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

    Kim, Hae-Young / Cuadros, Diego / Wilkinson, Eduan / Junqueira, Dennis M / Oliveira, Tulio de / Tanser, Frank

    PLOS global public health

    2022  Volume 2, Issue 3, Page(s) e0000055

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2022-03-09
    Publishing country United States
    Document type Journal Article
    ISSN 2767-3375
    ISSN (online) 2767-3375
    DOI 10.1371/journal.pgph.0000055
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Introductions of Human-Origin Seasonal H3N2, H1N2 and Pre-2009 H1N1 Influenza Viruses to Swine in Brazil.

    Tochetto, Caroline / Junqueira, Dennis M / Anderson, Tavis K / Gava, Danielle / Haach, Vanessa / Cantão, Mauricio E / Vincent Baker, Amy L / Schaefer, Rejane

    Viruses

    2023  Volume 15, Issue 2

    Abstract: In South America, the evolutionary history of influenza A virus (IAV) in swine has been obscured by historically low levels of surveillance, and this has hampered the assessment of the zoonotic risk of emerging viruses. The extensive genetic diversity of ...

    Abstract In South America, the evolutionary history of influenza A virus (IAV) in swine has been obscured by historically low levels of surveillance, and this has hampered the assessment of the zoonotic risk of emerging viruses. The extensive genetic diversity of IAV in swine observed globally has been attributed mainly to bidirectional transmission between humans and pigs. We conducted surveillance in swine in Brazil during 2011-2020 and characterized 107 H1N1, H1N2, and H3N2 IAVs. Phylogenetic analysis based on HA and NA segments revealed that human seasonal IAVs were introduced at least eight times into swine in Brazil since the mid-late 1980s. Our analyses revealed three genetic clades of H1 within the 1B lineage originated from three distinct spillover events, and an H3 lineage that has diversified into three genetic clades. The N2 segment from human seasonal H1N2 and H3N2 viruses was introduced into swine six times and a single introduction of an N1 segment from the human H1N1 virus was identified. Additional analysis revealed further reassortment with H1N1pdm09 viruses. All these introductions resulted in IAVs that apparently circulate only in Brazilian herds. These results reinforce the significant contributions of human IAVs to the genetic diversity of IAV in swine and reiterate the importance of surveillance of IAV in pigs.
    MeSH term(s) Humans ; Animals ; Swine ; Brazil/epidemiology ; Influenza A Virus, H3N2 Subtype/genetics ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A Virus, H1N2 Subtype/genetics ; Phylogeny ; Seasons ; Influenza A virus
    Language English
    Publishing date 2023-02-19
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15020576
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Factors influencing HIV-1 phylogenetic clustering.

    Junqueira, Dennis M / Sibisi, Zandile / Wilkinson, Eduan / de Oliveira, Tulio

    Current opinion in HIV and AIDS

    2019  Volume 14, Issue 3, Page(s) 161–172

    Abstract: Purpose of review: A major goal of public health in relation to HIV/AIDS is to prevent new transmissions in communities. Phylogenetic techniques have improved our understanding of the structure and dynamics of HIV transmissions. However, there is still ... ...

    Abstract Purpose of review: A major goal of public health in relation to HIV/AIDS is to prevent new transmissions in communities. Phylogenetic techniques have improved our understanding of the structure and dynamics of HIV transmissions. However, there is still no consensus about phylogenetic methodology, sampling coverage, gene target and/or minimum fragment size.
    Recent findings: Several studies use a combined methodology, which includes both a genetic or patristic distance cut-off and a branching support threshold to identify phylogenetic clusters. However, the choice about these thresholds remains an inherently subjective process, which affects the results of these studies. There is still a lack of consensus about the genomic region and the size of fragments that should be used, although there seems to be emerging a consensus that using longer segments, allied with the use of a realistic model of evolution and a codon alignment, increases the likelihood of inferring true transmission clusters. The pol gene is still the most used genomic region, but recent studies have suggested that whole genomes and/or sequences from nef and gp41 are also good targets for cluster reconstruction.
    Summary: The development and application of standard methodologies for phylogenetic clustering analysis will advance our understanding of factors associated with HIV transmission. This will lead to the design of more precise public health interventions.
    MeSH term(s) Animals ; Classification/methods ; Cluster Analysis ; Genome, Viral ; HIV Infections/virology ; HIV-1/classification ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Phylogeny ; Viral Proteins/genetics
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2019-04-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2502511-9
    ISSN 1746-6318 ; 1746-630X
    ISSN (online) 1746-6318
    ISSN 1746-630X
    DOI 10.1097/COH.0000000000000540
    Database MEDical Literature Analysis and Retrieval System OnLINE

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

    Cuadros, Diego F / de Oliveira, Tulio / Gräf, Tiago / Junqueira, Dennis M / Wilkinson, Eduan / Lemey, Philippe / Bärnighausen, Till / Kim, Hae-Young / Tanser, Frank

    PLOS global public health

    2022  Volume 2, Issue 2, Page(s) e0000105

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2022-02-22
    Publishing country United States
    Document type Journal Article
    ISSN 2767-3375
    ISSN (online) 2767-3375
    DOI 10.1371/journal.pgph.0000105
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Complete Genome Sequences of Two Bovine Alphaherpesvirus 5 Subtype C Strains from Southeast Brazil.

    Paim, Willian P / Campos, Fabrício S / Cibulski, Samuel P / Scheffer, Camila M / Tochetto, Caroline / Varela, Ana P M / Junqueira, Dennis M / Mayer, Fabiana Q / Romijn, Phyllis C / Pituco, Edviges M / Franco, Ana C / Spilki, Fernando R / Roehe, Paulo M

    Microbiology resource announcements

    2022  Volume 11, Issue 2, Page(s) e0122821

    Abstract: Bovine alphaherpesvirus 5 causes meningoencephalitis in cattle, belongs to ... ...

    Abstract Bovine alphaherpesvirus 5 causes meningoencephalitis in cattle, belongs to the
    Language English
    Publishing date 2022-02-10
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.01228-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics.

    Lima, Diane A / Cibulski, Samuel P / Tochetto, Caroline / Varela, Ana Paula M / Finkler, Fabrine / Teixeira, Thais F / Loiko, Márcia R / Cerva, Cristine / Junqueira, Dennis M / Mayer, Fabiana Q / Roehe, Paulo M

    Virus research

    2018  Volume 261, Page(s) 9–20

    Abstract: 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 ... ...

    Abstract 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.
    MeSH term(s) Animals ; Chickens ; Feces/virology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Malabsorption Syndromes/veterinary ; Malabsorption Syndromes/virology ; Metagenomics ; Poultry Diseases/virology ; Viruses/classification ; Viruses/genetics
    Language English
    Publishing date 2018-12-10
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2018.12.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: New insights into the in silico prediction of HIV protease resistance to nelfinavir.

    Antunes, Dinler A / Rigo, Maurício M / Sinigaglia, Marialva / de Medeiros, Rúbia M / Junqueira, Dennis M / Almeida, Sabrina E M / Vieira, Gustavo F

    PloS one

    2014  Volume 9, Issue 1, Page(s) e87520

    Abstract: 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 ...

    Abstract 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.
    MeSH term(s) Acquired Immunodeficiency Syndrome/drug therapy ; Acquired Immunodeficiency Syndrome/enzymology ; Acquired Immunodeficiency Syndrome/genetics ; Amino Acid Substitution ; Drug Resistance, Viral ; HIV Protease/chemistry ; HIV Protease/genetics ; HIV Protease Inhibitors/chemistry ; HIV-1/enzymology ; HIV-1/genetics ; Humans ; Mutation, Missense ; Nelfinavir/chemistry
    Chemical Substances HIV Protease Inhibitors ; HIV Protease (EC 3.4.23.-) ; Nelfinavir (HO3OGH5D7I)
    Language English
    Publishing date 2014-01-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0087520
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Rapid and Slow Progressors Show Increased IL-6 and IL-10 Levels in the Pre-AIDS Stage of HIV Infection.

    de Medeiros, Rúbia M / Valverde-Villegas, Jacqueline M / Junqueira, Dennis M / Gräf, Tiago / Lindenau, Juliana D / de Mello, Marineide G / Vianna, Priscila / Almeida, Sabrina E M / Chies, Jose Artur B

    PloS one

    2016  Volume 11, Issue 5, Page(s) e0156163

    Abstract: 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 ...

    Abstract 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.
    MeSH term(s) Acquired Immunodeficiency Syndrome/blood ; Adult ; Disease Progression ; Female ; Follow-Up Studies ; HIV Infections/blood ; HIV Infections/pathology ; HIV-1 ; Humans ; Interleukin-10/blood ; Interleukin-6/blood ; Male ; Middle Aged ; Prodromal Symptoms ; Retrospective Studies ; Time Factors
    Chemical Substances IL10 protein, human ; Interleukin-6 ; Interleukin-10 (130068-27-8)
    Language English
    Publishing date 2016-05-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0156163
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Temporal dynamics of HIV-1 circulating subtypes in distinct exposure categories in southern Brazil

    Almeida, Sabrina EM / de Medeiros, Rubia M / Junqueira, Dennis M / Gräf, Tiago / Passaes, Caroline PB / Bello, Gonzalo / Morgado, Mariza G / L Guimarães, Monick

    Virology journal. 2012 Dec., v. 9, no. 1

    2012  

    Abstract: BACKGROUND: The HIV-1 epidemic in Brazil is predominantly driven by subtype B. However, in Brazilian Southern region subtype C prevails and a relatively high AIDS incidence rate is observed. The aim of the present study was to assess the temporal ... ...

    Abstract BACKGROUND: The HIV-1 epidemic in Brazil is predominantly driven by subtype B. However, in Brazilian Southern region subtype C prevails and a relatively high AIDS incidence rate is observed. The aim of the present study was to assess the temporal dynamics of HIV-1 subtypes circulating in patients from distinct exposure categories in Southern Brazil. For this purpose 166 HIV-1 samples collected at the years of 1998 (group I) and 2005–2008 (group II) were analyzed. RESULTS: Analysis of group I revealed statistically significant (p < 0.05) associations between MSM and subtype B as well as between IDU and subtype C; while no statistical significant association between HIV-1 subtypes and exposure category was verified for group II. An overall temporal increase in the prevalence of subtype C and BC recombinants was observed in both HET and MSM populations, accompanied by a proportional decrease in the prevalence of the pure subtype B. CONCLUSIONS: The present study shows an association between HIV subtypes and exposure categories at the middle 1990s in Southern Brazil. Our findings suggest that MSM and IDU populations might have played a major role in the introduction and initial dissemination of subtypes B and C, respectively, in Southern Brazil. This study also suggests a trend towards homogenization of HIV-1 strains across distinct exposure categories as a consequence of an overall increase in the prevalence of subtype C and BC recombinants in both HET and MSM populations.
    Keywords Human immunodeficiency virus 1 ; homogenization ; patients ; temporal variation ; Brazil
    Language English
    Dates of publication 2012-12
    Size p. 306.
    Publishing place BioMed Central
    Document type Article
    ISSN 1743-422X
    DOI 10.1186/1743-422X-9-306
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Temporal dynamics of HIV-1 circulating subtypes in distinct exposure categories in southern Brazil

    Almeida Sabrina EM / de Medeiros Rubia M / Junqueira Dennis M / Gräf Tiago / Passaes Caroline PB / Bello Gonzalo / Morgado Mariza G / L Guimarães Monick

    Virology Journal, Vol 9, Iss 1, p

    2012  Volume 306

    Abstract: Abstract Background The HIV-1 epidemic in Brazil is predominantly driven by subtype B. However, in Brazilian Southern region subtype C prevails and a relatively high AIDS incidence rate is observed. The aim of the present study was to assess the temporal ...

    Abstract Abstract Background The HIV-1 epidemic in Brazil is predominantly driven by subtype B. However, in Brazilian Southern region subtype C prevails and a relatively high AIDS incidence rate is observed. The aim of the present study was to assess the temporal dynamics of HIV-1 subtypes circulating in patients from distinct exposure categories in Southern Brazil. For this purpose 166 HIV-1 samples collected at the years of 1998 (group I) and 2005–2008 (group II) were analyzed. Results Analysis of group I revealed statistically significant (p < 0.05) associations between MSM and subtype B as well as between IDU and subtype C; while no statistical significant association between HIV-1 subtypes and exposure category was verified for group II. An overall temporal increase in the prevalence of subtype C and BC recombinants was observed in both HET and MSM populations, accompanied by a proportional decrease in the prevalence of the pure subtype B. Conclusions The present study shows an association between HIV subtypes and exposure categories at the middle 1990s in Southern Brazil. Our findings suggest that MSM and IDU populations might have played a major role in the introduction and initial dissemination of subtypes B and C, respectively, in Southern Brazil. This study also suggests a trend towards homogenization of HIV-1 strains across distinct exposure categories as a consequence of an overall increase in the prevalence of subtype C and BC recombinants in both HET and MSM populations.
    Keywords HIV-1 ; Brazil ; Subtypes ; Exposure categories ; Temporal dynamics ; Microbiology ; QR1-502 ; Science ; Q ; DOAJ:Microbiology ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Medicine (General) ; R5-920 ; Medicine ; R ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
    Subject code 306
    Language English
    Publishing date 2012-12-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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