Dynamics and features of transmission clusters of HIV-1 subtypes in the state of São Paulo, Brazil.

Background: Molecular epidemiology techniques allow us to track the HIV-1 transmission dynamics. Herein, we combined genetic, clinical and epidemiological data collected during routine clinical treatment to evaluate the dynamics and characteristics of transmission clusters of the most prevalent HIV-1 subtypes in the state of São Paulo, Brazil. Methods: This was a cross-sectional study conducted with 2,518 persons living with HIV (PLWH) from 53 cities in São Paulo state between Jan 2004 to Feb 2015. The phylogenetic tree of protease/reverse transcriptase (PR/RT) regions was reconstructed by PhyML and ClusterPicker used to infer the transmission clusters based on Shimodaira-Hasegawa (SH) greater than 90% (phylogenetic support) and genetic distance less than 6%. Results: Of a total of 2,518 sequences, 2,260 were pure subtypes at the PR/RT region, being B (88%), F1 (8.1%), and C (4%). About 21.2% were naïve with a transmitted drug resistance (TDR) rate of 11.8%. A total of 414 (18.3%) of the sequences clustered. These clusters were less evident in subtype B (17.7%) and F1 (15.1%) than in subtype C (40.2%). Clustered sequences were from PLWH at least 5 years younger than non-clustered among subtypes B (p < 0.001) and C (p = 0.037). Men who have sex with men (MSM) predominated the cluster in subtype B (51%), C (85.7%), and F1 (63.6%; p < 0.05). The TDR rate in clustered patients was 15.4, 13.6, and 3.1% for subtypes B, F1, and C, respectively. Most of the infections in subtypes B (80%), C (64%), and F1 (59%) occurred within the state of São Paulo. The metropolitan area of São Paulo presented a high level of endogenous clustering for subtypes B and C. The São Paulo city had 46% endogenous clusters of subtype C. Conclusion: Our findings showed that MSM, antiretroviral therapy in Treatment-Naive (ART-naïve) patients, and HIV1-C, played an important role in the HIV epidemic in the São Paulo state. Further studies in transmission clusters are needed to guide the prevention intervention.

Performance evaluation of a Sars-CoV-2 rapid test and two automated immunoassays / Avaliação do desempenho de teste rápido e de dois imunoensaios automatizados para Sars-CoV-2

ABSTRACT Introduction: Due to urgency and demand of a response to the Covid-19 pandemic, numerous Sars-CoV-2 immunoassays have been rapidly developed. Objective: This study aimed at assessing the performance of rapid Sars-CoV-2 antibody test in comparison to high-throughput serological assays. Methods: A total of 86 serum samples were evaluated in the three assays: a lateral flow immunoassay - Wondfo Sars-CoV-2 Antibody Test (WRT) - and two chemiluminescence immunoassays: Elecsys Anti-Sars-CoV-2 (ECLIA), and Sars-CoV-2 IgG (CMIA-IgG). Results: The estimated diagnostic sensitivities of serological tests in the evaluation of serum samples from the epidemiological survey were: WRT 59% [95% confidence interval (CI) 43.4%-72.9%], ECLIA 66.7% (51%-79.4%), and CMIA-IgG 61.5% (47.1%-73%). Meanwhile, the estimated diagnostic specificity was for WRT 78.7% (95% CI 65.1%-88%), ECLIA 72.3% (58.2%-83.1%), and CMIA-IgG 76.6% (74%-95.5%). The sensitivity and specificity values were lower than manufacturers' claimed. Although 16.2% (14/86) of serological results were discordant among the three Sars-CoV-2 serological assays, the degree of agreement by the kappa index was adequate: WRT/CMIA-IgG [0.757 (95% CI 0.615-0.899)], WRT/ECLIA [0.715 (0.565-0.864)], and ECLIA/CMIA-IgG [0.858 (0.748-0.968)]. Conclusion: The serological testing may be a useful diagnostic tool, which reinforces its careful evaluation, and, as well as the correct time to use it.

RESUMEN Introducción: Debido a la urgencia y la demanda de una respuesta a la pandemia de Covid-19, se han desarrollado rápidamente numerosos inmunoensayos del Sars-CoV-2. Objetivo: Este estudio tuvo como objetivo evaluar el rendimiento de la prueba rápida de anticuerpos contra el Sars-CoV-2 en comparación con los ensayos serológicos de alto rendimiento. Métodos: Se evaluaron un total de 86 muestras de suero en los tres ensayos: un inmunoensayo de flujo lateral - Wondfo Sars-CoV-2 Antibody Test (TRW) - y dos inmunoensayos de quimioluminiscencia: Elecsys Anti-Sars-CoV-2 (ECLIA) y Sars-CoV-2 IgG (CMIA-IgG). Resultados: Las sensibilidades diagnósticas estimadas de las pruebas serológicas en la evaluación de muestras de suero de la encuesta epidemiológica fueron: WRT 59% [intervalo de confianza (IC) del 95%: 43,4%-72,9%], ECLIA 66,7% (51%-79,4%) y CMIA-IgG 61,5% (47,1%-73%). Mientras tanto, la especificidad diagnóstica estimada fue para WRT 78,7% (95% CI 65,1%-88%), ECLIA 72,3% (58,2%-83,1%) y CMIA-IgG 76,6% (74%-95,5%). Los valores de sensibilidad y especificidad fueron más bajos que los declarados por los fabricantes. Aunque el 16,2% (14/86) de los resultados fueron discordantes entre los tres ensayos serológicos del Sars-CoV-2, el grado de concordancia del índice kappa fue adecuado: WRT/CMIA-IgG [0,757 (IC del 95%: 0,615-0,899)], WRT/ECLIA [0,715 (0,565-0,864)] y ECLIA/CMIA-IgG [0,858 (0,748-0,968)]. Conclusión: La prueba serológica puede ser una herramienta diagnóstica útil, lo que refuerza su evaluación cuidadosa, así como el momento adecuado para usarla.

RESUMO Introdução: Em função da urgência e demanda de uma resposta à pandemia do novo coronavírus (Covid-19), vários testes de detecção de anticorpos para a síndrome respiratória aguda grave do coronavírus 2 (Sars-CoV-2) têm sido desenvolvidos. Objetivo: Este estudo teve como objetivo avaliar o desempenho do teste rápido utilizado em um inquérito epidemiológico para Sars-CoV-2 em comparação com outros ensaios sorológicos. Métodos: Foram avaliadas 86 amostras de soro em três ensaios sorológicos: um imunoensaio de fluxo lateral - Wondfo Sars-CoV-2 Antibody Test (TRW) - e dois imunoensaios de quimioluminescência: Elecsys anti-Sars-CoV-2 (ECLIA) e Sars-CoV-2 IgG (CMIA-IgG). Resultados: As sensibilidades diagnósticas estimadas dos testes sorológicos na avaliação dessas amostras foram: TRW 59% [95% intervalo de confiança (IC) 43,4%-72,9%], ECLIA 66,7% (51%-79,4%) e CMIA-IgG 61,5% (47,1%-73%). Enquanto isso, a especificidade diagnóstica estimada para TRW foi 78,7% (95% CI 65,1%-88%), ECLIA 72,3% (58,2%-83,1%) e CMIA-IgG 76,6% (74%-95,5%). Os valores de sensibilidade e especificidade foram inferiores aos afirmados pelos fabricantes. Embora 16,2% (14/86) dos resultados tenham sido discordantes entre os três ensaios serológicos para Sars-CoV-2, o grau de concordância pelo índice Kappa foi adequado: TRW/CMIA-IgG [0,757 (95% IC 0,615-0,899)], TRW/ECLIA [0,715 (0,565-0,864)] e ECLIA/CMIA-IgG [0,858 (0,748-0,968)]. Conclusão: O teste sorológico pode ser uma ferramenta diagnóstica útil, o que reforça sua avaliação criteriosa, bem como o momento correto de sua utilização.