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Su Y, Wu Y, Ye M, Zhao C, Li L, Cai J, Chakraborty T, Yang L, Wang D, Zhou L. Star1 gene mutation reveals the essentiality of 11-ketotestosterone and glucocorticoids for male fertility in Nile Tilapia (Oreochromis niloticus). Comp Biochem Physiol B Biochem Mol Biol 2024; 273:110985. [PMID: 38729293 DOI: 10.1016/j.cbpb.2024.110985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Steroidogenic acute regulatory protein (Star) plays an essential role in the biosynthesis of corticosteroids and sex steroids by mediating the transport of cholesterol from the outer to the inner membrane of mitochondria. Two duplicated Star genes, namely star1 and star2, have been identified in non-mammalian vertebrates. To investigate the roles of star genes in fish steriodogenesis, we generated two mutation lines of star1-/- and star1-/-/star2-/- in Nile tilapia (Oreochromis niloticus). Previous studies revealed that deficiency of star2 gene caused delayed spermatogenesis, sperm apoptosis and sterility in male tilapia. Our present data revealed that mutation of star genes impaired male fertility. Disordered seminiferous lobules and spermatic duct obstruction were found in the testis of both types of mutants. Moreover, significant decline in semen volume, sperm abnormality and impaired fertility were also detected in star1-/- and star1-/-/star2-/- males. In star1-/- male fish, lipid accumulation, up-regulation of steroidogenic enzymes, and significant decline of androgens were found. Additionally, hyperplasic interrenal cells, elevated steroidogenic gene expression level and decline of serum glucocorticoids were detected in star1 mutants. Intriguingly, either 11-KT or cortisol supplementation successfully rescued the impaired fertility of the star1-/- mutants. Taken together, these results further indicate that Star1 might play critical roles in the production of both 11-KT and glucocorticoids, which are indispensable for the maintenance of male fertility in fish.
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Affiliation(s)
- Yun Su
- Fisheries Engineering Institute, Chinese Academy of Fishery Sciences, Beijing, PR China; Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - You Wu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Maolin Ye
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Chenhua Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Lu Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Jing Cai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing 400715, PR China
| | | | - Lanying Yang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing 400715, PR China.
| | - Linyan Zhou
- Fisheries Engineering Institute, Chinese Academy of Fishery Sciences, Beijing, PR China.
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Zhou Y, Cui M, Hong Z, Huang S, Zhou S, Lyu H, Li J, Lin Y, Huang H, Tang W, Sun C, Huang W. High Genetic Diversity of HIV-1 and Active Transmission Clusters among Male-to-Male Sexual Contacts (MMSCs) in Zhuhai, China. Viruses 2023; 15:1947. [PMID: 37766353 PMCID: PMC10535991 DOI: 10.3390/v15091947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
Monitoring genetic diversity and recent HIV infections (RHIs) is critical for understanding HIV epidemiology. Here, we report HIV-1 genetic diversity and RHIs in blood samples from 190 HIV-positive MMSCs in Zhuhai, China. MMSCs with newly reported HIV were enrolled from January 2020 to June 2022. A nested PCR was performed to amplify the HIV polymerase gene fragments at HXB2 positions 2604-3606. We constructed genetic transmission network at both 0.5% and 1.5% distance thresholds using the Tamura-Nei93 model. RHIs were identified using a recent infection testing algorithm (RITA) combining limiting antigen avidity enzyme immunoassay (LAg-EIA) assay with clinical data. The results revealed that 19.5% (37/190) were RHIs and 48.4% (92/190) were CRF07_BC. Two clusters were identified at a 0.5% distance threshold. Among them, one was infected with CRF07_BC for the long term, and the other was infected with CRF55_01B recently. We identified a total of 15 clusters at a 1.5% distance threshold. Among them, nine were infected with CRF07_BC subtype, and RHIs were found in 38.8% (19/49) distributed in eight genetic clusters. We identified a large active transmission cluster (n = 10) infected with a genetic variant, CRF79_0107. The multivariable logistic regression model showed that clusters were more likely to be RHIs (adjusted OR: 3.64, 95% CI: 1.51~9.01). The RHI algorithm can help to identify recent or ongoing transmission clusters where the prevention tools are mostly needed. Prompt public health measures are needed to contain the further spread of active transmission clusters.
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Affiliation(s)
- Yi Zhou
- Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China;
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai 519060, China; (H.L.); (H.H.)
| | - Mingting Cui
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China;
| | - Zhongsi Hong
- Department of Infectious Diseases, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519001, China
| | - Shaoli Huang
- School of Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hang Lyu
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai 519060, China; (H.L.); (H.H.)
| | - Jiarun Li
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai 519060, China; (H.L.); (H.H.)
| | - Yixiong Lin
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai 519060, China; (H.L.); (H.H.)
| | - Huitao Huang
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai 519060, China; (H.L.); (H.H.)
| | - Weiming Tang
- Dermatology Hospital of Southern Medical University, Guangzhou 510315, China
- Southern Medical University Institute for Global Health and Sexually Transmitted Diseases, Guangzhou 510315, China
- University of North Carolina Project-China, Guangzhou 510315, China
| | - Caijun Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China;
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Wenyan Huang
- Department of HIV Prevention, Zhuhai Center for Disease Control and Prevention, Zhuhai 519060, China; (H.L.); (H.H.)
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Yamamoto T, Kaneshima T, Tsukano K, Michiue T. The heparan sulfate modification enzyme, Hs6st1, governs Xenopus neuroectodermal patterning by regulating distributions of Fgf and Noggin. Dev Biol 2023; 496:87-94. [PMID: 36739958 DOI: 10.1016/j.ydbio.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
The nervous system has various types of cells derived from three neuroectodermal regions: neural plate (NP), neural crest (NC), and preplacodal ectoderm (PPE). Differentiation of these regions is regulated by various morphogens. However, regulatory mechanisms of morphogen distribution in neural patterning are still debated. In general, an extracellular component, heparan sulfate (HS), is essential to regulate morphogen gradients by modulating morphogen binding. The present study focused on an HS modification enzyme, heparan sulfate 6-O-sulfotransferase 1 (Hs6st1), which is highly expressed during the neurula stage in Xenopus. Our present in situ hybridization analysis revealed that Hs6st1 is expressed in the lateral sensorial layer of neuroectoderm. Overexpression of Hs6st1 expands Sox3 (NP marker gene) expression, and slightly dampens FoxD3 (NC marker) expression. Hs6st1 knockout using the CRISPR/Cas9 system also expands the neural plate region, followed by retinal malformation. These results imply that 6-O sulfation, mediated by Hs6st1, selectively regulates morphogen distribution required for neuroectodermal patterning. Among morphogens required for patterning, Fgf8a accumulates on Hs6st1-expressing cells, whereas a secreted BMP antagonist, Noggin, diffuses away from those cells. Thus, cell-autonomous 6-O sulfation of HS at the sensorial layer of neuroectoderm also affects neuroectodermal patterning in neighboring regions, including neural plate and neural crest, not only through accumulation, but also through dispersal of specific morphogens.
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Affiliation(s)
- Takayoshi Yamamoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
| | - Toki Kaneshima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Kohei Tsukano
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Tatsuo Michiue
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Torres-Cifuentes DM, Antonio-Campos A, Farfán-Pira KJ, Sánchez-Cordero V, Rivas N, Alejandre-Aguilar R. Heteroduplex assay of cytochrome b expanding the toolbox for the identification of triatomine (Hemiptera: Reduviidae) vectors of Chagas disease. JOURNAL OF VECTOR ECOLOGY : JOURNAL OF THE SOCIETY FOR VECTOR ECOLOGY 2022; 47:235-238. [PMID: 36314680 DOI: 10.52707/1081-1710-47.2.235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Diana Milena Torres-Cifuentes
- Instituto de Investigación sobre la Salud Pública, Universidad de la Sierra Sur (UNSIS), Sistema de Universidades Estatales de Oaxaca (SUNEO). Guillermo Rojas Mijangos s/n, Col. Ciudad Universitaria, 70800 Miahuatlán de Porfirio Díaz, Oaxaca, Mexico
| | - Alberto Antonio-Campos
- Laboratorio de Entomología Médica, Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Calle Plan de Ayala s/n, Santo Tomás, Miguel Hidalgo, 11340, CDMX, Mexico
- Departamento de Zoología, Instituto de Biología. Universidad Nacional Autónoma de México, Copilco 3000. Ciudad Universitaria, Coyoacán, 04510, CDMX, Mexico
| | - Keity J Farfán-Pira
- Laboratorio de Biología del Desarrollo y de Sistemas, Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Col. San Pedro Zacatenco, Alcaldía Gustavo A. Madero, 07360, CDMX, Mexico
| | - Víctor Sánchez-Cordero
- Departamento de Zoología, Instituto de Biología. Universidad Nacional Autónoma de México, Copilco 3000. Ciudad Universitaria, Coyoacán, 04510, CDMX, Mexico
| | - Nancy Rivas
- Laboratorio de Entomología Médica, Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Calle Plan de Ayala s/n, Santo Tomás, Miguel Hidalgo, 11340, CDMX, Mexico
| | - Ricardo Alejandre-Aguilar
- Laboratorio de Entomología Médica, Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Calle Plan de Ayala s/n, Santo Tomás, Miguel Hidalgo, 11340, CDMX, Mexico,
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Biswas KK, Keremane ML, Marais LJ, Ramadugu C, Lee RF. Population dynamics of Citrus tristeza virus (CTV) in single aphid-transmitted sub-isolates of the South African GFMS12 isolate. FRONTIERS IN PLANT SCIENCE 2022; 13:1024556. [PMID: 36388600 PMCID: PMC9650399 DOI: 10.3389/fpls.2022.1024556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Grapefruit trees in South Africa have been cross protected against severe stem pitting genotypes of Citrus tristeza virus (CTV) since the 1920s using a mild strain initially called 'Nartia' but later referred to as grapefruit mild strain 12 (GFMS12). In the current study, the GFMS12 isolate was used as the source for single aphid transmissions (SAT) using Toxoptera citricida, commonly called the brown citrus aphid (BrCA). The BrCA-transmitted CTV sub-isolates were analyzed by the heteroduplex mobility assay (HMA), serological assays, genetic marker analysis (GMA), and selected sub-isolates were biologically indexed. Reverse transcription PCR of genomic regions was conducted using universal primers followed by cloning the PCR products, HMA and sequence analysis; nine genotypes of CTV were identified in the complex of GFMS12, including both severe and mild genotypes. A single BrCA transmitted up to six CTV genotypes simultaneously in one sub-isolate. The HMA was found to be a rapid, reliable tool for the identification of genotypes and can be useful in the development of CTV management strategies and budwood certification programs.
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Affiliation(s)
- K. K. Biswas
- Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, FL, United States
- Plant Protection, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - M. L. Keremane
- Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, FL, United States
- Agricultural Research Service, United States Department of Agriculture (USDA), Riverside, CA, United States
| | - L. J. Marais
- Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, FL, United States
| | - C. Ramadugu
- Botany & Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - R. F. Lee
- Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, FL, United States
- Agricultural Research Service, United States Department of Agriculture (USDA), Riverside, CA, United States
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6
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Da Silva RKM, Morais J, Foley BT, Bello G, Morgado MG, Guimarães ML. Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola. Front Microbiol 2022; 13:992640. [PMID: 36325024 PMCID: PMC9619209 DOI: 10.3389/fmicb.2022.992640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/14/2022] [Indexed: 12/03/2022] Open
Abstract
Angola, located in Central Africa, has around 320,000 (270,000–380,000) people living with human immunodeficiency virus (HIV)/AIDS, equivalent to 1% of the country’s population at the end of 2021. A previous study conducted in 2012, using Angolan samples collected between 2008 and 2010 revealed a high prevalence of HIV-1 recombinants, around 42% of sequences, with 21% showing the same UH profile in partial pol region which were grouped into a monophyletic cluster with high bootstrap support. Thus, the objective of the present work was to obtain complete genomes of those sequences and characterize them, aiming at a description of a new circulating recombinant form (CRF). Whole blood from nine HIV-1 UH pol-infected individuals had their genomic DNA extracted, and nested PCR was used to amplify seven overlapping fragments targeting the full-length HIV-1 genome. The final classification was based on maximum likelihood trees, and recombination analyses were performed using a bootscan from the Simplot program. BLAST and Los Alamos Database inspections were used to search other similar H-like pol sequences. Complete genome amplification was possible for three samples, partial genomes were obtained for the other three, and only pol was available for the remaining three sequences. Bootscan analysis of the two whole-genome and three partial genome sequences retrieved from people living with HIV/AIDS (PLHIVA) without epidemiological linkage showed the same complex recombination profile involving HIV-1 subtypes A/G/H/CRF27_cpx, with a total of six recombinant breakpoints, aiming to classify a new HIV-1 CRF124_cpx. We found no other full-length HIV-1 genomes with the same mosaic profile; however, we identified 33 partial pol sequences, mainly sampled from Angola between 2001 to 2019, with the same H-like profile. Bayesian analysis of H and H-like pol sequences indicates that CRF124_cpx probably originated in Angola at mid-1970s, indicating that this CRF has been circulating in the country for a long time. In summary, our study describes a new CRF circulating principally in Angola and highlights the importance of continuing molecular surveillance studies, especially in countries with high molecular diversity of HIV.
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Affiliation(s)
| | - Joana Morais
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação em Saúde, Ministério da Saúde de Angola, Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
| | - Brian Thomas Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariza Gonçalves Morgado
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Monick Lindenmeyer Guimarães
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- *Correspondence: Monick Lindenmeyer Guimarães,
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7
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The significance of NAD + metabolites and nicotinamide N-methyltransferase in chronic kidney disease. Sci Rep 2022; 12:6398. [PMID: 35430611 PMCID: PMC9013399 DOI: 10.1038/s41598-022-10476-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/28/2022] [Indexed: 11/09/2022] Open
Abstract
Dysregulation of nicotinamide adenine dinucleotide (NAD +) metabolism contributes to the initiation and progression of age-associated diseases, including chronic kidney disease (CKD). Nicotinamide N-methyltransferase (NNMT), a nicotinamide (NAM) metabolizing enzyme, regulates both NAD + and methionine metabolism. Although NNMT is expressed abundantly in the kidney, its role in CKD and renal fibrosis remains unclear. We generated NNMT-deficient mice and a unilateral ureter obstruction (UUO) model and conducted two clinical studies on human CKD to investigate the role of NNMT in CKD and fibrosis. In UUO, renal NNMT expression and the degraded metabolites of NAM increased, while NAD + and NAD + precursors decreased. NNMT deficiency ameliorated renal fibrosis; mechanistically, it (1) increased the DNA methylation of connective tissue growth factor (CTGF), and (2) improved renal inflammation by increasing renal NAD + and Sirt1 and decreasing NF-κB acetylation. In humans, along with CKD progression, a trend toward a decrease in serum NAD + precursors was observed, while the final NAD + metabolites were accumulated, and the level of eGFR was an independent variable for serum NAM. In addition, NNMT was highly expressed in fibrotic areas of human kidney tissues. In conclusion, increased renal NNMT expression induces NAD + and methionine metabolism perturbation and contributes to renal fibrosis.
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8
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Suzuki S, Sasaki K, Fukazawa T, Kubo T. Xenopus laevis il11ra.L is an experimentally proven interleukin-11 receptor component that is required for tadpole tail regeneration. Sci Rep 2022; 12:1903. [PMID: 35115663 PMCID: PMC8814168 DOI: 10.1038/s41598-022-05954-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/20/2022] [Indexed: 11/22/2022] Open
Abstract
Xenopus laevis tadpoles possess high regenerative ability and can regenerate functional tails after amputation. An early event in regeneration is the induction of undifferentiated cells that form the regenerated tail. We previously reported that interleukin-11 (il11) is upregulated immediately after tail amputation to induce undifferentiated cells of different cell lineages, indicating a key role of il11 in initiating tail regeneration. As Il11 is a secretory factor, Il11 receptor-expressing cells are thought to mediate its function. X. laevis has a gene annotated as interleukin 11 receptor subunit alpha on chromosome 1L (il11ra.L), a putative subunit of the Il11 receptor complex, but its function has not been investigated. Here, we show that nuclear localization of phosphorylated Stat3 induced by Il11 is abolished in il11ra.L knocked-out culture cells, strongly suggesting that il11ra.L encodes an Il11 receptor component. Moreover, knockdown of il11ra.L impaired tadpole tail regeneration, suggesting its indispensable role in tail regeneration. We also provide a model showing that Il11 functions via il11ra.L-expressing cells in a non-cell autonomous manner. These results highlight the importance of il11ra.L-expressing cells in tail regeneration.
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Affiliation(s)
- Shunya Suzuki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kayo Sasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Taro Fukazawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Takeo Kubo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Li T, Wong TKF, Ranjard L, Rodrigo AG. pgHMA: Application of the heteroduplex mobility assay analysis in phylogenetics and population genetics. Mol Ecol Resour 2021; 22:653-663. [PMID: 34551204 DOI: 10.1111/1755-0998.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 11/26/2022]
Abstract
The heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (a) there is a significant linear relationship (R2 = .992) between heteroduplex mobility and genetic distance, (b) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies, (c) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies, (d) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size, and (e) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends.
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Affiliation(s)
- Teng Li
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Thomas K F Wong
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Louis Ranjard
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,PlantTech Research Institute, Tauranga, New Zealand
| | - Allen G Rodrigo
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
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High Detection Rate of HIV Drug Resistance Mutations among Patients Who Fail Combined Antiretroviral Therapy in Manaus, Brazil. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5567332. [PMID: 34212033 PMCID: PMC8208851 DOI: 10.1155/2021/5567332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/10/2021] [Accepted: 05/27/2021] [Indexed: 02/08/2023]
Abstract
Virologic failure may occur because of poor treatment adherence and/or viral drug resistance mutations (DRM). In Brazil, the northern region exhibits the worst epidemiological scenarios for the human immunodeficiency virus (HIV). Thus, this study is aimed at investigating the genetic diversity of HIV-1 and DRM in Manaus. The cross-sectional study included people living with HIV on combined antiretroviral therapy and who had experienced virological failure during 2018-2019. Sequencing of the protease/reverse transcriptase (PR/RT) and C2V3 of the viral envelope gp120 (Env) regions was analyzed to determine subtypes/variants of HIV-1, DRMs, and tropism. Ninety-two individuals were analyzed in the study. Approximately 72% of them were male and 74% self-declared as heterosexual. Phylogenetic inference (PR/RT-Env) showed that most sequences were B subtype, followed by BF1 or BC mosaic genomes and few F1 and C sequences. Among the variants of subtype B at PR/RT, 84.3% were pandemic (BPAN), and 15.7% were Caribbean (BCAR). The DRMs most frequent were M184I/V (82.9%) for nucleoside reverse transcriptase inhibitors (NRTI), K103N/S (63.4%) for nonnucleoside reverse transcriptase inhibitor (NNRTI), and V82A/L/M (7.3%) for protease inhibitors (PI). DRM analysis depicted high levels of resistance for lamivudine and efavirenz in over 82.9% of individuals; although, low (7.7%) cross-resistance to etravirine was observed. A low level of resistance to protease inhibitors was found and included patients that take atazanavir/ritonavir (16.6%) and lopinavir (11.1%), which confirms that these antiretrovirals can be used—for most individuals. The thymidine analog mutations-2 (TAM-2) resistance pathway was higher in BCAR than in BPAN. Similar results from other Brazilian studies regarding HIV drug resistance were observed; however, we underscore a need for additional studies regarding subtype BCAR variants. Molecular epidemiology studies are an important tool for monitoring the prevalence of HIV drug resistance and can influence the public health policies.
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Giovanetti M, Ciccozzi M, Parolin C, Borsetti A. Molecular Epidemiology of HIV-1 in African Countries: A Comprehensive Overview. Pathogens 2020; 9:pathogens9121072. [PMID: 33371264 PMCID: PMC7766877 DOI: 10.3390/pathogens9121072] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) originated in non-human primates in West-central Africa and continues to be a major global public health issue, having claimed almost 33 million lives so far. In Africa, it is estimated that more than 20 million people are living with HIV/Acquired Immunodeficiency Syndrome (AIDS) and that more than 730,000 new HIV-1 infections still occur each year, likely due to low access to testing. The high genetic variability of HIV-1, due to a fast replication cycle and high mutation rate, may cause the generation of many viral variants in a single infected patient during a single day. Therefore, the active monitoring and characterization of the HIV-1 subtypes and recombinant forms circulating through African countries poses a significant challenge to more specific diagnoses, treatments, care, and intervention strategies. In this review, a concise characterization of all the subtypes and recombinant forms circulating in Africa is presented to highlight the magnitude of the HIV-1 threat among the African countries and to understand virus genetic diversity and dispersion dynamics better.
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Affiliation(s)
- Marta Giovanetti
- Reference Laboratory of Flavivirus, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
- Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Massimo Ciccozzi
- Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Cristina Parolin
- Department of Molecular, Medicine University of Padova, 35121 Padova, Italy;
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy
- Correspondence: ; Tel.: +39-06-49903082
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12
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Sterner ZR, Shewade LH, Mertz KM, Sturgeon SM, Buchholz DR. Glucocorticoid receptor is required for survival through metamorphosis in the frog Xenopus tropicalis. Gen Comp Endocrinol 2020; 291:113419. [PMID: 32032606 DOI: 10.1016/j.ygcen.2020.113419] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023]
Abstract
Stress hormones, also known as glucocorticoids, are critical for survival at birth in mammals due at least in part to their importance in lung maturation. However, because air breathing is not always required for amphibian survival and because stress hormones have no known developmental impact except to modulate the developmental actions of thyroid hormone (TH), the requirement for stress hormone signaling during metamorphosis is not well understoodi. Here, we produced a glucocorticoid receptor knockout (GRKO) Xenopus line with a frameshift mutation in the first exon of the glucocorticoid receptor. Induction by exogenous corticosterone (CORT, the frog stress hormone) of the CORT response genes, klf9 (Krüppel-like factor 9, also regulated by TH) and ush1g (Usher's syndrome 1G), was completely abrogated in GRKO tadpoles. Surprisingly, GRKO tadpoles developed faster than wild-type tadpoles until forelimb emergence and then developed more slowly until their death at the climax of metamorphosis. Growth rate was not affected in GRKO tadpoles, but they achieved a smaller maximum size. Gene expression analysis of the TH response genes, thrb (TH receptor beta) and klf9 showed reduced expression in the tail at metamorphic climax consistent with the reduced development rate. These results indicate that glucocorticoid receptor is required for survival through metamorphosis and support dual roles for GR signaling in control of developmental rate.
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Affiliation(s)
- Zachary R Sterner
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Leena H Shewade
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Kala M Mertz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Savannah M Sturgeon
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States.
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Leite TF, Delatorre E, Côrtes FH, Ferreira ACG, Cardoso SW, Grinsztejn B, de Andrade MM, Veloso VG, Morgado MG, Guimarães ML. Reduction of HIV-1 Reservoir Size and Diversity After 1 Year of cART Among Brazilian Individuals Starting Treatment During Early Stages of Acute Infection. Front Microbiol 2019; 10:145. [PMID: 30804915 PMCID: PMC6378917 DOI: 10.3389/fmicb.2019.00145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/21/2019] [Indexed: 01/13/2023] Open
Abstract
The aim of early combined antiretroviral therapy (cART) of HIV is to limit the seeding of the viral reservoir during the initial phase of infection and, consequently, decrease intrahost viral diversity. Here, we assessed the effect of early cART on size and complexity of the proviral reservoir. Peripheral blood mononuclear cell (PBMC) and plasma samples were obtained from ten HIV-infected Brazilian individuals diagnosed at the acute phase of infection, before (PREART) and 12 months (M12ART) after suppressive cART. HIV proviral reservoir size was determined by quantitative real-time PCR; intrahost viral diversity of the env C2-V3 region was assessed by single genome amplification or next-generation sequencing in PBMC and plasma, respectively. Mean nucleotide diversity (π) and normalized Shannon entropy (HSN) were used to infer the complexity of the viral population. Compared to PREART, M12ART saw an immunological recovery with a gain of ∼200 CD4+ T cells (P = 0.008) and a normalization of the CD4/CD8 ratio [1.0 (IQR: 0.88–1.18), P = 0.016], as well as a significant decrease in HIV-1 RNA (∼4 log, P = 0.004) and DNA (∼1 log, P = 0.002) levels. The median time to achieve viral suppression was 3 months (IQR: 2.8–5.8 months). The high intermixing between sequences from both visits suggests that the HIV-1 DNA reservoir remained remarkably stable under cART. After 1 year of cART, there was a minor reduction in proviral π (PreART = 0.20 vs. M12ART = 0.10; P = 0.156) but a significant decrease in HSN (PreART = 0.41 vs. M12ART = 0.25; P = 0.019). We found no correlation between π or HSN at PreART and the rate of HIV DNA decay, T CD4+ counts, or CD4/CD8 ratio at M12ART. Based on a small cohort of Brazilian infected individuals under early cART and analyses of the env region, 1 year of follow-up suggested a reservoir size reduction, allowed a significant decrease of HIV-1 complexity, and achieved immunological restoration regardless of the initial HIV-1 plasma viral load, CD4+ T cell counts, or HIV-1 subtype. However, further studies in the Brazilian setting aiming a longer follow-up and larger cohort are required in this field.
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Affiliation(s)
- Thaysse Ferreira Leite
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fernanda Heloise Côrtes
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Cristina Garcia Ferreira
- Laboratório de Pesquisa Clínica em DST e AIDS, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Sandra Wagner Cardoso
- Laboratório de Pesquisa Clínica em DST e AIDS, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Laboratório de Pesquisa Clínica em DST e AIDS, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Michelle Morata de Andrade
- Laboratório de Pesquisa Clínica em DST e AIDS, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Valdilea Gonçalves Veloso
- Laboratório de Pesquisa Clínica em DST e AIDS, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Mariza Gonçalves Morgado
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Monick Lindenmeyer Guimarães
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Dapp MJ, Kober KM, Chen L, Westfall DH, Wong K, Zhao H, Hall BM, Deng W, Sibley T, Ghorai S, Kim K, Chen N, McHugh S, Au L, Cohen M, Anastos K, Mullins JI. Patterns and rates of viral evolution in HIV-1 subtype B infected females and males. PLoS One 2017; 12:e0182443. [PMID: 29045410 PMCID: PMC5646779 DOI: 10.1371/journal.pone.0182443] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/18/2017] [Indexed: 12/18/2022] Open
Abstract
Biological sex differences affect the course of HIV infection, with untreated women having lower viral loads compared to their male counterparts but, for a given viral load, women have a higher rate of progression to AIDS. However, the vast majority of data on viral evolution, a process that is clearly impacted by host immunity and could be impacted by sex differences, has been derived from men. We conducted an intensive analysis of HIV-1 gag and env-gp120 evolution taken over the first 6–11 years of infection from 8 Women’s Interagency HIV Study (WIHS) participants who had not received combination antiretroviral therapy (ART). This was compared to similar data previously collected from men, with both groups infected with HIV-1 subtype B. Early virus populations in men and women were generally homogenous with no differences in diversity between sexes. No differences in ensuing nucleotide substitution rates were found between the female and male cohorts studied herein. As previously reported for men, time to peak diversity in env-gp120 in women was positively associated with time to CD4+ cell count below 200 (P = 0.017), and the number of predicted N-linked glycosylation sites generally increased over time, followed by a plateau or decline, with the majority of changes localized to the V1-V2 region. These findings strongly suggest that the sex differences in HIV-1 disease progression attributed to immune system composition and sensitivities are not revealed by, nor do they impact, global patterns of viral evolution, the latter of which proceeds similarly in women and men.
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Affiliation(s)
- Michael J. Dapp
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kord M. Kober
- Department of Physiological Nursing, University of California at San Francisco, California, United States of America
| | - Lennie Chen
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Dylan H. Westfall
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kim Wong
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Hong Zhao
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Breana M. Hall
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Wenjie Deng
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Thomas Sibley
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Suvankar Ghorai
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Katie Kim
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Natalie Chen
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Sarah McHugh
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lily Au
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Mardge Cohen
- The Core Center, Bureau of Health Services of Cook County, Chicago, Illinois, United States of America
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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15
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Pace of Coreceptor Tropism Switch in HIV-1-Infected Individuals after Recent Infection. J Virol 2017; 91:JVI.00793-17. [PMID: 28659473 DOI: 10.1128/jvi.00793-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/08/2017] [Indexed: 11/20/2022] Open
Abstract
HIV-1 entry into target cells influences several aspects of HIV-1 pathogenesis, including viral tropism, HIV-1 transmission and disease progression, and response to entry inhibitors. The evolution from CCR5- to CXCR4-using strains in a given human host is still unpredictable. Here we analyzed timing and predictors for coreceptor evolution among recently HIV-1-infected individuals. Proviral DNA was longitudinally evaluated in 66 individuals using Geno2pheno[coreceptor] Demographics, viral load, CD4+ and CD8+ T cell counts, CCR5Δ32 polymorphisms, GB virus C (GBV-C) coinfection, and HLA profiles were also evaluated. Ultradeep sequencing was performed on initial samples from 11 selected individuals. A tropism switch from CCR5- to CXCR4-using strains was identified in 9/49 (18.4%) individuals. Only a low baseline false-positive rate (FPR) was found to be a significant tropism switch predictor. No minor CXCR4-using variants were identified in initial samples of 4 of 5 R5/non-R5 switchers. Logistic regression analysis showed that patients with an FPR of >40.6% at baseline presented a stable FPR over time whereas lower FPRs tend to progressively decay, leading to emergence of CXCR4-using strains, with a mean evolution time of 27.29 months (range, 8.90 to 64.62). An FPR threshold above 40.6% determined by logistic regression analysis may make it unnecessary to further determine tropism for prediction of disease progression related to emergence of X4 strains or use of CCR5 antagonists. The detection of variants with intermediate FPRs and progressive FPR decay over time not only strengthens the power of Geno2pheno in predicting HIV tropism but also indirectly confirms a continuous evolution from earlier R5 variants toward CXCR4-using strains.IMPORTANCE The introduction of CCR5 antagonists in the antiretroviral arsenal has sparked interest in coreceptors utilized by HIV-1. Despite concentrated efforts, viral and human host features predicting tropism switch are still poorly understood. Limited longitudinal data are available to assess the influence that these factors have on predicting tropism switch and disease progression. The present study describes longitudinal tropism evolution in a group of recently HIV-infected individuals to determine the prevalence and potential correlates of tropism switch. We demonstrated here that a low baseline FPR determined by the Geno2pheno[coreceptor] algorithm can predict tropism evolution from CCR5 to CXCR4 coreceptor use.
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Avanzi VM, Vicente BA, Beloto NCP, Gomes-da-Silva MM, Ribeiro CEL, Tuon FF, Vidal LRR, Nogueira MB, Raboni SM. Profile of HIV subtypes in HIV/HBV- and HIV/HCV-coinfected patients in Southern Brazil. Rev Soc Bras Med Trop 2017; 50:470-477. [PMID: 28954067 DOI: 10.1590/0037-8682-0450-2016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/30/2017] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION: HIV and viral hepatitis infections are major causes of chronic disease worldwide and have some similarities with regard to routes of transmission, epidemiology, front barriers faced during access of treatment, and strategies for a global public health response. The objective was to describe the HIV-1 subtypes, viral tropism and single-nucleotide polymorphisms (SNPs) of interleukin 28B (IL28B) from a case series of HIV/viral hepatitis coinfected patients from southern Brazil. METHODS: Clinical and epidemiological data were evaluated by a review of medical records. Periodic blood draws were taken to determine the viral and host characteristics. RESULTS: This study included 38 patients with HIV/HBV or HIV/HCV coinfection; the median age was 49 years. Thirty-seven (97.4%) were on antiretroviral therapy, 32 (84.2%) had an undetectable viral load, a median CD4+ T-cell count of 452 cells/mm3. HIV-1 subtyping showed 47.4 and 31.6% of patients with subtypes C and B, respectively. Analysis of viral co-receptor usage showed a predominance of the R5 variant (64.7%), with no significant difference between the subtypes. Twenty patients with HIV/HCV coinfection were eligible to receive HCV therapy with pegylated-interferon-alpha plus ribavirin, and 10/20 (50%) of them achieved sustained virological response. SNPs of IL28B were evaluated in 93.3% of patients with HIV/HCV coinfection, and 17 (60.7%) presented the CC genotype. CONCLUSIONS: In the present case series, a higher frequency of HIV subtype C was found in coinfected patients. However such findings need to be prospectively evaluated with the inclusion of data from regional multicenter analyses.
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Affiliation(s)
- Valéria Miranda Avanzi
- Programa de Pós Graduação em Medicina Interna, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Bianca Arão Vicente
- Departamento de Doenças Infecciosas, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | | | | | - Clea Elisa Lopes Ribeiro
- Departamento de Doenças Infecciosas, Universidade Federal do Paraná, Curitiba, PR, Brasil
- Secretaria Municipal de Saúde de Curitiba, Divisão Epidemiologica, Curitiba, PR, Brasil
| | - Felipe Francisco Tuon
- Programa de Pós Graduação em Medicina Interna, Universidade Federal do Paraná, Curitiba, PR, Brasil
- Departamento de Doenças Infecciosas, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | | | | | - Sonia Mara Raboni
- Programa de Pós Graduação em Medicina Interna, Universidade Federal do Paraná, Curitiba, PR, Brasil
- Departamento de Doenças Infecciosas, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Reis MNDG, Bello G, Guimarães ML, Stefani MMA. Characterization of HIV-1 CRF90_BF1 and putative novel CRFs_BF1 in Central West, North and Northeast Brazilian regions. PLoS One 2017. [PMID: 28628667 PMCID: PMC5476242 DOI: 10.1371/journal.pone.0178578] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Brazilian AIDS epidemic has been characterized by an increasing rate of BF1 recombinants and so far eight circulating recombinant forms/CRFs_BF1 have been described countrywide. In this study, pol sequences (protease/PR, reverse transcriptase/RT) of 87 BF1 mosaic isolates identified among 828 patients living in six Brazilian States from three geographic regions (Central West, North, Northeast) were analyzed. Phylogenetic and bootscan analyses were performed to investigate the evolutionary relationship and mosaic structure of BF1 isolates. Those analyses showed that 20.7% of mosaics (18 out of 87) were CRFs-like isolates, mostly represented by CRF28/CRF29_BF-like viruses (14 out of 18). We also identified five highly supported clusters that together comprise 42 out of 87 (48.3%) BF1 sequences, each cluster containing at least five sequences sharing a similar mosaic structure, suggesting possible new unidentified CRFs_BF1. The divergence time of these five potential new CRFs_BF1 clusters was estimated using a Bayesian approach and indicate that they probably originated between the middle 1980s and the middle 1990s. DNA was extracted from whole blood and four overlapping fragments were amplified by PCR providing full/near full length genomes (FLG/NFLG) and partial genomes. Eleven HIV-1 isolates from Cluster # 5 identified in epidemiologically unlinked individuals living in Central West and North regions provided FLG/NFLG/partial genome sequences with identical mosaic structure. These viruses differ from any known CRF_BF1 reported to date and were named CRF90_BF1 by the Los Alamos National Laboratory. This is the 9th CRF_BF1 described in Brazil and the first one identified in Central West and North regions. Our results highlight the importance of continued molecular screening and surveillance studies, especially of full genome sequences to understand the evolutionary dynamics of the HIV-1 epidemic in a country of continental dimensions as Brazil.
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Affiliation(s)
- Mônica Nogueira da Guarda Reis
- Laboratório de Imunologia da AIDS e da Hanseníase, Instituto de Patologia Tropical e Saúde Pública, UFG, Goiânia, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Mariane Martins Araújo Stefani
- Laboratório de Imunologia da AIDS e da Hanseníase, Instituto de Patologia Tropical e Saúde Pública, UFG, Goiânia, Brazil
- * E-mail:
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Strand AE, Milligan BG, Pruitt CM. ARE POPULATIONS ISLANDS? ANALYSIS OF CHLOROPLAST DNA VARIATION IN
AQUILEGIA. Evolution 2017; 50:1822-1829. [DOI: 10.1111/j.1558-5646.1996.tb03568.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/1994] [Accepted: 11/03/1995] [Indexed: 11/30/2022]
Affiliation(s)
- Allan E. Strand
- Department of Biology New Mexico State University Las Cruces New Mexico 88003
| | - Brook G. Milligan
- Department of Biology New Mexico State University Las Cruces New Mexico 88003
| | - Casey M. Pruitt
- Department of Biology New Mexico State University Las Cruces New Mexico 88003
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Wagner TA, Huang HC, Salyer CE, Richardson KM, Weinberg A, Nachman S, Frenkel LM. H1N1 influenza vaccination in HIV-infected women on effective antiretroviral treatment did not induce measurable antigen-driven proliferation of the HIV-1 proviral reservoir. AIDS Res Ther 2017; 14:7. [PMID: 28193244 PMCID: PMC5307755 DOI: 10.1186/s12981-017-0135-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/26/2017] [Indexed: 01/03/2023] Open
Abstract
Objectives Antigen-induced activation and proliferation of HIV-1-infected cells is hypothesized to be a mechanism of HIV persistence during antiretroviral therapy. The objective of this study was to determine if proliferation of H1N1-specific HIV-infected cells could be detected following H1N1 vaccination. Methods This study utilized cryopreserved PBMC from a previously conducted trial of H1N1 vaccination in HIV-infected pregnant women. HIV-1 DNA concentrations and 437 HIV-1 C2V5 env DNA sequences were analyzed from ten pregnant women on effective antiretroviral therapy, before and 21 days after H1N1 influenza vaccination. Results HIV-1 DNA concentration did not change after vaccination (median pre- vs. post-vaccination: 95.77 vs. 41.28 copies/million PBMC, p = .37). Analyses of sequences did not detect evidence of HIV replication or proliferation of infected cells. Conclusions Antigenic stimulation during effective ART did not have a detectable effect on the genetic makeup of the HIV-1 DNA reservoir. Longitudinal comparison of the amount and integration sites of HIV-1 in antigen-specific cells to chronic infections (such as herpesviruses) may be needed to definitively evaluate whether antigenic stimulation induces proliferation of HIV-1 infected cells. Electronic supplementary material The online version of this article (doi:10.1186/s12981-017-0135-1) contains supplementary material, which is available to authorized users.
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20
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Benko Z, Liang D, Li G, Elder RT, Sarkar A, Takayama J, Ghosh AK, Zhao RY. A fission yeast cell-based system for multidrug resistant HIV-1 proteases. Cell Biosci 2017; 7:5. [PMID: 28096973 PMCID: PMC5225522 DOI: 10.1186/s13578-016-0131-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 12/16/2016] [Indexed: 02/03/2023] Open
Abstract
Background HIV-1 protease (PR) is an essential enzyme for viral production. Thus, PR inhibitors (PIs) are the most effective class of anti-HIV drugs. However, the main challenge to the successful use of PI drugs in patient treatment is the emergence of multidrug resistant PRs (mdrPRs). This study aimed to develop a fission yeast cell-based system for rapid testing of new PIs that combat mdrPRs. Results Three mdrPRs were isolated from HIV-infected patients that carried seven (M7PR), ten (M10PR) and eleven (M11PR) PR gene mutations, respectively. They were cloned and expressed in fission yeast under an inducible promoter to allow the measurement of PR-specific proteolysis and drug resistance. The results showed that all three mdrPRs maintained their abilities to proteolyze HIV viral substrates (MA↓CA and p6) and to confer drug resistance. Production of these proteins in the fission yeast caused cell growth inhibition, oxidative stress and altered mitochondrial morphologies that led to cell death. Five investigational PIs were used to test the utility of the established yeast system with an FDA-approved PI drug Darunavir (DRV) as control. All six compounds suppressed the wildtype PR (wtPR) and the M7PR-mediated activities. However, none of them were able to suppress the M10PR or the M11PR. Conclusions The three clinically isolated mdrPRs maintained their viral proteolytic activities and drug resistance in the fission yeast. Furthermore, those viral mdrPR activities were coupled with the induction of growth inhibition and cell death, which could be used to test the PI activities. Indeed, the five investigational PIs and DRV suppressed the wtPR in fission yeast as they did in mammalian cells. Significantly, two of the high level mdrPRs (M10PR and M11PR) were resistant to all of the existing PI drugs including DRV. This observation underscores the importance of continued searching for new PIs against mdrPRs. Electronic supplementary material The online version of this article (doi:10.1186/s13578-016-0131-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zsigmond Benko
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201 USA ; Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, SAS, 84005 Bratislava, Slovakia
| | - Dong Liang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Ge Li
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Robert T Elder
- Children's Memorial Institute for Education and Research, Northwestern University Feinberg School of Medicine, Chicago, IL 10164 USA
| | - Anindya Sarkar
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Jun Takayama
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Richard Y Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201 USA ; Department of Microbiology-Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA ; Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201 USA ; Children's Memorial Institute for Education and Research, Northwestern University Feinberg School of Medicine, Chicago, IL 10164 USA
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21
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Leite TCNF, Campos DP, Coelho AB, Teixeira SLM, Veloso V, Morgado MG, Guimarães ML. Impact of HIV-1 Subtypes on AIDS Progression in a Brazilian Cohort. AIDS Res Hum Retroviruses 2017; 33:41-48. [PMID: 27418261 DOI: 10.1089/aid.2016.0126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Viral and host factors are known to play a role in the different patterns of AIDS progression. The cocirculation of HIV-1 subtypes B, F1, BBR, and BF1; the occasional detection of HIV-1 subtype D; and an increasing prevalence of subtype C and other recombinant forms have been described in Rio de Janeiro, Brazil. The aim of this study was to evaluate the potential association of HIV-1 subtypes circulating among HIV-1+ individuals in Rio de Janeiro with AIDS disease progression. For this purpose, 246 HIV-1 individuals under clinical and laboratory follow-up from 1986 to 2011 were classified according to their progression to AIDS in typical progressors (n = 133), rapid progressors (n = 95), and long-term nonprogressors (n = 18). The env-gp120 region was amplified and sequenced. Neighbor-joining phylogenetic inferences were performed in Mega 6 and bootscan analysis was performed in Simplot 3.5.1. The Kaplan-Meier method and Cox modeling were performed to determine the time until an AIDS-defining event based on the HIV-1 subtypes/variants. Similar AIDS progression rates were observed among individuals infected with HIV-1 subtype B and variant BBR. However, a direct association between more rapid AIDS progression and HIV-1 subtypes, D and BF1, was confirmed in the multivariate analysis, corroborating previous results. Our findings contribute to the investigation of the possible influence of HIV-1 subtypes in AIDS outcome.
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Affiliation(s)
| | - Dayse Pereira Campos
- Evandro Chagas Nacional Institute of Infectious Diseases, FIOCRUZ, Rio de Janeiro, Brazil
| | - Alessandra Brum Coelho
- Evandro Chagas Nacional Institute of Infectious Diseases, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Valdilea Veloso
- Evandro Chagas Nacional Institute of Infectious Diseases, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariza Gonçalves Morgado
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
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22
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Andersson M, Turesson H, Nicolia A, Fält AS, Samuelsson M, Hofvander P. Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts. PLANT CELL REPORTS 2017; 36:117-128. [PMID: 27699473 PMCID: PMC5206254 DOI: 10.1007/s00299-016-2062-3] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/27/2016] [Indexed: 05/14/2023]
Abstract
Altered starch quality with full knockout of GBSS gene function in potato was achieved using CRISPR-Cas9 technology, through transient transfection and regeneration from isolated protoplasts. Site-directed mutagenesis (SDM) has shown great progress in introducing precisely targeted mutations. Engineered CRISPR-Cas9 has received increased focus compared to other SDM techniques, since the method is easily adapted to different targets. Here, we demonstrate that transient application of CRISPR-Cas9-mediated genome editing in protoplasts of tetraploid potato (Solanum tuberosum) yielded mutations in all four alleles in a single transfection, in up to 2 % of regenerated lines. Three different regions of the gene encoding granule-bound starch synthase (GBSS) were targeted under different experimental setups, resulting in mutations in at least one allele in 2-12 % of regenerated shoots, with multiple alleles mutated in up to 67 % of confirmed mutated lines. Most mutations resulted in small indels of 1-10 bp, but also vector DNA inserts of 34-236 bp were found in 10 % of analysed lines. No mutations were found in an allele diverging one bp from a used guide sequence, verifying similar results found in other plants that high homology between guide sequence and target region near the protospacer adjacent motif (PAM) site is essential. To meet the challenge of screening large numbers of lines, a PCR-based high-resolution fragment analysis method (HRFA) was used, enabling identification of multiple mutated alleles with a resolution limit of 1 bp. Full knockout of GBSS enzyme activity was confirmed in four-allele mutated lines by phenotypic studies of starch. One remaining wild-type (WT) allele was shown sufficient to maintain enough GBSS enzyme activity to produce significant amounts of amylose.
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Affiliation(s)
- Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, SE-23053, Alnarp, Sweden
| | - Helle Turesson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, SE-23053, Alnarp, Sweden
| | - Alessandro Nicolia
- ENEA Research Centre Casaccia, SSPT-BIOAG-BIOTEC, Via Anguillarese, 301, 00123, Rome, Italy
| | - Ann-Sofie Fält
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, SE-23053, Alnarp, Sweden
| | | | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, SE-23053, Alnarp, Sweden.
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23
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Lebedev AV, Kazennova EV, Zverev SY, Nistratova YI, Laga VY, Tumanov AS, Glushchenko NV, Yarygina EI, Bobkova MR. Analysis of the env gene variability of the IDU-A HIV-1 variant in the outbreak of the HIV infection epidemic in Perm region of Russia (1996-2011). ACTA ACUST UNITED AC 2016. [DOI: 10.18821/0507-4088-2016-61-5-222-229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- A. V. Lebedev
- «Federal Research Centre of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya»; K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology
| | - E. V. Kazennova
- «Federal Research Centre of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya»
| | - S. Ya. Zverev
- Perm Regional Center for Prevention and Control of AIDS and Infectious Diseases
| | - Yu. I. Nistratova
- Perm Regional Center for Prevention and Control of AIDS and Infectious Diseases
| | - V. Yu. Laga
- «Federal Research Centre of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya»
| | - A. S. Tumanov
- «Federal Research Centre of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya»
| | - N. V. Glushchenko
- «Federal Research Centre of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya»
| | - E. I. Yarygina
- K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology
| | - M. R. Bobkova
- «Federal Research Centre of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya»
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24
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Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality. PLoS Pathog 2016; 12:e1005689. [PMID: 27494508 PMCID: PMC4975415 DOI: 10.1371/journal.ppat.1005689] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/18/2016] [Indexed: 01/01/2023] Open
Abstract
In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings. Although antiretroviral therapy effectively blocks HIV-1 replication, the virus persists indefinitely in a reservoir of latently infected cells. This reservoir is a major barrier to HIV-1 cure. Recent studies have identified the proliferation of latently infected cells as a mechanism that may contribute to the lifelong persistence of HIV-1. In contrast with cellular proliferation, viral replication is highly error-prone; therefore, the detection of identical viral genomes in distinct host cells provides evidence that those cells are the progeny of an infected cell that underwent clonal expansion. For this reason, the accurate and reliable identification of identical HIV-1 genomes derived from distinct cells is critical for understanding HIV-1 persistence and advancing cure research. Studies of HIV-1 clonal expansion often present clonality of short, subgenomic sequences as evidence for the clonality of full viral genomes. In this study, we quantified the relationship between sequence identity in short regions and sequence identity of near-full-length genomes to demonstrate that no subgenomic region completely captures the diversity of the full viral genome. Consequently, identical subgenomic sequences are not proof of identical full-length HIV-1 genomes. In the context of these findings, we developed a method to evaluate identical subgenomic sequences as possible evidence for clonal expansion.
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25
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Zhang X, McGown LB. Sequence-based separation of single-stranded DNA at high salt concentrations in capillary zone electrophoresis. Electrophoresis 2016; 37:2017-24. [DOI: 10.1002/elps.201600138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Xueru Zhang
- Department of Chemistry and Chemical Biology Rensselaer Polytechnic Institute; Troy NY USA
| | - Linda B. McGown
- Department of Chemistry and Chemical Biology Rensselaer Polytechnic Institute; Troy NY USA
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26
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Quantification of designer nuclease induced mutation rates: a direct comparison of different methods. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 3:16047. [PMID: 27419195 PMCID: PMC4934480 DOI: 10.1038/mtm.2016.47] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/21/2016] [Accepted: 05/23/2016] [Indexed: 02/08/2023]
Abstract
Designer nucleases are broadly applied to induce site-specific DNA double-strand breaks (DSB) in genomic DNA. These are repaired by nonhomologous end joining leading to insertions or deletions (in/dels) at the respective DNA-locus. To detect in/del mutations, the heteroduplex based T7-endonuclease I -assay is widely used. However, it only provides semi-quantitative evidence regarding the number of mutated alleles. Here we compared T7-endonuclease I- and heteroduplex mobility assays, with a quantitative polymerase chain reaction mutation detection method. A zinc finger nuclease pair specific for the human adeno-associated virus integration site 1 (AAVS1), a transcription activator-like effector nuclease pair specific for the human DMD gene, and a zinc finger nuclease- and a transcription activator-like effector nuclease pair specific for the human CCR5 gene were explored. We found that the heteroduplex mobility assays and T7-endonuclease I - assays detected mutations but the relative number of mutated cells/alleles can only be estimated. In contrast, the quantitative polymerase chain reaction based method provided quantitative results which allow calculating mutation and homologous recombination rates in different eukaryotic cell types including human peripheral blood mononuclear cells. In conclusion, our quantitative polymerase chain reaction based mutation detection method expands the array of methods for in/del mutation detection and facilitates quantification of introduced in/del mutations for a genomic locus containing a mixture of mutated and unmutated DNA.
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27
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Lebedev AV, Neshumaev DA, Kazennova EV, Lapovok IA, Laga VY, Tumanov AS, Glushchenko NV, Plotnikova YK, Ponomareva OA, Yarygina EI, Bobkova MR. [Comparative analysis of genetic variants of the HIV-1 circulating in the Irkutsk region in 1999 and 2012]. Vopr Virusol 2016; 61:112-118. [PMID: 36494944 DOI: 10.18821/0507-4088-2016-61-3-112-118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 07/12/2020] [Indexed: 12/13/2022]
Abstract
The pol and env genome regions of the HIV-1 genetic variants circulating in the irkutsk region of russia in 1999 and 2012 were compared. The results of this work showed the dominance of the HIV-1 subtype a IDU-A genetic variant (100%) in this region. No primary resistance mutations in the pol gene in the treatment-naive patients were found. The heterogeneity of the viral population was found to be significantly increased based on the pol and env analysis among HIV-variants isolated in 2012 (12.88% and 2.16%) from the intravenous drug users as compared to HIV-variants that caused the outbreak of the HIV infection in 1999 (1.64% and 0.47%). In addition, the comparison of genetic distances of the pol and env gene sequences in the viruses isolated in 2012 from the HIV-positive persons infected through heterosexual intercourse and intravenous drug use demonstrated that the transmission route influenced the variability of the virus population. Among the viruses of IDU-A variant circulating in the area in 2012 the prevalence of X4-tropic variants was 24.7%.
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Affiliation(s)
- A V Lebedev
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya».,Moscow State Academy of Veterinary Medicine and Biotechnology
| | | | - E V Kazennova
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - I A Lapovok
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - V Y Laga
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - A S Tumanov
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - N V Glushchenko
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | | | | | - E I Yarygina
- Moscow State Academy of Veterinary Medicine and Biotechnology
| | - M R Bobkova
- D.I. Ivanovsky Institute of Virology «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
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28
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Li F, Scott MJ. CRISPR/Cas9-mediated mutagenesis of the white and Sex lethal loci in the invasive pest, Drosophila suzukii. Biochem Biophys Res Commun 2015; 469:911-6. [PMID: 26721433 DOI: 10.1016/j.bbrc.2015.12.081] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 12/18/2015] [Indexed: 02/07/2023]
Abstract
Drosophila suzukii (commonly called spotted wing Drosophila) is an invasive pest of soft-skinned fruit (e.g. blueberries, strawberries). A high quality reference genome sequence is available but functional genomic tools, such as used in Drosophila melanogaster, remain to be developed. In this study we have used the CRISPR/Cas9 system to introduce site-specific mutations in the D. suzukii white (w) and Sex lethal (Sxl) genes. Hemizygous males with w mutations develop white eyes and the mutant genes are transmissible to the next generation. Somatic mosaic females that carry mutations in the Sxl gene develop abnormal genitalia and reproductive tissue. The D. suzukii Sxl gene could be an excellent target for a Cas9-mediated gene drive to suppress populations of this highly destructive pest.
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Affiliation(s)
- Fang Li
- Department of Entomology, North Carolina State University, Campus Box 7613, Raleigh 27695-7613, NC, USA
| | - Maxwell J Scott
- Department of Entomology, North Carolina State University, Campus Box 7613, Raleigh 27695-7613, NC, USA.
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29
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Zhao Q, Zhang C, Jiang Y, Wen Y, Pan P, Li Y, Zhang G, Zhang L, Qiu M. Short Communication: Investigating a Chain of HIV Transmission Events Due to Homosexual Exposure and Blood Transfusion Based on a Next Generation Sequencing Method. AIDS Res Hum Retroviruses 2015; 31:1225-9. [PMID: 26355677 DOI: 10.1089/aid.2015.0178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This study investigates a chain of HIV transmission events due to homosexual exposure and blood transfusion in China. The MiSeq platform, a next generation sequencing (NGS) system, was used to obtain genetic details of the HIV-1 env region (336 base pairs). Evolutionary analysis combined with epidemiologic evidence suggests a transmission chain from patient T3 to T2 through homosexual exposure and subsequently to T1 through blood transfusion. More importantly, a phylogenetic study suggested a likely genetic bottleneck for HIV in homosexual transmission from T3 to T2, while T1 inherited the majority of variants from T2. The result from the MiSeq platform is consistent with findings from the epidemiologic survey. The MiSeq platform is a powerful tool for tracing HIV transmissions and intrapersonal evolution.
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Affiliation(s)
- Qi Zhao
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Chen Zhang
- 2 National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Yan Jiang
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Yujie Wen
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Pinliang Pan
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Yang Li
- 2 National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Guiyun Zhang
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Lei Zhang
- 3 Research Center for Public Health, School of Medicine, Tsinghua University , Beijing, China
- 4 Melbourne Sexual Health Centre , Alfred Health, Melbourne, Victoria, Australia
- 5 Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University , Melbourne, Victoria, Australia
| | - Maofeng Qiu
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
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30
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Delgado E, Cuevas MT, Domínguez F, Vega Y, Cabello M, Fernández-García A, Pérez-Losada M, Castro MÁ, Montero V, Sánchez M, Mariño A, Álvarez H, Ordóñez P, Ocampo A, Miralles C, Pérez-Castro S, López-Álvarez MJ, Rodríguez R, Trigo M, Diz-Arén J, Hinojosa C, Bachiller P, Hernáez-Crespo S, Cisterna R, Garduño E, Pérez-Álvarez L, Thomson MM. Phylogeny and Phylogeography of a Recent HIV-1 Subtype F Outbreak among Men Who Have Sex with Men in Spain Deriving from a Cluster with a Wide Geographic Circulation in Western Europe. PLoS One 2015; 10:e0143325. [PMID: 26599410 PMCID: PMC4658047 DOI: 10.1371/journal.pone.0143325] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 11/03/2015] [Indexed: 11/18/2022] Open
Abstract
We recently reported the rapid expansion of an HIV-1 subtype F cluster among men who have sex with men (MSM) in the region of Galicia, Northwest Spain. Here we update this outbreak, analyze near full-length genomes, determine phylogenetic relationships, and estimate its origin. For this study, we used sequences of HIV-1 protease-reverse transcriptase and env V3 region, and for 17 samples, near full-length genome sequences were obtained. Phylogenetic analyses were performed via maximum likelihood. Locations and times of most recent common ancestors were estimated using Bayesian inference. Among samples analyzed by us, 100 HIV-1 F1 subsubtype infections of monophyletic origin were diagnosed in Spain, including 88 in Galicia and 12 in four other regions. Most viruses (n = 90) grouped in a subcluster (Galician subcluster), while 7 from Valladolid (Central Spain) grouped in another subcluster. At least 94 individuals were sexually-infected males and at least 71 were MSM. Seventeen near full-length genomes were uniformly of F1 subsubtype. Through similarity searches and phylogenetic analyses, we identified 18 viruses from four other Western European countries [Switzerland (n = 8), Belgium (n = 5), France (n = 3), and United Kingdom (n = 2)] and one from Brazil, from samples collected in 2005–2011, which branched within the subtype F cluster, outside of both Spanish subclusters, most of them corresponding to recently infected individuals. The most probable geographic origin and age of the Galician subcluster was Ferrol, Northwest Galicia, around 2007, while the Western European cluster probably emerged in Switzerland around 2002. In conclusion, a recently expanded HIV-1 subtype F cluster, the largest non-subtype B cluster reported in Western Europe, continues to spread among MSM in Spain; this cluster is part of a larger cluster with a wide geographic circulation in diverse Western European countries.
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Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Francisco Domínguez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Yolanda Vega
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Marina Cabello
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Marcos Pérez-Losada
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Vairão, Portugal
| | - María Ángeles Castro
- Department of Internal Medicine, Complejo Hospitalario Universitario de A Coruña, A Coruña, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Mariño
- Infectious Diseases Unit, Department of Internal Medicine, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain
| | - Hortensia Álvarez
- Infectious Diseases Unit, Department of Internal Medicine, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain
| | - Patricia Ordóñez
- Department of Microbiology, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain
| | - Antonio Ocampo
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | - Celia Miralles
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | - Sonia Pérez-Castro
- Department of Microbiology, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | | | - Raúl Rodríguez
- Department of Internal Medicine, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Matilde Trigo
- Department of Microbiology, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain
| | - Julio Diz-Arén
- Department of Internal Medicine, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain
| | - Carmen Hinojosa
- Department of Internal Medicine, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Pablo Bachiller
- Department of Internal Medicine, Hospital Universitario Río Hortega, Valladolid, Spain
| | - Silvia Hernáez-Crespo
- Department of Clinical Microbiology and Infection Control, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain
| | - Ramón Cisterna
- Department of Clinical Microbiology and Infection Control, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain
| | - Eugenio Garduño
- Department of Microbiology, Hospital Infanta Cristina, Badajoz, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- * E-mail:
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Assessing the HIV-1 Epidemic in Brazilian Drug Users: A Molecular Epidemiology Approach. PLoS One 2015; 10:e0141372. [PMID: 26536040 PMCID: PMC4633026 DOI: 10.1371/journal.pone.0141372] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/06/2015] [Indexed: 11/24/2022] Open
Abstract
Person who inject illicit substances have an important role in HIV-1 blood and sexual transmission and together with person who uses heavy non-injecting drugs may have less than optimal adherence to anti-retroviral treatment and eventually could transmit resistant HIV variants. Unfortunately, molecular biology data on such key population remain fragmentary in most low and middle-income countries. The aim of the present study was to assess HIV infection rates, evaluate HIV-1 genetic diversity, drug resistance, and to identify HIV transmission clusters in heavy drug users (DUs). For this purpose, DUs were recruited in the context of a Respondent-Driven Sampling (RDS) study in different Brazilian cities during 2009. Overall, 2,812 individuals were tested for HIV, and 168 (6%) of them were positive, of which 19 (11.3%) were classified as recent seroconverters, corresponding to an estimated incidence rate of 1.58%/year (95% CI 0.92–2.43%). Neighbor joining phylogenetic trees from env and pol regions and bootscan analyses were employed to subtype the virus from132 HIV-1-infected individuals. HIV-1 subtype B was prevalent in most of the cities under analysis, followed by BF recombinants (9%-35%). HIV-1 subtype C was the most prevalent in Curitiba (46%) and Itajaí (86%) and was also detected in Brasília (9%) and Campo Grande (20%). Pure HIV-1F infections were detected in Rio de Janeiro (9%), Recife (6%), Salvador (6%) and Brasília (9%). Clusters of HIV transmission were assessed by Maximum likelihood analyses and were cross-compared with the RDS network structure. Drug resistance mutations were verified in 12.2% of DUs. Our findings reinforce the importance of the permanent HIV-1 surveillance in distinct Brazilian cities due to viral resistance and increasing subtype heterogeneity all over Brazil, with relevant implications in terms of treatment monitoring, prophylaxis and vaccine development.
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32
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Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Toki S. CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochem Biophys Res Commun 2015; 467:76-82. [PMID: 26408904 DOI: 10.1016/j.bbrc.2015.09.117] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 12/11/2022]
Abstract
Site-directed mutagenesis using genetic approaches can provide a wealth of resources for crop breeding as well as for biological research. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 endonuclease (CRISPR/Cas9) system is a novel strategy used to induce mutations in a specific genome region; the system functions in a variety of organisms, including plants. Here, we report application of the CRISPR/Cas9 system to efficient mutagenesis of the tomato genome. In this study, we targeted the tomato RIN gene, which encodes a MADS-box transcription factor regulating fruit ripening. Three regions within the gene were targeted and mutations consisting either of a single base insertion or deletion of more than three bases were found at the Cas9 cleavage sites in T0 regenerated plants. The RIN-protein-defective mutants produced incomplete-ripening fruits in which red color pigmentation was significantly lower than that of wild type, while heterologous mutants expressing the remaining wild-type gene reached full-ripening red color, confirming the important role of RIN in ripening. Several mutations that were generated at three independent target sites were inherited in the T1 progeny, confirming the applicability of this mutagenesis system in tomato.
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Affiliation(s)
- Yasuhiro Ito
- National Food Research Institute, NARO, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
| | - Ayako Nishizawa-Yokoi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masaki Endo
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masafumi Mikami
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan; Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Yokohama, Kanagawa 236-0027, Japan
| | - Seiichi Toki
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan; Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Yokohama, Kanagawa 236-0027, Japan; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Yokohama, Kanagawa 244-0813, Japan
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Muterko A, Kalendar R, Cockram J, Balashova I. Discovery, evaluation and distribution of haplotypes and new alleles of the Photoperiod-A1 gene in wheat. PLANT MOLECULAR BIOLOGY 2015; 88:149-164. [PMID: 25851614 DOI: 10.1007/s11103-015-0313-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 03/29/2015] [Indexed: 06/04/2023]
Abstract
Photoperiod response in wheat is determined to a large extent by the homoeologous series of Photoperiod 1 (Ppd1) genes. In this study, Ppd-A1 genomic sequences from the 5' UTR and promoter region were analysed in 104 accessions of six tetraploid wheat species (Triticum dicoccoides, T. dicoccum, T. turgidum, T. polonicum, T. carthlicum, T. durum) and 102 accessions of six hexaploid wheat species (T. aestivum, T. compactum, T. sphaerococcum, T. spelta, T. macha, T. vavilovii). This data was supplemented with in silico analysis of publicly available sequences from 46 to 193 accessions of diploid and tetraploid wheat, respectively. Analysis of a region of the Ppd-A1 promoter identified thirteen haplotypes, which were divided in two haplogroups. Distribution of the Ppd-A1 haplogroups and haplotypes in wheat species, and their geographical distributions were analysed. Polymerase chain reaction combined with a heteroduplex mobility assay was subsequently used to efficiently discriminate between Ppd-A1 alleles, allowing identification of the Ppd-A1b haplotypes and haplogroups. The causes of anomalous migration of Ppd-A1 heteroduplexes in gels were found to be the localization of mismatches relative to the center of fragment, the cumulative effect of neighbouring polymorphic sites, and the location of mismatches within A/T-tracts. Analysis of the Ppd-A1 5' UTR in hexaploid wheat revealed a novel mutation within the "photoperiod critical" region in a subset of T. compactum accessions. This putative photoperiod insensitive allele (designated Ppd-A1a.4) includes a 684 bp deletion which spans region in common with deletions previously identified in other photoperiod insensitive Ppd1 alleles.
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Affiliation(s)
- Alexandr Muterko
- Department of Genomics and Biotechnology, Plant Breeding and Genetics Institute - National Center of Seed and Cultivar Investigation, Ovidiopolskaya Road 3, Odessa, 65036, Ukraine,
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Chéret A, Bacchus-Souffan C, Avettand-Fenoël V, Mélard A, Nembot G, Blanc C, Samri A, Sáez-Cirión A, Hocqueloux L, Lascoux-Combe C, Allavena C, Goujard C, Valantin MA, Leplatois A, Meyer L, Rouzioux C, Autran B. Combined ART started during acute HIV infection protects central memory CD4+ T cells and can induce remission. J Antimicrob Chemother 2015; 70:2108-20. [PMID: 25900157 DOI: 10.1093/jac/dkv084] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/13/2015] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Therapeutic control of HIV replication reduces the size of the viral reservoir, particularly among central memory CD4+ T cells, and this effect might be accentuated by early treatment. METHODS We examined the effect of ART initiated at the time of the primary HIV infection (early ART), lasting 2 and 6 years in 11 and 10 patients, respectively, on the HIV reservoir in peripheral resting CD4+ T cells, sorted into naive (TN), central memory (TCM), transitional memory (TTM) and effector memory (TEM) cells, by comparison with 11 post-treatment controllers (PTCs). RESULTS Between baseline and 2 years, CD4+ T cell subset numbers increased markedly (P < 0.004) and HIV DNA levels decreased in all subsets (P < 0.009). TTM cells represented the majority of reservoir cells at both timepoints, T cell activation status normalized and viral diversity remained stable over time. The HIV reservoir was smaller after 6 years of early ART than after 2 years (P < 0.019), and did not differ between PTCs and patients treated for 6 years. One patient, who had low reservoir levels in all T cell subsets after 2 years of treatment similar to the levels in PTCs, spontaneously controlled viral replication during 18 months off treatment. CONCLUSIONS Early prolonged ART thus limits the size of the HIV reservoir, protects long-lived cells from persistent infection and may enhance post-treatment control.
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Affiliation(s)
- Antoine Chéret
- EA 7327 Paris-Descartes University, Sorbonne Paris-Cité, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France Infectious Diseases Department, Dron Hospital, Tourcoing, France
| | - Charline Bacchus-Souffan
- Pierre & Marie Curie University Paris VI, INSERM UMR-S 945 Immunity & Infection, Pitié-Salpêtrière Hospital, Paris, France
| | - Veronique Avettand-Fenoël
- EA 7327 Paris-Descartes University, Sorbonne Paris-Cité, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France Infectious Diseases Department, Dron Hospital, Tourcoing, France
| | - Adeline Mélard
- EA 7327 Paris-Descartes University, Sorbonne Paris-Cité, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France Infectious Diseases Department, Dron Hospital, Tourcoing, France
| | - Georges Nembot
- Epidemiology and Public Health Department, Inserm U1018, AP-HP, Le Kremlin-Bicêtre Hospital, University Paris Sud, Le Kremlin-Bicêtre, France
| | - Catherine Blanc
- CyPS Flow Cytometry Platform, Pierre & Marie Curie University, Pitié-Salpêtrière Hospital, Paris, France
| | - Assia Samri
- Pierre & Marie Curie University Paris VI, INSERM UMR-S 945 Immunity & Infection, Pitié-Salpêtrière Hospital, Paris, France
| | - Asier Sáez-Cirión
- Pasteur Institute, Regulation of Retroviral Infections Unit, Paris, France
| | | | | | | | - Cécile Goujard
- Internal Medicine Department, AP-HP, Le Kremlin-Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Marc Antoine Valantin
- Infectious Diseases Department, AP-HP, Pitié-Salpêtrière Hospital, University Paris XII, Paris, France
| | - Anne Leplatois
- Infectious Diseases Department, l'Archet Hospital, Nice, France
| | - Laurence Meyer
- Epidemiology and Public Health Department, Inserm U1018, AP-HP, Le Kremlin-Bicêtre Hospital, University Paris Sud, Le Kremlin-Bicêtre, France
| | - Christine Rouzioux
- EA 7327 Paris-Descartes University, Sorbonne Paris-Cité, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France Infectious Diseases Department, Dron Hospital, Tourcoing, France
| | - Brigitte Autran
- Pierre & Marie Curie University Paris VI, INSERM UMR-S 945 Immunity & Infection, Pitié-Salpêtrière Hospital, Paris, France
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Sakkhachornphop S, Kijak GH, Beyrer C, Razak MH, Sanders-Buell E, Jittiwutikarn J, Suriyanon V, Robb ML, Kim JH, Celentano DD, McCutchan FE, Tovanabutra S. An effective tool for identifying HIV-1 subtypes B, C, CRF01_AE, their recombinant forms, and dual infections in Southeast Asia by the multi-region subtype specific PCR (MSSP) assay. J Virol Methods 2015; 217:70-8. [PMID: 25725414 DOI: 10.1016/j.jviromet.2015.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 02/05/2015] [Accepted: 02/14/2015] [Indexed: 01/14/2023]
Abstract
The RV144 Thai vaccine trial has been the only vaccine study to show efficacy in preventing HIV infection. Ongoing molecular surveillance of HIV-1 in Southeast Asia is vital for vaccine development and evaluation. In this study a novel tool, the multi-region subtype specific PCR (MSSP) assay, that was able to identify subtypes B, C, CRF01_AE for Thailand, other Southeast Asian countries, India and China is described. The MSSP assay is based on a nested PCR strategy and amplifies eight short regions distributed along the HIV-1 genome using subtype-specific primers. A panel of 41 clinical DNA samples obtained primarily from opiate users in northern Thailand was used to test the assay performance. The MSSP assay provided 73-100% sensitivity and 100% specificity for the three subtypes in each genome region. The assay was then field-tested on 337 sera from HIV infected northern Thai drug users collected between 1999 and 2002. Subtype distribution was CRF01_AE 77.4% (n=261), subtype B 3.3% (n=11), CRF01_AE/B recombinant 12.2% (n=41), CRF01_AE/C recombinant 0.6% (n=2), and non-typeable 6.5% (n=22). The MSSP assay is a simple, cost-effective, and accurate genotyping tool for laboratory settings with limited resources and is sensitive enough to capture the recombinant genomes and dual infections.
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Affiliation(s)
| | - Gustavo H Kijak
- U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA
| | - Chris Beyrer
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Myat Htoo Razak
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA
| | | | - Vinai Suriyanon
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Merlin L Robb
- U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA
| | - Jerome H Kim
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - David D Celentano
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Francine E McCutchan
- U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD 20910, USA.
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Junqueira DM, Medeiros RMD, Leite TCNF, Guimarães ML, Gräf T, Pinto AR, Almeida SEDM. Detection of the B"-GWGR variant in the southernmost region of Brazil: unveiling the complexity of the human immunodeficiency virus-1 subtype B epidemic. Mem Inst Oswaldo Cruz 2014; 108:735-40. [PMID: 24037196 PMCID: PMC3970682 DOI: 10.1590/0074-0276108062013010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/26/2013] [Indexed: 12/17/2022] Open
Abstract
Typical human immunodeficiency virus-1 subtype B (HIV-1B) sequences present a GPGR signature at the tip of the variable region 3 (V3) loop; however, unusual motifs harbouring a GWGR signature have also been isolated. Although epidemiological studies have detected this variant in approximately 17-50% of the total infections in Brazil, the prevalence of B"-GWGR in the southernmost region of Brazil is not yet clear. This study aimed to investigate the C2-V3 molecular diversity of the HIV-1B epidemic in southernmost Brazil. HIV-1 seropositive patients were ana-lysed at two distinct time points in the state of Rio Grande do Sul (RS98 and RS08) and at one time point in the state of Santa Catarina (SC08). Phylogenetic analysis classified 46 individuals in the RS98 group as HIV-1B and their molecular signatures were as follows: 26% B"-GWGR, 54% B-GPGR and 20% other motifs. In the RS08 group, HIV-1B was present in 32 samples: 22% B"-GWGR, 59% B-GPGR and 19% other motifs. In the SC08 group, 32 HIV-1B samples were found: 28% B"-GWGR, 59% B-GPGR and 13% other motifs. No association could be established between the HIV-1B V3 signatures and exposure categories in the HIV-1B epidemic in RS. However, B-GPGR seemed to be related to heterosexual individuals in the SC08 group. Our results suggest that the established B"-GWGR epidemics in both cities have similar patterns, which is likely due to their geographical proximity and cultural relationship.
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Affiliation(s)
- Dennis Maletich Junqueira
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde,, Porto AlegreRS, Brasil
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37
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Rawson JMO, Mansky LM. Retroviral vectors for analysis of viral mutagenesis and recombination. Viruses 2014; 6:3612-42. [PMID: 25254386 PMCID: PMC4189041 DOI: 10.3390/v6093612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 12/29/2022] Open
Abstract
Retrovirus population diversity within infected hosts is commonly high due in part to elevated rates of replication, mutation, and recombination. This high genetic diversity often complicates the development of effective diagnostics, vaccines, and antiviral drugs. This review highlights the diverse vectors and approaches that have been used to examine mutation and recombination in retroviruses. Retroviral vectors for these purposes can broadly be divided into two categories: those that utilize reporter genes as mutation or recombination targets and those that utilize viral genes as targets of mutation or recombination. Reporter gene vectors greatly facilitate the detection, quantification, and characterization of mutants and/or recombinants, but may not fully recapitulate the patterns of mutagenesis or recombination observed in native viral gene sequences. In contrast, the detection of mutations or recombination events directly in viral genes is more biologically relevant but also typically more challenging and inefficient. We will highlight the advantages and disadvantages of the various vectors and approaches used as well as propose ways in which they could be improved.
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Affiliation(s)
- Jonathan M O Rawson
- Institute for Molecular Virology, University of Minnesota, Moos Tower 18-242, 515 Delaware St SE, Minneapolis, MN 55455, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Moos Tower 18-242, 515 Delaware St SE, Minneapolis, MN 55455, USA.
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Shcherbakova NS, Shalamova LA, Delgado E, Fernández-García A, Vega Y, Karpenko LI, Ilyichev AA, Sokolov YV, Shcherbakov DN, Pérez-Álvarez L, Thomson MM. Short communication: Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia. AIDS Res Hum Retroviruses 2014; 30:912-9. [PMID: 25050828 DOI: 10.1089/aid.2014.0075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A(FSU)) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A(FSU), which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.
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Affiliation(s)
- Nadezhda S. Shcherbakova
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Lyudmila A. Shalamova
- Department of Zoonotic Infections and Influenza, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Yolanda Vega
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Larissa I. Karpenko
- Laboratory of Recombinant Vaccine, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Alexander A. Ilyichev
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Yuri V. Sokolov
- Center for Prevention and Control of AIDS and Infectious Diseases, Koltsovo, Novosibirsk, Russia
| | | | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Abstract
UNLABELLED Recall T cell responses to HIV-1 antigens are used as a surrogate for endogenous cellular immune responses generated during infection. Current methods of identifying antigen-specific T cell reactivity in HIV-1 infection use bulk peripheral blood mononuclear cells (PBMC) yet ignore professional antigen-presenting cells (APC) that could reveal otherwise hidden responses. In the present study, peptides representing autologous variants of major histocompatibility complex (MHC) class I-restricted epitopes from HIV-1 Gag and Env were used as antigens in gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) and polyfunctional cytokine assays. Here we show that dendritic cells (DC) enhanced T cell reactivity at all stages of disease progression but specifically restored T cell reactivity after combination antiretroviral therapy (cART) to early infection levels. Type 1 cytokine secretion was also enhanced by DC and was most apparent late post-cART. We additionally show that DC reveal polyfunctional T cell responses after many years of treatment, when potential immunotherapies would be implemented. These data underscore the potential efficacy of DC immunotherapy that aims to awaken a dormant, autologous, HIV-1-specific CD8+ T cell response. IMPORTANCE Assessment of endogenous HIV-1-specific T cell responses is critical for generating immunotherapies for subjects on cART. Current assays ignore the ability of dendritic cells to reveal these responses and may therefore underestimate the breadth and magnitude of T cell reactivity. As DC do not prime new responses in these assays, it can be assumed that the observed responses are not detected without appropriate stimulation. This is important because dogma states that HIV-1 mutates to evade host recognition and that CD8+ cytotoxic T lymphocyte (CTL) failure is due to the inability of T cells to recognize the autologous virus. The results presented here indicate that responses to autologous virus are generated during infection but may need additional stimulation to be effective. Detecting the breadth and magnitude of HIV-1-specific T cell reactivity generated in vivo is of the utmost importance for generating effective DC immunotherapies.
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Carnegie NB, Wang R, Novitsky V, De Gruttola V. Linkage of viral sequences among HIV-infected village residents in Botswana: estimation of linkage rates in the presence of missing data. PLoS Comput Biol 2014; 10:e1003430. [PMID: 24415932 PMCID: PMC3886896 DOI: 10.1371/journal.pcbi.1003430] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 11/25/2013] [Indexed: 11/30/2022] Open
Abstract
Linkage analysis is useful in investigating disease transmission dynamics and the effect of interventions on them, but estimates of probabilities of linkage between infected people from observed data can be biased downward when missingness is informative. We investigate variation in the rates at which subjects' viral genotypes link across groups defined by viral load (low/high) and antiretroviral treatment (ART) status using blood samples from household surveys in the Northeast sector of Mochudi, Botswana. The probability of obtaining a sequence from a sample varies with viral load; samples with low viral load are harder to amplify. Pairwise genetic distances were estimated from aligned nucleotide sequences of HIV-1C env gp120. It is first shown that the probability that randomly selected sequences are linked can be estimated consistently from observed data. This is then used to develop estimates of the probability that a sequence from one group links to at least one sequence from another group under the assumption of independence across pairs. Furthermore, a resampling approach is developed that accounts for the presence of correlation across pairs, with diagnostics for assessing the reliability of the method. Sequences were obtained for 65% of subjects with high viral load (HVL, n = 117), 54% of subjects with low viral load but not on ART (LVL, n = 180), and 45% of subjects on ART (ART, n = 126). The probability of linkage between two individuals is highest if both have HVL, and lowest if one has LVL and the other has LVL or is on ART. Linkage across groups is high for HVL and lower for LVL and ART. Adjustment for missing data increases the group-wise linkage rates by 40–100%, and changes the relative rates between groups. Bias in inferences regarding HIV viral linkage that arise from differential ability to genotype samples can be reduced by appropriate methods for accommodating missing data. The analysis of viral genomes has great potential for investigating transmission of disease, including the identification of risk factors and transmission clusters, and can thereby aid in targeting interventions. To make use of genetic data in this way, it is necessary to make inferences about population-level patterns of viral linkage. As with any rigorous statistical inference from sampled data to a population, it is important to consider the effect of the sampling strategy and the occurrence of missing data on the final inferences made. In this paper we highlight the effects of missing data on the resulting estimates of population level linkage rates and develop methods for adjusting for the presence of missing data. As an example, we consider comparing the rates of linkage of HIV sequences from subjects with high viral load, low viral load, or on antiretroviral treatment, and show that comparative inferences are compromised when adjustment is not made for missing sequences and bias in inferences can be reduced with proper adjustment.
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Affiliation(s)
- Nicole Bohme Carnegie
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
| | - Rui Wang
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Victor De Gruttola
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Novitsky V, Bussmann H, Logan A, Moyo S, van Widenfelt E, Okui L, Mmalane M, Baca J, Buck L, Phillips E, Tim D, McLane MF, Lei Q, Wang R, Makhema J, Lockman S, DeGruttola V, Essex M. Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana. PLoS One 2013; 8:e80589. [PMID: 24349005 PMCID: PMC3859477 DOI: 10.1371/journal.pone.0080589] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/04/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Determining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities. METHODS To reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C env sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010-2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C env sequences and bootstrap support of splits. RESULTS The overall proportion of clustered HIV-1C env sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non-Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters. CONCLUSIONS The study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages.
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Affiliation(s)
- Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | | | - Andrew Logan
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Lillian Okui
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Mompati Mmalane
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Jeannie Baca
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Lauren Buck
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Eleanor Phillips
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - David Tim
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Mary Fran McLane
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Quanhong Lei
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Rui Wang
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph Makhema
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Shahin Lockman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Victor DeGruttola
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - M. Essex
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Pimentel VF, Morgado MG, Bello G, Guimarães MD, Castilho EA, Veloso VG, Guimarães ML. Temporal trends and molecular epidemiology of HIV type 1 infection in Rio de Janeiro, Brazil. AIDS Res Hum Retroviruses 2013; 29:1553-61. [PMID: 23987184 DOI: 10.1089/aid.2013.0050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
HIV-1 molecular epidemiology studies carried out in Rio de Janeiro, Brazil have identified the prevalence of subtypes B, F1 and BF1 recombinants. A high percentage of HIV-1 subtype B isolates in Rio de Janeiro harbor the GWG motif at the V3 tip (B'' variant) instead of the canonical GPG motif (B variant). To trace the dynamics of the HIV-1 variants over time in different exposure categories in Rio de Janeiro, the HIV-1 proviral DNA from heterosexual men (HET) and men who have sex with men (MSM) from two distinct time periods (1990-1992 and 2008-2010) were extracted, and the env-gp120 region was amplified. Neighbor-joining phylogenetic analysis was performed to determine the viral subtype, and Bayesian analysis was used to trace the HIV-1 transmission networks. A predominance of subtype B was observed in both study periods, independent of the exposure risk category. An increase of non-B subtypes was observed in the HET group, but these subtypes were maintained among the MSM group. The distribution of HIV-1 subtype B signatures in the first and second periods studied were, respectively, HET (GPG) [44.8-51.5%], (GWG) [13.8-33.3%], and (GXG) [41.4-15.2%] and MSM (GPG) [34-50%], (GWG) [55.3-30.6%], and (GXG) [10.7-19.4%]. In the first period, an association between GWG and MSM was verified while a significant reduction of this association was observed during the second period. The phylogenetic tree and the BaTS program detected the clustering of isolates only according to the B signatures but not by exposure risk category. Our findings indicate a stable prevalence of HIV-1 subtypes B and F over time in Rio de Janeiro and further suggest that the B'' subclade of subtype B was possibly introduced into the MSM group in this area of Brazil.
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Shankarappa R, Mullins JI. Inferring viral population structures using heteroduplex mobility and DNA sequence analyses. J Virol Methods 2013; 194:169-77. [PMID: 23994080 DOI: 10.1016/j.jviromet.2013.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022]
Abstract
Heteroduplex mobility (HMA) and tracking assays (HTA) are used to assess genetic relationships between DNA molecules. While distinguishing relationships between clonal or nearly clonal molecules is relatively straightforward, inferring population structures is more complex. To address this issue, HIV-1 quasispecies with varying levels of diversity were studied using both HTA and DNA sequencing. Viral diversity estimates and the temporal features of virus evolution were found to be generally concordant between HTA and DNA sequencing. In addition, the distribution of pairwise differences and the rates of virus divergence were similar between the two methods. These findings support the use of HTA to characterize variant populations of DNA and strengthen previous inferences concerning the evolution of HIV-1 over the course of infection.
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Affiliation(s)
- Raj Shankarappa
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, United States
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Bacchus C, Cheret A, Avettand-Fenoël V, Nembot G, Mélard A, Blanc C, Lascoux-Combe C, Slama L, Allegre T, Allavena C, Yazdanpanah Y, Duvivier C, Katlama C, Goujard C, Seksik BCP, Leplatois A, Molina JM, Meyer L, Autran B, Rouzioux C. A single HIV-1 cluster and a skewed immune homeostasis drive the early spread of HIV among resting CD4+ cell subsets within one month post-infection. PLoS One 2013; 8:e64219. [PMID: 23691172 PMCID: PMC3653877 DOI: 10.1371/journal.pone.0064219] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/10/2013] [Indexed: 12/30/2022] Open
Abstract
Optimizing therapeutic strategies for an HIV cure requires better understanding the characteristics of early HIV-1 spread among resting CD4+ cells within the first month of primary HIV-1 infection (PHI). We studied the immune distribution, diversity, and inducibility of total HIV-DNA among the following cell subsets: monocytes, peripheral blood activated and resting CD4 T cells, long-lived (naive [TN] and central-memory [TCM]) and short-lived (transitional-memory [TTM] and effector-memory cells [TEM]) resting CD4+T cells from 12 acutely-infected individuals recruited at a median 36 days from infection. Cells were sorted for total HIV-DNA quantification, phylogenetic analysis and inducibility, all studied in relation to activation status and cell signaling. One month post-infection, a single CCR5-restricted viral cluster was massively distributed in all resting CD4+ subsets from 88% subjects, while one subject showed a slight diversity. High levels of total HIV-DNA were measured among TN (median 3.4 log copies/million cells), although 10-fold less (p = 0.0005) than in equally infected TCM (4.5), TTM (4.7) and TEM (4.6) cells. CD3−CD4+ monocytes harbored a low viral burden (median 2.3 log copies/million cells), unlike equally infected resting and activated CD4+ T cells (4.5 log copies/million cells). The skewed repartition of resting CD4 subsets influenced their contribution to the pool of resting infected CD4+T cells, two thirds of which consisted of short-lived TTM and TEM subsets, whereas long-lived TN and TCM subsets contributed the balance. Each resting CD4 subset produced HIV in vitro after stimulation with anti-CD3/anti-CD28+IL-2 with kinetics and magnitude varying according to subset differentiation, while IL-7 preferentially induced virus production from long-lived resting TN cells. In conclusion, within a month of infection, a clonal HIV-1 cluster is massively distributed among resting CD4 T-cell subsets with a flexible inducibility, suggesting that subset activation and skewed immune homeostasis determine the conditions of viral dissemination and early establishment of the HIV reservoir.
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Affiliation(s)
- Charline Bacchus
- Pierre-and-Marie-Curie University Paris 06, Laboratory Immunity and Infection UMR_S 945, F-75013, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Laboratory Immunity and Infection UMR_S 945, F-75013, Paris, France
| | - Antoine Cheret
- Paris-Descartes University, Sorbonne Paris-Cité, EA 3620, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France
- Infectious Diseases Department, Gustave Dron Hospital, Tourcoing, France
| | - Véronique Avettand-Fenoël
- Paris-Descartes University, Sorbonne Paris-Cité, EA 3620, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France
| | - Georges Nembot
- Epidemiology and Public Health Department, Inserm U1018, Le Kremlin-Bicêtre Hospital, Paris, France
| | - Adeline Mélard
- Paris-Descartes University, Sorbonne Paris-Cité, EA 3620, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France
| | - Catherine Blanc
- CyPS Flow Cytometry Platform, Pierre & Marie Curie University, Pitié-Salpêtrière Hospital, Paris, France
| | - Caroline Lascoux-Combe
- Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Saint-Louis Hospital, Paris, France
| | - Laurence Slama
- Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Tenon Hospital, Paris, France
| | - Thierry Allegre
- Department of Hematology, Aix-en-Provence Hospital, Aix-en-Provence, France
| | | | - Yazdan Yazdanpanah
- Infectious Diseases Department, Gustave Dron Hospital, Tourcoing, France
| | - Claudine Duvivier
- Pasteur Institute, Medical Center, Necker-Pasteur Infectious Diseases Center, Paris, France
| | - Christine Katlama
- Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France
| | - Cécile Goujard
- Internal Medicine and Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre Hospital, Paris, France
| | - Bao Chau Phung Seksik
- Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Bichat Hospital, Paris, France
| | - Anne Leplatois
- Infectious Diseases Department, L’Archet Hospital, Nice, France
| | - Jean-Michel Molina
- Sorbonne Paris-Cité University, Institut National de la Santé et de la Recherche Médicale U941, Infectious Diseases Unit, Saint-Louis Hospital, Paris, France
| | - Laurence Meyer
- Epidemiology and Public Health Department, Inserm U1018, Le Kremlin-Bicêtre Hospital, Paris, France
| | - Brigitte Autran
- Pierre-and-Marie-Curie University Paris 06, Laboratory Immunity and Infection UMR_S 945, F-75013, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Laboratory Immunity and Infection UMR_S 945, F-75013, Paris, France
- * E-mail:
| | - Christine Rouzioux
- Paris-Descartes University, Sorbonne Paris-Cité, EA 3620, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France
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Freitas FB, Esteves A, Piedade J, Parreira R. Novel multiregion hybridization assay for the identification of the most prevalent genetic forms of the human immunodeficiency virus type 1 circulating in Portugal. AIDS Res Hum Retroviruses 2013; 29:318-28. [PMID: 22935093 DOI: 10.1089/aid.2012.0025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The most efficient method for HIV-1 genetic characterization involves full-genome sequencing, but the associated costs, technical features, and low throughput preclude it from being routinely used for the analysis of large numbers of viral strains. Multiregion hybridization assays (MHA) represent an alternative for a consistent genetic analysis of large numbers of viral strains. Classically, MHA rely on the amplification by real-time PCR of several regions scattered along the HIV-1 genome, and on their characterization with clade-specific TaqMan probes (also known as hydrolysis probes). In this context, the aim of our study was the development of a technical variant of an MHA (vMHA(B/G/02)) for genotyping the most prevalent genetic forms of HIV-1 circulating in Portugal. Different sets of primers were designed for universal and clade-specific amplifications of several sections of the viral genome: gag, pol(Pr), pol(RT), vpu, env(gp120), and env(gp41). vMHA(B/G/02) was implemented using a real-time PCR-based approach, with detection dependent on the use of SYBR Green I. As an alternative, a technically less demanding strategy based on conventional PCR and agarose gel analysis of the reaction products was also developed. This method performed with overall good sensitivity and specificity (>91%) when a convenience sample of 45 plasma-derived HIV-1 strains was analyzed. Apart from the detection of subtype B, G, CRF02_AG, and CRF14_BG viruses, several unique B/G recombinant were also detected. Curiously, recombinant viruses including CRF02_AG sequences were not detected in the group of samples analyzed.
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Affiliation(s)
- Ferdinando B. Freitas
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Aida Esteves
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - João Piedade
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ricardo Parreira
- Unidade de Microbiologia Médica-Grupo de Virologia/Unidade de Parasitologia e Microbiologia Médicas, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
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Gaspareto KV, Mello FMMDA, Dias JRC, Meneguetti VAF, Storti MEG, Ferreira JLDP, Lança AM, Rodrigues R, Brígido LFDM, Teixeira JJV, Bertolini DA. Genetic diversity and primary resistance among HIV-1-positive patients from Maringá, Paraná, Brazil. Rev Inst Med Trop Sao Paulo 2012; 54:207-13. [PMID: 22850992 DOI: 10.1590/s0036-46652012000400005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 05/03/2012] [Indexed: 11/21/2022] Open
Abstract
The objective of this study is to identify subtypes of Human Immunodeficiency Virus type 1 (HIV-1) and to analyze the presence of mutations associated to antiretroviral resistance in the protease (PR) and reverse transcriptase (RT) regions from 48 HIV-1 positive treatment naïve patients from an outpatient clinic in Maringá, Paraná, Brazil. Sequencing was conducted using PR, partial RT and group-specific antigen gene (gag) nested PCR products from retrotranscribed RNA. Transmitted resistance was determined according to the Surveillance Drug Resistance Mutation List (SDRM) algorithm. Phylogenetic and SimPlot analysis of concatenated genetic segments classified sequences as subtype B 19/48 (39.6%), subtype C 12/48 (25%), subtype F 4/48 (8.3%), with 13/48 (27.1%) recombinant forms. Most recombinant forms were B mosaics (B/F 12.5%, B/C 10.4%), with one C/F (2.1%) and one complex B/C/F mosaic (2.1%). Low levels of transmitted resistance were found in this study, 2/48 (2.1% to NRTIs and 2.1% for PI). This preliminary data may subsidize the monitoring of the HIV evolution in the region.
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Affiliation(s)
- Karine Vieira Gaspareto
- Laboratório de Retrovírus, Centro de Virologia, Instituto Adolfo Lutz, São Paulo, SP, Brazil
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Manigart O, Boeras DI, Karita E, Hawkins PA, Vwalika C, Makombe N, Mulenga J, Derdeyn CA, Allen S, Hunter E. A gp41-based heteroduplex mobility assay provides rapid and accurate assessment of intrasubtype epidemiological linkage in HIV type 1 heterosexual transmission Pairs. AIDS Res Hum Retroviruses 2012; 28:1745-55. [PMID: 22587371 DOI: 10.1089/aid.2012.0023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A critical step in HIV-1 transmission studies is the rapid and accurate identification of epidemiologically linked transmission pairs. To date, this has been accomplished by comparison of polymerase chain reaction (PCR)-amplified nucleotide sequences from potential transmission pairs, which can be cost-prohibitive for use in resource-limited settings. Here we describe a rapid, cost-effective approach to determine transmission linkage based on the heteroduplex mobility assay (HMA), and validate this approach by comparison to nucleotide sequencing. A total of 102 HIV-1-infected Zambian and Rwandan couples, with known linkage, were analyzed by gp41-HMA. A 400-base pair fragment within the envelope gp41 region of the HIV proviral genome was PCR amplified and HMA was applied to both partners' amplicons separately (autologous) and as a mixture (heterologous). If the diversity between gp41 sequences was low (<5%), a homoduplex was observed upon gel electrophoresis and the transmission was characterized as having occurred between partners (linked). If a new heteroduplex formed, within the heterologous migration, the transmission was determined to be unlinked. Initial blind validation of gp-41 HMA demonstrated 90% concordance between HMA and sequencing with 100% concordance in the case of linked transmissions. Following validation, 25 newly infected partners in Kigali and 12 in Lusaka were evaluated prospectively using both HMA and nucleotide sequences. Concordant results were obtained in all but one case (97.3%). The gp41-HMA technique is a reliable and feasible tool to detect linked transmissions in the field. All identified unlinked results should be confirmed by sequence analyses.
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Affiliation(s)
- Olivier Manigart
- Rwanda Zambia HIV Research Group (RZHRG), Projet San Francisco (PSF), Kigali, Rwanda
- Emory University, Atlanta, Georgia
- RZHRG, Zambia Emory University HIV Research Project (ZEHRP), Lusaka, Zambia
| | | | - Etienne Karita
- Rwanda Zambia HIV Research Group (RZHRG), Projet San Francisco (PSF), Kigali, Rwanda
| | | | - Cheswa Vwalika
- RZHRG, Zambia Emory University HIV Research Project (ZEHRP), Lusaka, Zambia
| | - Nathan Makombe
- Rwanda Zambia HIV Research Group (RZHRG), Projet San Francisco (PSF), Kigali, Rwanda
| | - Joseph Mulenga
- RZHRG, Zambia Emory University HIV Research Project (ZEHRP), Lusaka, Zambia
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HIV-1 subtypes and recombinants in Northern Tanzania: distribution of viral quasispecies. PLoS One 2012; 7:e47605. [PMID: 23118882 PMCID: PMC3485255 DOI: 10.1371/journal.pone.0047605] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/13/2012] [Indexed: 11/25/2022] Open
Abstract
This study analyzed the distribution and prevalence of HIV-1 subtypes, multiplicity of HIV-1 infection, and frequency of inter-subtype recombination among HIV-1-infected female bar and hotel workers in Moshi, Kilimanjaro Region, Tanzania, from 2004 to 2007. The HIV-1 viral sequences spanning the V1-C5 region of HIV-1 env gp120 were analyzed from 50 subjects by single genome amplification and sequencing (SGA/S) technique. A total of 1740 sequences were amplified and sequenced from the HIV-1 proviral DNA template. The median env sequences analyzed per subject per two time points was 38 (IQR 28–50) over one year of HIV infection. In a subset of 14 subjects, a total of 239 sequences were obtained from HIV-1 RNA template at the baseline visit. The most prevalent HIV-1 subtypes were A1 (56%) and C (30%), while HIV-1 subtype D and inter-subtype recombinant viruses were found in 6% and 8% of subjects respectively. Transmission of multiple HIV-1 variants was evident in 27% of the subjects infected with pure HIV-1 subtypes A1, C, or D. The HIV-1 inter-subtype recombinants were found in 8% including HIV-1 C/A, D/A, and complex mosaic recombinants. Multiple viral variants were found in two subjects infected with inter-subtype recombinants. One subject harbored quasispecies of both pure HIV-1 A1 and C/A recombinant. The other subject was infected with two complex mosaic inter-subtype recombinant variants belonging to subtype D. HIV-1 multiple infections and ongoing recombination contribute significantly to the genetic diversity of circulating HIV-1 in Tanzania and have important implications for vaccine design and the development of therapeutic strategies.
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Telan EFO, Samonte GMJ, Abellanosa-Tac-An IP, Alesna ET, Leaño PSA, Emphasis YEE, Tsuneki A, Matsumoto K, Kageyama S. The early phase of an HIV epidemic in a population exposed previously to HCV in the Philippines. J Med Virol 2012; 83:941-7. [PMID: 21503904 DOI: 10.1002/jmv.22070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Human immunodeficiency virus (HIV) sentinel surveillance program for injecting drug users has been conducted in Metro Cebu, the Philippines. A low prevalence (0-0.52%) of anti-HIV-positivity had been detected in this population from 2002 to 2007. However, a 10-fold increase in HIV prevalence was detected in the 2009 national HIV sentinel surveillance program. It prompted an additional outreach program to be conducted in Metro Cebu in January 2010, which recorded the highest HIV prevalence rate ever documented in the Philippines (75%, 44/59). HIV genes from fourteen 2009 to 2010 Metro Cebu strains were clustered closely in the phylogenetic tree, but no other strain collected outside Metro Cebu and none stored in the International Nucleotide Sequence Database was allocated to the same phylogenetic cluster. All these HIV infections have emerged in the anti-hepatitis C virus (HCV)-positive population (100%, 62/62) in Metro Cebu from 2009 to 2010. The five HCV strains from the individuals harboring the closely related HIV strains were categorized into different subtypes. These results strongly suggest that HIV infections occurred recently and spread rapidly among injecting drug users, while HCV had been circulating previously among them. Considering the fact that injecting drug use was the first mode of HIV transmission in Asia, extensive monitoring of injecting drug users and associated bridging populations is necessary. Therefore, HCV-guided characterization of the spread of HIV to populations that are vulnerable to blood-borne infections could play an important role in alerting health authorities to the early phase of an HIV epidemic.
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Ragupathy V, Casado C, Jacob SM, Samuel NM, Lopez-Galindez C. Circulation of HIV-1 subtype A within the subtype C HIV-1 epidemic in Tamil Nadu, India. J Med Virol 2012; 84:1507-13. [PMID: 22930495 DOI: 10.1002/jmv.23383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The HIV-1 epidemic in India is caused mainly by subtype C viruses that are transmitted sexually and by injecting drug use. The state of Tamil Nadu in Southern India has an HIV-1 median prevalence of 16.8% among injecting drug users, 6.6% in men who have sex with men, and 4.6% in female sex workers. In the rural district of Namakkal, a prevalence >3% was detected among antenatal women. The goal of this study was to determine the HIV-1 molecular epidemiology in Tamil Nadu. Blood samples were collected from 40 high-risk HIV-seropositive individuals from Chennai and Namakkal. HIV-1 subtype was determined by envelope nucleotide sequencing. Among the samples studied, 85% were subtype C, however, a cluster of subtype A samples (12.5%) and one subtype E recombinant form CRF01_AE (close to the Thailand strains) were detected. The average genetic distance of subtype C samples from Chennai and Namakkal were 9.44 ± 0.77% and 11.8 ± 0.7%, respectively indicating an evolved epidemic. This pilot study confirmed that subtype C was predominant in these regions but an outbreak of subtype A was detected in Namakkal. These results stress the importance of periodic monitoring of circulating HIV-1 subtypes in South India.
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Affiliation(s)
- Viswanath Ragupathy
- Department of Experimental Medicine, Tamil Nadu Dr MGR Medical University, Chennai, Tamil Nadu, India.
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