Open-source real-time quantitative RT-PCR-based on a RNA standard for the assessment of SARS-CoV-2 viral load.

BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target genes by molecular methods has been chosen as the main approach to identify individuals with Coronavirus disease 2019 (COVID-19) infection. OBJECTIVES: In this study, we developed an open-source RNA standard-based real-time quantitative RT-PCR (RT-qPCR) assay for quantitative diagnostics of SARS-CoV-2 from nasopharynx, oropharynx, saliva and plasma samples. METHODS AND FINDINGS: We evaluated three SARS-CoV-2 target genes and selected the RNA-dependent RNA polymerase (RdRp) gene, given its better performance. To improve the efficiency of the assay, a primer gradient containing 25 primers forward and reverse concentration combinations was performed. The forward and reverse primer pairs with 400 nM and 500 nM concentrations, respectively, showed the highest sensitivity. The LOD95% was ~60 copies per reaction. From the four biological matrices tested, none of them interfered with the viral load measurement. Comparison with the AllplexTM 2019-nCoV assay (Seegene) demonstrated that our test presents 90% sensitivity and 100% specificity. MAIN CONCLUSIONS: We developed an efficient molecular method able to measure absolute SARS-CoV-2 viral load with high replicability, sensitivity and specificity in different clinical samples.

The impact of socioeconomic status on HPV infection among young Brazilians in a nationwide multicenter study.

The aim of this study is to evaluate genital human papillomavirus (HPV) infection according to socioeconomic categories in Brazil. This cross-sectional, nationwide study included 7,694 sexually active women and men aged 16-25 years. Individuals of all socioeconomic groups in all 26 Brazilian capitals and the Federal District were enrolled through public primary care units between September 2016 and November 2017. All participants answered a standardized interview administered by trained primary care health professionals. Socioeconomic class was analyzed using a pricing classification system for the Brazilian public that divides the market exclusively in terms of economic class based on the ownership of assets and the education level. Cervical samples were obtained using a Digene® HC2 DNA Collection, and penile/scrotum samples were obtained using a wet Dacron swab. HPV typing (overall and high-risk) was performed in a central lab. Of the 7,694 participants (47.85% women), 17.92% belonged to class A-B, 56.08% to class C, and 26.00% to class D-E. The prevalence of overall HPV was similar among the social classes: 51.16% for classes A-B, 53.39% for class C, and 55.47% for classes D-E (P = 0.479). Similar results were found for high-risk HPV. After adjustments, the presence of HPV in individuals with a brown skin color belonging to classes A-B was 57.00% higher [prevalence ratio 1.57 (95%: 1.23, 2.01)] than that in whites and had no impact on the other social classes. In conclusion, HPV infection affects all socioeconomic classes in Brazil, evidencing the importance of offering the HPV vaccine to the entire population.

Open-source real-time quantitative RT-PCR-based on a RNA standard for the assessment of SARS-CoV-2 viral load

BACKGROUND Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target genes by molecular methods has been chosen as the main approach to identify individuals with Coronavirus disease 2019 (COVID-19) infection. OBJECTIVES In this study, we developed an open-source RNA standard-based real-time quantitative RT-PCR (RT-qPCR) assay for quantitative diagnostics of SARS-CoV-2 from nasopharynx, oropharynx, saliva and plasma samples. METHODS AND FINDINGS We evaluated three SARS-CoV-2 target genes and selected the RNA-dependent RNA polymerase (RdRp) gene, given its better performance. To improve the efficiency of the assay, a primer gradient containing 25 primers forward and reverse concentration combinations was performed. The forward and reverse primer pairs with 400 nM and 500 nM concentrations, respectively, showed the highest sensitivity. The LOD95% was ~60 copies per reaction. From the four biological matrices tested, none of them interfered with the viral load measurement. Comparison with the AllplexTM 2019-nCoV assay (Seegene) demonstrated that our test presents 90% sensitivity and 100% specificity. MAIN CONCLUSIONS We developed an efficient molecular method able to measure absolute SARS-CoV-2 viral load with high replicability, sensitivity and specificity in different clinical samples.

Community burden and prognostic impact of reduced kidney function among patients hospitalized with acute decompensated heart failure: The Atherosclerosis Risk in Communities (ARIC) Study Community Surveillance.

BACKGROUND: Kidney dysfunction is prevalent and impacts prognosis in patients with acute decompensated heart failure (ADHF). However, most previous reports were from a single hospital, limiting their generalizability. Also, contemporary data using new equation for estimated glomerular filtration rate (eGFR) are needed. METHODS AND RESULTS: We analyzed data from the ARIC Community Surveillance for ADHF conducted for residents aged ≥55 years in four US communities between 2005-2011. All ADHF cases (n = 5, 391) were adjudicated and weighted to represent those communities (24,932 weighted cases). The association of kidney function (creatinine-based eGFR by the CKD-EPI equation and blood urea nitrogen [BUN]) during hospitalization with 1-year mortality was assessed using logistic regression. Based on worst and last serum creatinine, there were 82.5% and 70.6% with reduced eGFR (<60 ml/min/1.73m2) and 37.4% and 26.6% with severely reduced eGFR (<30 ml/min/1.73m2), respectively. Lower eGFR (regardless of last or worst eGFR), particularly eGFR <30 ml/min/1.73m2, was significantly associated with higher 1-year mortality independently of potential confounders (odds ratio 1.60 [95% CI 1.26-2.04] for last eGFR 15-29 ml/min/1.73m2 and 2.30 [1.76-3.00] for <15 compared to eGFR ≥60). The association was largely consistent across demographic subgroups. Of interest, when both eGFR and BUN were modeled together, only BUN remained significant. CONCLUSIONS: Severely reduced eGFR (<30 ml/min/1.73m2) was observed in ~30% of ADHF cases and was an independent predictor of 1-year mortality in community. For prediction, BUN appeared to be superior to eGFR. These findings suggest the need of close attention to kidney dysfunction among ADHF patients.