The role of high-risk geographies in the perpetuation of the HIV epidemic in rural South Africa: A spatial molecular epidemiology study

In this study, we hypothesize that HIV geographical clusters (geospatial areas with significantly higher numbers of HIV positive individuals) can behave as the highly connected nodes in the transmission network. Using data come from one of the most comprehensive demographic surveillance systems in Africa, we found that more than 70% of the HIV transmission links identified were directly connected to an HIV geographical cluster located in a peri-urban area. Moreover, we identified a single central large community of highly connected nodes located within the HIV cluster. This module was composed by nodes highly connected among them, forming a central structure of the network that was also connected with the small sparser modules located outside of the HIV geographical cluster. Our study supports the evidence of the high level of connectivity between HIV geographical high-risk populations and the entire community.

The geography and inter-community configuration of new sexual partnership formation in a rural South African population over fourteen years (2003-2016)

Understanding spatial configuration of sexual network structure is critical for effective use of HIV preventative interventions in a community. However, this has never been described at the population level for any setting in sub-Saharan Africa. We constructed the comprehensive geospatial sexual network among new heterosexual partnerships in rural KwaZulu-Natal, South Africa. In the Africa Health Research Institute (AHRI)'s population-based surveillance, we identified stable sexual partnerships among individuals (≥15 years) from 2003 to 2016. Sexual partnerships and residency were recorded via household surveys (every 4-6 months). We geolocated residents and migration events and mapped the geospatial linkages of sexual partners at the start of sexual partnerships. In a grid composed by 108 cells (nodes; 3kmx3km per cell) covering the surveillance area (438km2), we calculated the degree of connectivity and centrality of the nodes and examined their association with HIV prevalence and incidence per cell. Of 2401 new sexual partnerships, 21% (n = 495) had both partners living within the surveillance area at the start of sexual partnerships, and 76% (376/495) were linked to the geographic HIV cluster with high HIV prevalence identified in a peri-urban community. Overall, 57 nodes had at least one connection to another node. The nodes in the peri-urban cluster had higher connectivity (mean = 19, range: 9-32), compared to outside the cluster (6, range: 1-16). The node's degree of connectivity was positively associated with HIV prevalence of the cell (Pearson correlation coefficient = 0.67; p <0.005). The peri-urban cluster contained nine of the 10 nodes that composed of a single large central module in the community. About 17% of sexual partnerships (n = 421) were formed between a resident and a non-resident partner who out-migrated. Most of these non-resident partners lived in KwaZulu-Natal (86.7%), followed by Gauteng (9.7%), and the median distance between a resident and a non-resident partner was 50.1km (IQR: 23.2-177.2). We found that the peri-urban HIV cluster served as the highly connected central node of the network for sexual partnership formation. The network was also connected beyond the surveillance area across South Africa. Understanding spatial sexual network can improve the provision of spatially targeted and effective interventions.

The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics

Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. A number of known and unknown representatives of Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, as well as novel uncharacterized CRESS-DNA viruses, were identified. However, the distribution of sequence reads of viral genomes identified in diseased or healthy birds revealed no statistically significant differences. These findings indicate no association between the occurrence of MAS and enteric viruses. The viral genomes reported in the present study, including a variety of novel viruses, seem part of the normal intestinal microbiota of chickens.

Columbid circoviruses detected in free ranging pigeons from Southern Brazil: insights on PiCV evolution

Pigeon circovirus (PiCV) is taxonomically classified as a member of the Circovirus genus, family Circoviridae. The virus contains a single stranded DNA genome of approximately 2 kb, with minor length variations among different isolates. The occurrence of PiCV infections in pigeons (Columba livia) has been documented worldwide over the past 20 years; however, in Brazil there were still no reports on PiCV detection. This study identifies seven PiCV genomes recovered from domestic pigeons of South Brazil through high-throughput sequencing and shows a high frequency of PiCV infection, through quantitative real-time PCR. Phylogenetic classification was performed by maximum likelihood analysis of the full genomes, ORF V1 (Rep) and ORF C1 (Cap). The results show that either full genome or Cap based analysis allowed PiCV classification into five major clades (groups A to E), where Brazilian sequences were classified as A, C or D. Recombination analyses were carried out with Simplot and RDP4 and the results show that both Rep and Cap ORFs contain several recombination hotspots, pointing to an important role for such events in PiCV evolution.

Rapid and Slow Progressors Show Increased IL-6 and IL-10 Levels in the Pre-AIDS Stage of HIV Infection

Cytokines are intrinsically related to disease progression in HIV infection. We evaluated the plasma levels of Th1/Th2/Th17 cytokines in extreme progressors, including slow (SPs) and rapid (RPs) progressors, who were thus classified based on clinical and laboratory follow-up covering a period of time before the initiation of HAART, ranging from 93–136.5 months for SPs and 7.5–16.5 months for RPs. Analyses were also performed based on the different stages of HIV infection (chronic, pre-HAART individuals—subjects sampled before initiating HAART but who initiated therapy from 12 to 24 months—and those receiving HAART). The plasma cytokine levels of 16 HIV-infected rapid progressors and 25 slow progressors were measured using a Human Th1/Th2/Th17 CBA kit. The IL-6 and IL-10 plasma levels differed significantly between the stages of HIV infection. The IL-6 levels were higher in slow progressors pre-HAART than in chronically infected SPs and HIV-seronegative individuals. The IL-10 levels were higher in slow progressors pre-HAART than in slow progressors receiving HAART and HIV-seronegative controls, and in rapid progressors, the IL-10 levels were higher in pre-HAART subjects than in HIV-seronegative controls. The results reflect the changes in the cytokine profile occurring during different clinical stages in HIV+ subjects. Our results suggest an association between increased IL-6 and IL-10 levels and pre-HAART stages independent of the slow or rapid progression status of the subjects. Thus, increased IL-6 and IL-10 levels could indicate a global inflammatory status and could be used as markers of the disease course in HIV-infected individuals.

New insights into the in silico prediction of HIV protease resistance to nelfinavir

The Human Immunodeficiency Virus type 1 protease enzyme (HIV-1 PR) is one of the most important targets of antiretroviral therapy used in the treatment of AIDS patients. The success of protease-inhibitors (PIs), however, is often limited by the emergence of protease mutations that can confer resistance to a specific drug, or even to multiple PIs. In the present study, we used bioinformatics tools to evaluate the impact of the unusual mutations D30V and V32E over the dynamics of the PR-Nelfinavir complex, considering that codons involved in these mutations were previously related to major drug resistance to Nelfinavir. Both studied mutations presented structural features that indicate resistance to Nelfinavir, each one with a different impact over the interaction with the drug. The D30V mutation triggered a subtle change in the PR structure, which was also observed for the well-known Nelfinavir resistance mutation D30N, while the V32E exchange presented a much more dramatic impact over the PR flap dynamics. Moreover, our in silico approach was also able to describe different binding modes of the drug when bound to different proteases, identifying specific features of HIV-1 subtype B and subtype C proteases.