylogenetic analysis, using a fixed distance of 0.05, was 9.2, 9.0, 7.3 and 5.6 years for MSM-, HET-, HET/IDU-, and IDU-pairs, respectively. Decreasing the cophenetic distance threshold from 0.05 to 0.01 significantly decreased the mean age difference. Similarly, repeated sampling of 100 per cent down to 1 per cent of the tips revealed an increased age difference at lower sample proportions. HIV-transmission is age-assortative, but the age difference of transmission pairs detected by phylogenetic analyses depends on both sampling proportion and distance criterion. The mean age difference decreases when using more conservative distance thresholds, implying an underestimation of age-assortativity when using liberal distance criteria. Similarly, overestimation of the mean age difference occurs for pairs from sparsely sampled trees, as it is often the case in sub-Saharan Africa