Recent HIV infections: evaluation of a simple identification score for newly diagnosed patients.

OBJECTIVE: Recognize incident infection to better characterize the groups that fuel HIV epidemic. We propose a simple score to identify recent infections among newly diagnosed patients as a HIV surveillance tool. METHODS: Newly diagnosed patients were defined as recent infections when a negative serological test in the previous year was available. Laboratory tests, such as the avidity index (Bio-Rad, according to the CEPHIA protocol), chemiluminescent intensity (CMIA, architect, Abbott), and the nucleotide ambiguity index of partial pol sequences were used as proxies of recency. A simple score based on clinical symptoms of acute retroviral syndrome during the previous year, CD4+ T cell count, and viral load at admission was tested to assess the predictive power, using receiver operating characteristic (ROC) curves, to identify recent cases of infection. RESULTS: We evaluated 204 recently diagnosed patients who were admitted to the Ambulatório de Referência em Moléstias Infecciosas de Santo André (Santo André Reference Infectious Diseases Outpatient Clinic), in the metropolitan region of São Paulo, Brazil, recruited between 2011 and 2018. An HIV-negative test in the year prior to enrollment was documented in 37% of participants. The proportion of cases classified as recent infections (less than one year), according to the laboratory proxies were: 37% (67/181) for an avidity index < 40%, 22% (30/137) for a CMIA < 200, and 68% (124/181) for an ambiguity index < 0.5%. Using different combinations of recency definitions, our score showed an area under the ROC curve from 0.66 to 0.87 to predict recency. CONCLUSIONS: Using data from patients' interviews and routine laboratory tests at admission, a simple score may provide information on HIV recency and thus, a proxy for HIV incidence to guide public policies. This simple for the Brazilian public health system and other low- and middle-income countries.

A simple algorithm for selecting cases to investigate acute and early HIV infections in low- and middle-income countries.

We documented the outcome of an over 10-year (2011-2021) effort to diagnose acute and early HIV infections (AEHI) in an Infectious Diseases Outpatient Clinic with limited resources. Of a total of 132, 119 HIV-RNA tests were performed from 2017 to 2020, 12 cases were identified, using a simple algorithm: risk exposure of 6 weeks or less before the visit and/or symptoms compatible with acute retroviral syndrome 7-30 days after exposure and/or undetermined 3rd generation rapid diagnostic test or serology. AEHI diagnoses varied from 2.4% among asymptomatic to 25% for undetermined serology cases using this simple screening applicable to different settings.

Recent HIV infections: evaluation of a simple identification score for newly diagnosed patients

ABSTRACT OBJECTIVE Recognize incident infection to better characterize the groups that fuel HIV epidemic. We propose a simple score to identify recent infections among newly diagnosed patients as a HIV surveillance tool. METHODS Newly diagnosed patients were defined as recent infections when a negative serological test in the previous year was available. Laboratory tests, such as the avidity index (Bio-Rad, according to the CEPHIA protocol), chemiluminescent intensity (CMIA, architect, Abbott), and the nucleotide ambiguity index of partial pol sequences were used as proxies of recency. A simple score based on clinical symptoms of acute retroviral syndrome during the previous year, CD4+ T cell count, and viral load at admission was tested to assess the predictive power, using receiver operating characteristic (ROC) curves, to identify recent cases of infection. RESULTS We evaluated 204 recently diagnosed patients who were admitted to the Ambulatório de Referência em Moléstias Infecciosas de Santo André (Santo André Reference Infectious Diseases Outpatient Clinic), in the metropolitan region of São Paulo, Brazil, recruited between 2011 and 2018. An HIV-negative test in the year prior to enrollment was documented in 37% of participants. The proportion of cases classified as recent infections (less than one year), according to the laboratory proxies were: 37% (67/181) for an avidity index < 40%, 22% (30/137) for a CMIA < 200, and 68% (124/181) for an ambiguity index < 0.5%. Using different combinations of recency definitions, our score showed an area under the ROC curve from 0.66 to 0.87 to predict recency. CONCLUSIONS Using data from patients' interviews and routine laboratory tests at admission, a simple score may provide information on HIV recency and thus, a proxy for HIV incidence to guide public policies. This simple for the Brazilian public health system and other low- and middle-income countries.

Major drug resistance mutations to HIV-1 protease inhibitors (PI) among patients exposed to PI class failing antiretroviral therapy in São Paulo State, Brazil.

BACKGROUND: Protease inhibitors (PI) are especially important in salvage therapy. Previous treatment failure with a PI containing regimen may elicit resistance mutations, reducing PI susceptibility and limiting treatment options. The aim of this study was to describe major PI mutations among patients exposed to at least one PI to evaluate predictors of mutation emergence and the impact of subtypes on resistance. METHODOLOGY: Partial HIV-1 pol sequences (Sanger Sequencing) from patients exposed to PI with virological failure were genotyped from January 2014 to December 2017. Drug resistance mutations (DRM), antiretroviral susceptibility (GSS) and subtypes, along clinical and laboratory parameters, were evaluated using logistic regression to access the predictors of mutation emergence. RESULTS: In 27.5% (466/1696) of the cases at least one major PI mutations was identified, most commonly M46 (14.7%), V82 (13.8%) and I54 (13.3%). Mutations to NRTI and NNRTI were observed in 69.6% and 59.9%, respectively, of the 1696 sequences. Full activity to darunavir was predicted in 88% (1496/1696), but was only 57% among those with at least one PI-DRM. Subtype C sequences had less major PI-DRMs (10%, 9/87) compared to B (28%, 338/1216) or F (35%, 58/168) (p <0.001) but adjusted analysis suggested that this association is not independent from a shorter treatment time and fewer regimens (OR 0.59, Confidence Interval 95: 0.2-2.5, p = 0.48). Subtype F, together with NRTI mutations and longer time on treatment was associated to presence of PI-DRM, to a lower darunavir GSS and to mutations at codon I50. CONCLUSIONS: Among patients with PI-DRM, full activity to darunavir was compromised in almost half of the cases and efforts to detect failure at earlier time are warranted, particularly for HIV-1 subtype F that showed association to the emergence of resistance, with potential impact in protease inhibitors sequencing. Furthermore, NRTI mutations may serve as an indicative of sufficient adherence to allow PI-DRM emergence.

Prevalence of HIV-1 transmitted drug resistance and viral suppression among recently diagnosed adults in São Paulo, Brazil.

HIV-1 transmitted drug resistance (TDR) mutations may reduce the efficacy of antiretroviral therapy (ART), but pre-treatment testing to determine the virus genotype can improve the efficacy of ART. Unfortunately, issues related to cost and logistics of pre-treatment testing limit its use in resource-limited settings. We studied 596 ART-naive individuals who were newly diagnosed from 2014 to 2016 in São Paulo, Brazil, to evaluate TDR and virological outcome after 48 weeks of genotype-guided therapy. One or more TDR (based on the WHO surveillance list) was observed in 10.9% (CI 95%, 8.6-13.6) of the sequences, the most common of which was the K103 N mutation, which confers resistance to first-generation drugs of the non-nucleoside reverse transcriptase inhibitor (NNRTI) antiretroviral drug class. Dual-class (1%, 6/596) and triple-class (0.34%, 2/596) resistance were uncommon. After 48 weeks of treatment with ART, infection was suppressed to below 200 copies/mL in most patients (95%), with full suppression (RNA target not detected) in 65%. The following characteristics at patient enrollment were independently associated with a lack of full suppression: CD4 T cell counts below 500 cells/µL, viremia above 100,000 copies/mL, older age, and TDR to NNRTI. The rates of resistance were intermediate, but genotype-guided therapy resulted in high rates of viral suppression. The observed resistance profile should not be an obstacle to the use of the dolutegravir-based regimen now recommended in Brazil, but genotype testing may be warranted before initiating first-generation NNRTI-based regimens.

Monitoramento da infecção pelo HIV-!: estudo da prevalência de mutações de resistência transmitida aos antirretroviarais, análise molecular e de testes sorológicos para identificação de infecção recente em pacientes no Estado de São Paulo / Monitoring of HIV-! infection: study of the prevalence of resistance mutations transmitted to antiretroviral drugs, molecular analysis and serological tests to identify recent infection in patients in the State of São Paulo

O diagnóstico laboratorial de infecção pelo HIV, assim como a identificação de subtipos virais e de mutações de resistência transmitida a drogas (TDRM, transmitted drug reisitence mutation) são importantes para o controle e monitoramento de epidemia do HIV. No presente estudo, eles foram pesquisados em amostras de sangue de indivíduos provenientes...(AU)

High Prevalence of Drug Resistance Mutations Among Patients Failing First-Line Antiretroviral Therapy and Predictors of Virological Response 24 Weeks After Switch to Second-Line Therapy in São Paulo State, Brazil.

Universal antiretroviral treatment with sustained viral suppression benefits patients and reduces HIV transmission. Effectiveness of therapy may be limited by antiretroviral drug resistance. Information on the resistance profile at treatment failure and its impact on antiretroviral drugs may subsidize subsequent treatment strategies. Partial pol sequences from 319 patients failing first-line therapy were analyzed for resistance associated mutations (RAMs) and HIV subtype. Demographic data, CD4 T cell count, viral load, and antiretroviral regimens and mutational profile at first-line failure were also investigated for associations to the response to second-line regimens. RAMs at the reverse transcriptase gene were frequent. Most sequences (88%) showed at least one mutation. A higher number of reverse transcriptase RAMs were associated to lower CD4 T cell counts and the use of tenofovir/lamivudine in first line. Among 205 with follow-up data, 76.6% were virally suppressed (below 200 copies/ml) after 24 weeks of second-line therapy. Most cases initiated second line with a regimen genotypic susceptibility score ≥2, but it did not predict viral suppression, that was independently associated with higher CD4 T cell counts and with the presence of nucleos(t)ide analog reverse transcriptase inhibitor (NRTI) RAMs. This study documented extensive resistance at first-line failure in this area in Brazil, highlights the risks of low CD4 T cell counts to second-line therapy, and supports the notion that recycled NRTIs may contribute to viral suppression even when genotypic resistance is present.

Undiagnosed acute HIV infection identified through RNA testing of pooled serum samples obtained during a dengue outbreak in São Paulo, Brazil.

INTRODUCTION:: Improving HIV diagnostics and treatment is necessary to end the AIDS epidemic. Pooled plasma can be used to identify patients with acute HIV disease, even before serological tests. During dengue outbreaks, patients having symptoms common to other acute viral diseases might seek medical care. METHODS:: We evaluated HIV RNA in pooled seronegative dengue samples. RESULTS:: After excluding individuals with a known HIV diagnosis, an HIV-1 prevalence of 0.73% [95% confidence interval (CI) 0.23-1.76; 4/546 samples] was found. CONCLUSIONS:: Promoting strategies to diagnose these individuals and provide them with medical treatment might be instrumental for controlling the HIV epidemic.

Undiagnosed acute HIV infection identified through RNA testing of pooled serum samples obtained during a dengue outbreak in São Paulo, Brazil

Abstract INTRODUCTION: Improving HIV diagnostics and treatment is necessary to end the AIDS epidemic. Pooled plasma can be used to identify patients with acute HIV disease, even before serological tests. During dengue outbreaks, patients having symptoms common to other acute viral diseases might seek medical care. METHODS: We evaluated HIV RNA in pooled seronegative dengue samples. RESULTS: After excluding individuals with a known HIV diagnosis, an HIV-1 prevalence of 0.73% [95% confidence interval (CI) 0.23-1.76; 4/546 samples] was found. CONCLUSIONS: Promoting strategies to diagnose these individuals and provide them with medical treatment might be instrumental for controlling the HIV epidemic.

Undiagnosed acute HIV infection identified through RNA testing of pooled serum samples obtained during a gengue outbreak in São Paulo, Brazil

INTRODUCTION: Improving HIV diagnostics and treatment is necessary to end the AIDS epidemic. Pooled plasma can be used to identify patients with acute HIV disease, even before serological tests. During dengue outbreaks, patients having symptoms common to other acute viral diseases might seek medical care. METHODS: We evaluated HIV RNA in pooled seronegative dengue samples. RESULTS: After excluding individuals with a known HIV diagnosis, an HIV-1 prevalence of 0.73% [95% confidence interval (CI) 0.23-1.76; 4/546 samples] was found. CONCLUSIONS: Promoting strategies to diagnose these individuals and provide them with medical treatment might be instrumental for controlling the HIV epidemic. Keywords: HIV; Acute disease; Dengue

Transmitted Drug Resistance Among Recently Diagnosed Adults and Children in São Paulo, Brazil.

Transmitted drug resistance mutations (TDRM) have been a constant threat to treatment efficacy. We evaluated TDRM in plasma RNA of 217 antiretroviral therapy-naive patients from sites in the São Paulo metropolitan area, collected from 2012 to 2014. The partial HIV-1 polymerase region was sequenced using Big Dye terminators at an ABI 3130 Genetic Analyzer. TDRM was defined according to the Stanford database calibrated population resistance (CPR v.6.0), but other drug resistance mutations (DRM) considered at the IAS list (IAS, 2014) and at the Stanford HIV Database Genotyping Resistance Interpretation (GRI-HIVdb) were also described. Out of 78% (170/217) of patients with information on the time of diagnosis, most (83%, 141/170) had been recently diagnosed, with the first positive HIV serology at a median of 58 days (IQR 18-184). Subtype B predominated (70%), followed by subtype F (10%), BF (7.5%), C (7.5%), and BC (5%). TDRMs were observed in 9.2% (20/217, CI 95% 5.9% to 13.6%), mostly (5.2%) to nonnucleoside reverse transcriptase inhibitor (NNRTI) antiretroviral class. Among children and adolescents, only a single patient showed TDRMs. Additional non-CPR mutations were observed: 11.5% (25/217) according to IAS or 4.6% (10/217) according to GRI-HIVdb. Overall, 23.5% (51/217) of the cases had one or more DRM identified. TDRM prevalence differed significantly among some sites. These trends deserve continuous and systematic surveillance, especially with the new policies of treatment as prevention being implemented in the country.

Transmitted drug resistance among recently diagnosed adults and children in São Paulo, Brazil

Transmitted drug resistance mutations (TDRM) have been a constant threat to treatment efficacy. We evaluated TDRM in plasma RNA of 217 antiretroviral therapy-naive patients from sites in the São Paulo metropolitan area, collected from 2012 to 2014. The partial HIV-1 polymerase region was sequenced using Big Dye terminators at an ABI 3130 Genetic Analyzer. TDRM was defined according to the Stanford database calibrated population resistance (CPR v.6.0), but other drug resistance mutations (DRM) considered at the IAS list (IAS, 2014) and at the Stanford HIV Database Genotyping Resistance Interpretation (GRI-HIVdb) were also described. Out of 78% (170/217) of patients with information on the time of diagnosis, most (83%, 141/170) had been recently diagnosed, with the first positive HIV serology at a median of 58 days (IQR 18-184). Subtype B predominated (70%), followed by subtype F (10%), BF (7.5%), C (7.5%), and BC (5%). TDRMs were observed in 9.2% (20/217, CI 95% 5.9% to 13.6%), mostly (5.2%) to nonnucleoside reverse transcriptase inhibitor (NNRTI) antiretroviral class. Among children and adolescents, only a single patient showed TDRMs. Additional non-CPR mutations were observed: 11.5% (25/217) according to IAS or 4.6% (10/217) according to GRI-HIVdb. Overall, 23.5% (51/217) of the cases had one or more DRM identified. TDRM prevalence differed significantly among some sites. These trends deserve continuous and systematic surveillance, especially with the new policies of treatment as prevention being implemented in the country.

An HIV-1 transmission case possibly associated with manicure care.

A recently diagnosed 22-year-old female with no history of transmission risk factors prompted a thorough investigation of possible alternative risk factors. As the patient had evidence of advanced disease and laboratory data compatible with long-standing infection, past events were reviewed. About 10 years ago the patient shared manicure utensils with an older cousin, later known to be HIV infected; this prompted the phylogenetic analysis of the HIV sequences of both patients. Phylogenetic analyses of partial HIV-1 polymerase and envelope sequences from both patients revealed highly related sequences, with an estimated common ancestor date (about 11 years ago) that coincided with the putative sharing of manicure instruments, during a time in which the cousin was not virally suppressed. Taken together, the information about the infection of this patient suggests the use of shared manicure instruments as an alternative route of fomite HIV-1 transmission.

Prevalência de infecção por HTLV-1 e HTLV-2 em pacientes infectados pelo HIV em serviço especializado de São Paulo / Prevalence of HTLV-1 and HTLV-2 in patients infected with HIV from a Reference Center of São Paulo

Os HTLV-1, HTLV-2 e HIV compartilham as mesmas vias de transmissão e as prevalências de coinfecção HIV/HTLV-1 e HIV-HTLV-2 variam de acordo com a região geográfica, a população de estudo e a época em que foi realizada a pesquisa. Altas taxas de coinfecção foram detectadas em pacientes com Aids em São Paulo na década de 1990 e foram associadas ao uso de drogas injetáveis (UDI). Neste estudo foi determinada a prevalência e os fatores de risco para a coinfecção HIV/HTLV em pacientes do CRT-DST/Aids de São Paulo. Amostras de sangue de 1.608 pacientes que aceitaram participar do estudo foram encaminhadas ao Instituto Adolfo Lutz para pesquisa de anticorpos anti-HTLV-1/2 por ensaio imunoenzimático e Western Blot (WB) e para pesquisa de DNA proviral pela PCR em tempo real pol. Na triagem sorológica, 51 soros resultaram reagentes para HTLV. Destes, pelo WB, 23 (1,43%) confirmaram infecção HTLV-1, 12 (0,75%) HTLV-2 e 6 (0,37%) HTLV não tipado. Pela PCR houve detecção de mais um caso de HTLV-1 (total 1,49%) e cinco casos de HTLV-2 (total 1,06%). Houve associação entre infecção HTLV-1/2 e gênero feminino (p=0.0027), cor negro/pardo (p=0.0332), infecção pelo HBV (p=0.0019), HCV e UDI (p<0.0000). A PCR em tempo real foi útil para confirmar casos com resultado HTLV não tipado e Indeterminado pelo WB e pode ser usada como primeiro teste confirmatório seguido do WB. A baixa prevalência de coinfecção HIV/HTLV no presente estudo parece estar relacionada a mudanças na população exposta ao HIV e na troca de cocaína injetável por crack no momento atual...

Genotypic tropism prediction from paired cell and plasma using single and replicate sequences.

HIV-1 tropism determination is necessary prior to CCR5 antagonist use as antiretroviral therapy. Genotypic prediction of coreceptor use is a practical alternative to phenotypic tests. Cell DNA and plasma RNA-based prediction has shown discordance in many studies. We evaluate paired cell and plasma either as single or replicate V3 sequences to assess prediction comparability. The HIV-1 partial env region was sequenced and tropism was predicted using geno2pheno and position-specific scoring matrices (PSSM). Nucleotide ambiguities at V3 were quantified and genetic distance (Protdist) was determined using BioEdit. Wilcoxon signed-rank test, t tests, and Spearman correlation were performed with Prism GraphPad5.0. Results are expressed as medians, with a level of significance of p<0.05, two tailed. Single (n=28) or replicate (n=26) paired cell/plasma sequences were obtained from 54 patients. Although the clonalfalse-positive rate (FPR) value from both compartments strongly correlated (r=0.86 p<0.0001), discordance in tropism prediction was observed in both singles and replicates using geno2pheno or PSSM. Applying clonalFPR(10%) 46% (25/54) were X4 tropic, with a plasma/cell discordance of 11% in singles and 23% in replicates. Genetic distance (p<0.0001) and clonalFPR value dispersion (p=0.003) were significantly higher among replicate sequences from cells. Discordance of viral tropism prediction is not uncommon and the use of replicates does not decrease its occurrence, but improves X4 sensitivity. Sequences from provirus had greater genetic distance and dispersion of clonalFPR values. This may suggest that DNA replicate assays may better represent the diversity of HIV-1 variants, but the clinical significance of these findings needs further evaluation.

Predição do tropismo viral do HIV-1 utilizando plasma e célula em amostras de sangue de pessoas vivendo com HIV/AIDS / Prediction of HIV-1 viral tropism using plasma and cell from blood sample from people living with HV/AIDS

O HIV-1 geralmente utiliza o receptor CD4 em conjunto com um correceptor principal, CCR5 ou CXCR4, na etapa fundamental de entrada na célula hospedeira, determinando assim o tropismo viral por células que expressam estas moléculas. Diferenças no tropismo de HIV-1 têm contribuído para a compreensão da patogênese do HIV e são necessárias para suportar a decisão médica em relação ao uso de antagonistas do CCR5. O teste fenotípico de tropismo determina diretamente esta característica biológica, porém os custos e a complexidade restringem a sua utilização, sendo assim, a predição genotípica tem sido proposta como uma alternativa. O objetivo desse estudo foi padronizar e avaliar um teste de predição genotípica do tropismo. Foi adaptado para o nosso laboratório o protocolo desenvolvido pelo Centro de Excelência em HIV/Aids da Columbia Britânica (CECB)usando sequência em replicatas, avaliamos os parâmetros que possam influenciar na predição do tropismo e comparamos a predição na célula e no plasma. Produtos de PCR e plasma enviados pelo CECB foram sequenciados e analisados de forma independente no CECB e no IAL, com alta concordância. Sequências da V3 do envelope viral de 81 pacientes com consentimento informado mostraram uma correlação entre o número de ambiguidades e o menor valor de FPR, uma tendência a ter uma maior distância genética inter-sequência entre os isolados preditos como X4 e sem correlação entre o número de repetições de sequências e o menor FPR. Estudamos também diferenças na origem do material genético viral (RNA viral ou DNA pró-viral) e sua influência sobre a predição de tropismo. Em 56 amostras pareadas observou-se uma tendência na ocorrência de mais X4 em DNA pró-viral de células. Nós observamos maior distância genética entre as sequências de célula em comparação com as de plasma, e documentamos as discrepâncias na determinação do tropismo viral utilizando diferentes cut offs de uso clínico. Nosso trabalho permitiu o desenvolvimento...

Evaluation of genotypic prediction of HIV-1 tropism using population sequencing of replicates.

Determination of human immunodeficiency virus tropism has contributed to the understanding of the pathogenesis of HIV and is necessary prior to the use of CCR5 antagonists. Replicate V3 sequences may generate different sequences and improve viral tropism prediction. The diversity of HIV was evaluated to access its influence on prediction. Plasma RNA was retro-transcribed and amplified using a one-step protocol, followed by nested PCR and sequencing using an ABI3130XL. Eighty-one patients, 74% male and 26% female, with a median age of 44 years had either a single sequence (n=50) or 2-4 replicates (n=31) evaluated. Most patients (92%) had used multiple anti-retroviral regimens. Tropism prediction was performed using the Geno2pheno clonal option. The number of ambiguous nucleotides, the deduced non-synonymous amino acids at V3 and the genetic distance were quantified. Using a 20% false positive rate (FPR) cut-off, 41/81 (50.6%) was predicted as X4. TCD4 was lower, 226 cells/mm(3) (IQR 82-378), in patients infected with X4; TCD4 for R5 was 324 cells/mm(3) (IQR 200-538, p<0.05). The number of ambiguous nucleotides correlated with a lower FPR value (p<0.0027). Although different sequences may be generated, the number of replicates was not associated to a lower FPR or X4 assignment, and may allow a better prediction of this biological characteristic. Ambiguous nucleotides correlate inversely to a lower FPR.