scholarly journals Evolution in the Courtroom: Using Phylogenetics to Investigate Legal Claims of HIV Transmission

2020 ◽  
Author(s):  
Benjamin Toups ◽  
Jeremy M. Brown
Keyword(s):  
Biological Sciences ◽  
Dna Sequences ◽  
Hiv Transmission ◽  
Rapid Evolution ◽  
Rapid Rate ◽  
The Public ◽  
Rates Of Evolution ◽  
Immunodeficiency Virus ◽  
Hiv 1 ◽  
Fast Rates

DNA sequences have become ubiquitous across the biological sciences and are even embedded in the public psyche, perhaps most famously in the context of forensic science. A human being’s DNA changes very little over his or her lifetime, and this inherent stability lends itself well to positively identifying individuals using DNA samples. However, not all genomes are so stable, even over short timespans. One particularly dramatic example is human immunodeficiency virus (HIV-1). Unlike the human genome, the HIV-1 genome has an extraordinarily high mutation rate. This, in combination with recombination, rapid proliferation, and strong selection exerted by host immune systems, leads to exceptionally fast rates of evolution. The result of these interacting processes is a population of diverse and dynamically evolving HIV-1 genomes in the host, which is one reason why the virus is so difficult to eradicate. HIV-1’s rapid rate of evolution also prevents the use of standard DNA fingerprinting techniques that rely on stable, unchanging genomes to connect the infections in different individuals, but such rapid evolution does lend itself particularly well to phylogenetic analysis.

scholarly journals Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia

Viruses ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 482 ◽  
Author(s):  
Francesca Di Giallonardo ◽  
Angie N. Pinto ◽  
Phillip Keen ◽  
Ansari Shaik ◽  
Alex Carrera ◽  
...  
Keyword(s):  
Hiv Transmission ◽  
New South ◽  
New South Wales ◽  
Incidence Rates ◽  
Effective Control ◽  
South Wales ◽  
Immunodeficiency Virus ◽  
Hiv 1 ◽  
Local Transmission

Australia’s response to the human immunodeficiency virus type 1 (HIV-1) pandemic led to effective control of HIV transmission and one of the world’s lowest HIV incidence rates—0.14%. Although there has been a recent decline in new HIV diagnoses in New South Wales (NSW), the most populous state in Australia, there has been a concomitant increase with non-B subtype infections, particularly for the HIV-1 circulating recombinant form CRF01_AE. This aforementioned CRF01_AE sampled in NSW, were combined with those sampled globally to identify NSW-specific viral clades. The population growth of these clades was assessed in two-year period intervals from 2009 to 2017. Overall, 109 NSW-specific clades were identified, most comprising pairs of sequences; however, five large clades comprising ≥10 sequences were also found. Forty-four clades grew over time with one or two sequences added to each in different two-year periods. Importantly, while 10 of these clades have seemingly discontinued, the remaining 34 were still active in 2016/2017. Seven such clades each comprised ≥10 sequences, and are representative of individual sub-epidemics in NSW. Thus, although the majority of new CRF01_AE infections were associated with small clades that rarely establish ongoing chains of local transmission, individual sub-epidemics are present and should be closely monitored.

scholarly journals Detecção de HIV/AIDS por meio de teste rápido: estudo comparativo

2019 ◽  
Vol 9 (26) ◽  
pp. 95
Author(s):  
Alecsandra Bezerra Monteiro de Oliveira ◽  
Carmem Gabriela Gomes de Figueiredo ◽  
Maria Soraya Pereira Franco Adriano
Keyword(s):  
Rapid Test ◽  
Hiv Diagnosis ◽  
Adequate Treatment ◽  
The Public ◽  
Primary Health ◽  
Immunodeficiency Virus ◽  
Rapid Tests ◽  
The City ◽  
Hiv 1 ◽  
Hiv Aids

Dada a importância do teste rápido para diagnóstico da infecção pelo vírus da Imunodeficiência Humana (HIV), determinamos o número de testes rápidos (TR) realizados e reagentes entre 2015 e 2016 pela seção de DST/Aids do município de João Pessoa/PB, Brasil. Dos 77130 TR realizados pelo Serviço de Atendimento Especializado/Centro de Testagem e Acompanhamento e Rede Cegonha de João Pessoa/PB/Brasil, 45.91 % e 54.09% foram executados 2015 e 2016 respectivamente. Em todo o período 445 foram reagentes para o HIV ½, sendo os meses de maio, julho e novembro de 2016 os que apresentaram maior taxa de detecção (n=34, n=39, n=23 respectivamente). Verificamos um aumento de 15,1% de testes rápidos realizados e de 35,8% de testes reagentes no ano 2016 para o HIV 1/2 permitindo a detecção precoce já na atenção primária à saúde e o acesso ao tratamento adequado dos pacientes através de ações previstas nas políticas públicas vigentes no país.Descritores: HIV, Diagnóstico, Promoção da Saúde. Detection of HIV/AIDs through rapid test: a comparative studyAbstract: Given the importance of the rapid test for diagnosis of Human Immunodeficiency Virus (HIV) infection, we determined the number of rapid tests (RT) performed and reagents between 2015 and 2016 by the DST/AIDS section of the city of João Pessoa/PB, Brazil. Of the 77130 TR carried out by the Specialized Attendance Service/Center for Testing and Monitoring and Stork Network of João Pessoa/PB/Brazil, 45.91% and 54.09% were executed in 2015 and 2016 respectively. In the whole period, 445 were HIV 1/2 reagents, with May, July and November 2016 having the highest detection rate (n=34, n=39, n=23 respectively). We verified a 15.1% increase in rapid tests performed and 35.8% in reagent tests in the year 2016 for HIV 1/2, allowing for early detection in primary health care and access to adequate treatment of patients through actions foreseen in the public policies in force in the country.Descriptors: HIV, Diagnosis, Health Promotion. Detección del VIH/SIDA por medio de prueba rápida: estudio comparativoResumen: Dada la importancia de la prueba rápida para el diagnóstico de la infección por el virus de la Inmunodeficiencia Humana (VIH), determinamos el número de pruebas rápidas (TR) realizadas y reactivas entre 2015 y 2016 por la sección de ITS/Sida del municipio de João Pessoa/PB, Brasil. De los 77130 TR realizados por el Servicio de Atención Especializada/Centro de Pruebas y Seguimiento y Red Cigüeña de João Pessoa/PB/Brasil, el 45.91% y el 54.09% fueron ejecutados 2015 y 2016 respectivamente. En todo el período 445 fueron reactivos para el VIH 1/2, siendo los meses de mayo, julio y noviembre de 2016 los que presentaron mayor tasa de detección (n=34, n=39, n=23, respectivamente). Hemos comprobado un aumento del 15,1% de pruebas rápidas realizadas y del 35,8% de pruebas reactivas en el año 2016 para el VIH 1/2, permitiendo la detección precoz ya en la atención primaria a la salud y el acceso al tratamiento adecuado de los pacientes a través de acciones previstas en las políticas públicas vigentes en el país.Descriptores: VIH, Diagnóstico, Promoción de la Salud.

scholarly journals Human immunodeficiency virus and tuberculosis in Argentina: prevalence, genotypes and risk factors

2008 ◽  
Vol 57 (2) ◽  
pp. 190-197 ◽  
Author(s):  
Maria A. Pando ◽  
Cristina De Salvo ◽  
Christian T. Bautista ◽  
Lindsay Eyzaguirre ◽  
Gladys Carrion ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Highly Active Antiretroviral Therapy ◽  
Hiv Transmission ◽  
Treponema Pallidum ◽  
Risk Groups ◽  
Highly Active ◽  
Subtype B ◽  
Human T Cell ◽  
Immunodeficiency Virus ◽  
Hiv 1

The objective of this study was to determine the prevalence and genetic variability of human immunodeficiency virus type 1 (HIV-1) and other sexually transmitted infections (STIs) among 205 patients with clinical diagnosis of tuberculosis (TB) in Buenos Aires in 2001. Infections with hepatitis B virus (HBV), HIV-1, hepatitis C virus (HCV), Treponema pallidum and human T-cell lymphotropic virus types I/II were diagnosed in 37/187 (19.8 %), 35/205 (17.1 %), 22/187 (11.8 %), 13/187 (7.0 %) and 4/181 (2.2 %) patients, respectively. Almost one in three participants (33.1 %) presented at least one infection in addition to TB. Multiresistance to TB drugs (isoniazid plus rifampicin) was detected in the isolates recovered from three patients. Injecting drug use was detected as the main risk factor for HIV, HBV and HCV infections. Of ten patients who died, eight were infected with HIV. HIV genetic characterization showed the presence of two different subtypes. Env subtype F was found in 13/24 samples (54.2 %) and subtype B in 11/24 samples (45.8 %) by heteroduplex mobility assay. Sequencing of the protease/RT region was performed in ten samples: three were characterized as subtype B and seven as B/F recombinants by bootscanning analysis. Phylogenetic analysis of four full-length sequences showed that three were the circulating recombinant form CRF12_BF. The results of this study suggest an urgent need to detect HIV infection in high-risk groups to prevent future HIV transmission as well as morbidity and mortality associated with TB by providing highly active antiretroviral therapy (HAART) and/or TB treatment. Collaboration between TB and HIV programmes seems to be the best approach to decrease the incidence of these diseases, especially in high-prevalence HIV settings.

scholarly journals Population Level Analysis of Human Immunodeficiency Virus Type 1 Hypermutation and Its Relationship with APOBEC3G and vif Genetic Variation

2006 ◽  
Vol 80 (18) ◽  
pp. 9259-9269 ◽  
Author(s):  
Craig Pace ◽  
Jean Keller ◽  
David Nolan ◽  
Ian James ◽  
Silvana Gaudieri ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Amino Acid ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Dna Sequences ◽  
Population Level ◽  
Immunodeficiency Virus ◽  
Hiv 1 ◽  
Level Analysis

ABSTRACT APOBEC3G and APOBEC3F restrict human immunodeficiency virus type 1 (HIV-1) replication in vitro through the induction of G→A hypermutation; however, the relevance of this host antiviral strategy to clinical HIV-1 is currently not known. Here, we describe a population level analysis of HIV-1 hypermutation in near-full-length clade B proviral DNA sequences (n = 127). G→A hypermutation conforming to expected APOBEC3G polynucleotide sequence preferences was inferred in 9.4% (n = 12) of the HIV-1 sequences, with a further 2.4% (n = 3) conforming to APOBEC3F, and was independently associated with reduced pretreatment viremia (reduction of 0.7 log10 copies/ml; P = 0.001). Defective vif was strongly associated with HIV-1 hypermutation, with additional evidence for a contribution of vif amino acid polymorphism at residues important for APOBEC3G-vif interactions. A concurrent analysis of APOBEC3G polymorphism revealed this gene to be highly conserved at the amino acid level, although an intronic allele (6,892 C) was marginally associated with HIV-1 hypermutation. These data indicate that APOBEC3G-induced HIV-1 hypermutation represents a potent host antiviral factor in vivo and that the APOBEC3G-vif interaction may represent a valuable therapeutic target.

scholarly journals The Central Role of Nondisclosed Men Who Have Sex With Men in Human Immunodeficiency Virus-1 Transmission Networks in Guangzhou, China

2020 ◽  
Vol 7 (5) ◽  
Author(s):  
Huanchang Yan ◽  
Weiyun He ◽  
Liping Huang ◽  
Hao Wu ◽  
Yuanhao Liang ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Hiv Transmission ◽  
Central Position ◽  
Sex Behavior ◽  
Transmission Networks ◽  
Immunodeficiency Virus ◽  
Sex With Men ◽  
Centrality Analysis ◽  
Hiv 1

Abstract Background Men who have sex with men (MSM) are vulnerable risk group for human immunodeficiency virus (HIV)-1 infection. However, some MSM do not disclose their same-sex behavior and could impact the transmission and prevention of HIV-1 infection. Here, we evaluated the role of nondisclosed MSM in HIV-1 transmission in Guangzhou, China. Methods The HIV-1 pol sequences were obtained from HIV-infected subjects from 2008 to 2015. A transmission network was constructed using HIV TRAnsmission Cluster Engine (HIV-TRACE) at a pairwise genetic distance of 0.5%. The position of nondisclosed MSM in the network was determined by centrality analysis. Results Nondisclosed MSM were inferred in 9.92% (61 of 615) of slightly older, self-reported non-MSM (P = .006). They were more likely to be married (P = .002) and less educated (P < .001) than the MSM with whom they clustered. Closeness centrality was bigger for nondisclosed MSM than for MSM (P < .001), indicating the central position of nondisclosed MSM in the networks. The average shortest path length was smaller for nondisclosed MSM than for MSM (P < .001), whereas radiality was bigger for nondisclosed MSM than for MSM, suggesting a relatively greater contribution of nondisclosed MSM in transmitting HIV-1 than MSM. Assortativity analysis indicated that nondisclosed MSM were more likely to link each other with coefficient of 0.025. Conclusions Nondisclosed MSM are a specific group, and they play an important role in HIV-1 transmission. They could be bisexual and might increase the risk of HIV-1 infection to their sex partners. Therefore, specific prevention and intervention targeting nondisclosed MSM are urgently needed.

scholarly journals Photochemical inactivation of cell-associated human immunodeficiency virus in platelet concentrates

Blood ◽  
1993 ◽  
Vol 82 (1) ◽  
pp. 292-297 ◽  
Author(s):  
L Lin ◽  
H Londe ◽  
CV Hanson ◽  
G Wiesehahn ◽  
S Isaacs ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Dna Adducts ◽  
Dna Sequences ◽  
Uv Light ◽  
Platelet Concentrates ◽  
Long Wavelength ◽  
Hla Dq ◽  
Immunodeficiency Virus ◽  
Cellular Dna ◽  
Hiv 1

Photochemical decontamination (PCD) of platelet concentrates, with adequate preservation of platelet function, has been shown using 8- methoxypsoralen (8-MOP) and long wavelength UV light (UVA). To further evaluate this technique, models for the inactivation of pathogenic human cell-associated viruses and integrated proviral sequences are required. We have assessed the ability of the PCD technique to inactivate cell-associated human immunodeficiency virus 1 (HIV-1) in platelet concentrates. We correlated PCD inhibition of HIV-1 infectivity with 8-MOP-DNA adduct formation in contaminating nucleated cells, and measured the inhibition of polymerase chain reaction (PCR)- mediated amplification of cellular DNA sequences as a surrogate for inactivation of integrated proviral nucleic acid sequences. After PCD treatment (8-MOP 300 micrograms/mL, UVA 17 mW/cm2) for 60 minutes, 0.5 x 10(6) plaque-forming units (PFU)/mL of cell-associated HIV-1 were inactivated and no virus was detectable by infectivity assay. After 60 minutes of PCD, 15 8-MOP-DNA adducts per 1,000 bp were formed, while in the absence of UVA, no adducts were formed. PCR-mediated amplification of a 242-bp cellular DNA sequence (HLA-DQ-alpha) was inhibited when greater than eight psoralen-DNA adducts per 1,000 bp were present. These studies indicate that high titers of cell-associated HIV-1 in platelet concentrates were inactivated by PCD, and the numbers of 8-MOP- DNA adducts in nucleated cells were sufficient to inhibit amplification of DNA segments that encode for as few as 80 amino acids. Based on the frequency of 8-MOP-DNA adducts, for the 10-kb HIV-1 genome, the probability of an integrated genome without at least one 8-MOP adduct after 60 minutes of PCD was 10(-33).

scholarly journals Incidence of Human Immunodeficiency Virus Antibody in a Prenatal Population at a Community Hospital

1999 ◽  
Vol 6 (1) ◽  
pp. 140-141 ◽  
Author(s):  
Thomas S. Alexander ◽  
Joanne Lee ◽  
Belinda Yen-Lieberman
Keyword(s):  
Human Immunodeficiency Virus ◽  
Hiv Transmission ◽  
Community Hospital ◽  
Hiv Infections ◽  
Enzyme Linked Immunosorbent Assay ◽  
Hiv Screening ◽  
Virus Antibody ◽  
Immunodeficiency Virus ◽  
Positive Results ◽  
Hiv 1

ABSTRACT Prenatal human immunodeficiency virus (HIV) screening may reduce vertical HIV transmission. We screened 4,419 prenatal sera and found 38 repeatedly reactive specimens with an HIV-1–HIV-2 enzyme-linked immunosorbent assay. Western blot analysis confirmed four of these specimens as positive for HIV-1 antibodies. Screening detects previously unidentified HIV infections, but false-positive results may also occur.

Comment from the CDC

1996 ◽  
Vol 17 (10) ◽  
pp. 674-674 ◽  
Author(s):  
David M. Bell
Keyword(s):  
Lower Risk ◽  
Hiv Transmission ◽  
Public Health Service ◽  
Antiretroviral Drugs ◽  
Average Risk ◽  
Limited Data ◽  
Infected Blood ◽  
The Public ◽  
Skin Exposure ◽  
Immunodeficiency Virus

Dr. Glatt makes some thoughtful observations, and his recommendations are similar in many respects to those developed by the Public Health Service (PHS) with advice from expert consultants. However, the PHS did not recommend that new antiretroviral drugs be used routinely to treat lower-risk exposures, because relatively limited data are available on the safety and tolerability of the newer drugs and because the overwhelming majority of workers with lower-risk exposures will not become infected. (The average risk of human immunodeficiency virus [HIV] transmission is 0.3% after a percutaneous exposure to HIV-infected blood and less than that for a mucous membrane or skin exposure.)

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