BACKGROUND The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) has changed unevenly over time around the world. Although whole genome sequencing is the gold standard for virus characterisation, the discovery of alpha VOC causing spike gene target failure (SGTF) result, when tested using an reverse transcription real-time polymerase chain reaction (RT-qPCR) assay, has provided a simple tool for tracking the frequencies of variants. OBJECTIVES The aim of this study was to investigate if a multiplex RT-qPCR assay (BioM 4Plex VOC) could be used to detect SARS-CoV-2 and to perform a VOC screening test in a single reaction tube. Here, we present the multicentre study evaluating this assay. METHODS Twelve laboratories have participated in the multicentre study. The BioM 4Plex VOC was distributed to them with detailed instructions of how to perform the test. They were asked to test the BioM 4Plex VOC in parallel with their routine Commercial SARS-CoV-2 diagnostic assay. Additionally, they were requested to select SARS-CoV-2-positive samples with genome sequenced and lineage definition according to PANGO lineage classification. FINDINGS The BioM 4Plex VOC and commercial RT-PCR assay are equally effective in detecting SARS-CoV-2. Results revealed a specificity of 96.5-100% [95% confidence interval (CI)], a sensitivity of 99.8-100% (95% CI), and an accuracy of 99.8-100% (95% CI). A 99% concordance rate was found between results from the BioM 4Plex VOC and that from available genome sequencing data. MAIN CONCLUSIONS The BioM 4Plex VOC provides an effective solution to detect SARS-CoV-2 infections and screening for VOCs in a single reaction. It is a straightforward method to help us monitor the frequency and distribution of VOCs and develop strategies to better cope with the pandemics. SARSCoV2 SARSCoV SARS CoV (SARS-CoV-2 (VOCs world characterisation SGTF (SGTF result realtime real RTqPCR RT qPCR (RT-qPCR Plex SARS-CoV- tube Here Additionally SARSCoV2positive SARSCoVpositive positive classification RTPCR PCR SARSCoV2. 2. 96.5100% 965100 96.5 100% 96 5 100 96.5-100 95% 95 [95 CI, CI , (CI)] 99.8100% 998100 99.8 99 8 99.8-100 (95 CI) CI. . data pandemics (SARS-CoV- SARS-CoV 5100 96.5100 96510 965 96. 9 10 96.5-10 [9 (CI) 8100 99.8100 99810 998 99. 99.8-10 (9 (SARS-CoV 510 96.510 9651 1 96.5-1 [ (CI 810 99.810 9981 99.8-1 ( 51 96.51 96.5- 81 99.81 99.8-

Abstract Since the first reported case of COVID-19 in Brazil, the public and private educational system started to close. Up to November 2020, scientific discussions about the return of schooling activities have been rarely performed by the national scientific community and police-makers. The great delay of school returning in Brazil contrasts with successful international strategies of school reopening worldwide and seems counterintuitive with the reopening of non-essential activities. Here, important issues to be considered before and during school reopening are reviewed and discussed. COVID-19 testing is essential to avoid disease spreading, but high cost of individual RT-qPCRs impairs an extensive testing strategy for school returning. To reduce costs and increase the speed of diagnosis, we tested the efficiency of a pooled-sample PCR strategy in a cohort of the educational staff in the city of Macaé/RJ, finding five asymptomatic individuals (0,66%) among the 754 people tested. Thus, a polled-sample PCR testing strategy of the educational staff might prevent infection spreading in schools at a reasonable cost. We discuss how our test strategy could be coupled with internationally recognized safety rules to allow for a safe school return and how countries from different world regions are dealing with educational activities during COVID-19 pandemic.

ABSTRACT In response to the Zika epidemics in Brazil, the ZDC molecular assay (Bio-Manguinhos) was developed and registered at the Brazilian Regulatory Agency of Health Surveillance - ANVISA. The circulation of Zika (ZIKV) Dengue (DENV) and Chikungunya (CHIKV) viruses and their clinical similarities are challenges to correctly diagnose these viruses. The simultaneous detection of ZIKV, DENV and CHIKV is an important tool for diagnosis and surveillance. Here, we present the analytical and clinical performance evaluation of ZDC molecular assay (Bio-Manguinhos) at the public health laboratories three years after its registration at ANVISA. The clinical performance demonstrates the ZDC molecular assay (Bio-Manguinhos) has 100% sensitivity and 100% specificity to detect and discriminate ZIKV, CHIKV, and DENV from clinical plasma samples. The ZDC molecular assay (Bio-Manguinhos) results were highly reproducible and no cross-reactivity was seen during testing with a panel of other infectious agents. In conclusion, the ZDC molecular assay (Bio-Manguinhos) is an accurate and reliable tool to monitor Zika, dengue and chikungunya infections in countries like Brazil with simultaneous circulation of the three viruses.

Abstract Hepatitis C virus (HCV) infection is a worldwide health problem. Nowadays, direct-acting antiviral agents (DAAs) are the main treatment for HCV; however, the high level of virus variability leads to the development of resistance-associated variants (RAVs). Thus, assessing RAVs in infected patients is important for monitoring treatment efficacy. The aim of our study was to investigate the presence of naturally occurring resistance mutations in HCV NS3 and NS5 regions in treatment-naïve patients. Ninety-six anti-HCV positive serum samples from blood donors at the Center of Hematology and Hemotherapy of Santa Catarina State (HEMOSC) were collected retrospectively in 2013 and evaluated in this study. HCV 1a (37.9%), 1b (25.3%), and 3a (36.8%) subtypes were found. The frequency of patients with RAVs in our study was 6.9%. The HCV NS5b sequencing reveled 1 sample with L320F mutation and 4 samples with the C316N/R polymorphism. The analysis of the NS3 region revealed the D168A/G/T (3.45%), S122G (1.15%), and V55A (2.3%) mutations. All samples from genotype 3a (36.8%) presented the V170 I/V non-synonymous mutation. In conclusion, we have shown that mutations in NS3 and NS5b genes are present in Brazilian isolates from therapy-naïve HCV patients.

Abstract Recent reports indicate that besides respiratory and systemic symptoms among coronavirus disease (COVID-19) patients, the disease has a wide spectrum of neurological manifestations (encephalitis, meningitis, myelitis, acute disseminated encephalomyelitis, metabolic and acute hemorrhagic necrotizing encephalopathy, cerebrovascular diseases, Guillain-Barré syndrome, polyneuritis cranialis, dysautonomia, and myopathies). The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can spread from the respiratory system to the central nervous system, using transneuronal and hematogenous mechanisms. Although not every COVID-19 patient will test positive for the virus in the cerebrospinal fluid exam, the appearance of neurological symptoms associated with SARS-CoV-2 infection reveals the importance of understanding the neurologic manifestations and capacity for neural invasion associated with the pathogen. These aspects are relevant for correct diagnosis and treatment, and for the potential development of vaccines. This review highlights the latest evidence of SARS-CoV-2 infection with a focus on neurological involvement and potential neuropathogenesis mechanisms.

ABSTRACT The Brazilian Public Health Service provides freely αPEG-IFN to treat patients infected with HCV. The primary goal of HCV therapy is the long-term elimination of HCV from the blood to reduce the risk of HCV associated complications and death. Patient viremia affects the treatment duration and response, thus influencing clinical decisions. We developed a high-throughput method to perform the quantification of RNA hepatitis C virus (HCV) virus load in plasma samples to monitor patients under treatment. The method is based on a duplex detection, in a one-step real-time RT-PCR assay and it has been validated according to the rules established by the official Brazilian regulatory agency (ANVISA). This new method was compared to a commercial kit (Cobas/Taqman HCV Test v2.0 - Roche), showing virus load results with significant correlation between them (p= 0,012) using commercial and clinical panels. In addition, 611 samples from patients treated with peguilated alfa-interferon (αPEG-IFN) from different regions of Brazil were analyzed. Our one-step real-time RT-PCR assay demonstrated good performance in viral load measurement and in treatment course monitoring, with acceptable sensitivity and specificity values.

Antiretroviral therapy (ART) has reduced morbidity and mortality related to human immunodeficiency virus (HIV) infection, but in spite of this advance, HIV mutations decrease antiretroviral susceptibility, thus contributing to treatment failure in patients. Genotyping HIV-1 allows the selection of new drugs after initial drug failure. This study evaluated the genotypic profile of HIV-1 isolates from treated (drug-experienced) patients in Paraná, Brazil. The prevalence of mutations in reverse transcriptase (RT) and protease (PR) genes were assessed. We analyzed 467 genotypes of patients with HIV-1 viral loads above 1,000 copies/mL. Mutations at HIV-1 RT and PR genes and previously used ART regimens were recorded. The most prevalent RT mutations were: 184V (68.31%), 215YF (51.6%), 103NS (46%), 41L (39.4%), 67N (38.54%), 210W (23.5%), 190ASE (23.2%), and 181C (17.4%). PR mutations were 90M (33.33%), 82ATFS (29%), 46I (26.8%) and 54V (22.2%). The prevalence of mutations was in line with previous national and international reports, except to nonnucleoside analogue reverse transcriptase inhibitors related mutations, which were more prevalent in this study. Previous exposure to antiretroviral drugs was associated with genotypic resistance to specific drugs, leading to treatment failure in HIV patients.

OBJECTIVE: Because epidemiological data on circulating HIV subtypes among HIV-positive patients in the state of Paraná were not known until now, the aims of this study were to describe the genetic diversity profile of HIV-1 in treated patients in Paraná, Brazil, and report the differences in protease (PR) and reverse transcriptase (RT) mutations in HIV-1 subtypes. PATIENTS AND METHODS: A cross-sectional study was conducted from 2003 to 2006. Plasma viral RNA of 389 patients was extracted and PR and RT genes were polymerase chain reaction-amplified and sequenced. Sequences were subtyped and examined for antiretroviral resistance mutations. Data on gender of patient harboring the viruses and past history of antiretroviral treatment were also collected. RESULTS: Most viruses were either subtype B (61.44%) or subtype C (20.57%). Subtype C and F were more frequent in women (p < 0.00). The prevalence of subtypes was similar over the years studied. The most frequent RT mutations in all subtypes were M184V and mutations at codons 215, 41, 103, 67, 219, and 190. Mutations 41L, 210W, 215YF, and 74V were significantly more prevalent on subtype B, and the mutation 106M was significantly more prevalent on subtype C. The most frequent major PI mutations in all subtypes occurred at codons 46, 82, and 90. PR mutations 32I, 46I, and 84V were significantly more prevalent on subtype B. The minor PI mutations on codons 36, 93, and 63 were more prevalent on subtypes F, C, and B, respectively. CONCLUSION: We concluded that the predominant strain of HIV-1 in Paraná is subtype B, followed by subtype C. Some mutations at PR and TR had subtype predominance in accordance with other authors' report.

OBJETIVO: avaliar a proliferação de células T e a produção de citocinas em gestantes infectadas pelo HIV-1 e seu impacto na replicação viral in vitro. MÉTODOS: sangue periférico de 12 gestantes infectadas pelo HIV-1 e de seus neonatos, bem como de 10 gestantes HIV-1 negativas, foi colhido e a quantidade de linfócitos TCD4+ e TCD8+ periféricos foi avaliada por citometria de fluxo. Para obter plasma ou células mononucleares periféricas (PBMC), as amostras foram centrifugadas na ausência ou presença de um gradiente de Ficoll-Hypaque, respectivamente. As PBMC foram mantidas em cultura por sete dias na presença de fito-hemaglutinina mais IL-2 recombinante e a resposta linfoproliferativa de células T foi analisada pelo método de exclusão em azul de Trypan. Em alguns experimentos, as culturas foram mantidas na presença adicional de anticorpo anti-IL-10. Os plasmas e sobrenadantes das culturas de PBMC ativadas foram submetidos à análise da produção de citocinas, pelo método ELISA indireto, e a carga viral, detectada pelo RT-PCR. RESULTADOS: independente da carga viral plasmática, a resposta linfoproliferativa em culturas de células obtidas de gestantes infectadas pelo HIV foi inferior às amostras normais [4,2±0,37 vs 2,4±0,56 (x 10(6)) células/mL; p<0.005]. Tanto em gestantes normais quanto em pacientes com cargas virais baixas, os níveis de IL-10 foram mais elevados que os das gestantes com elevada replicação viral (9.790±3.224 vs 1.256±350 pg/mL; p=0.002). Níveis elevados de TNF-alfa no soro (7.200±2.440 vs 510±476 pg/mL) e nas culturas de células (21.350±15.230 vs 1.256±350 pg/mL) correlacionaram-se à carga viral plasmática elevada e a infecção neonatal. O bloqueio da IL-10 endógena com anticorpos anti-IL-10 aumentou a replicação do HIV-1 em cultura de células. CONCLUSÃO: nossos resultados sugerem que a IL-10 exerce influência negativa na replicação viral, o que provavelmente contribui para reduzir o risco de infecção vertical.

PURPOSE: to evaluate T cell proliferation and cytokine production in HIV-1-infected pregnant women and their impact on in vitro virus replication. METHODS: peripheral blood from 12 HIV-1-infected pregnant women and from their neonates was collected. As control, 10 samples from non-infected pregnants were also colleted. The CD4+ and CD8+ T cell counts were assayed by flow cytometry. Peripheral blood mononuclear cells (PBMC) and plasma were obtained by centrifugation with and without Ficoll-Hypaque gradient, respectively. The freshly purified PBMC were kept in cultures for seven days with PHA plus r-IL-2, and the lymphoproliferative response was assayed by Trypan blue dye exclusion. In some experiments we added anti-IL-10 monoclonal antibody. The plasma samples and supernatants from cell cultures were stored to determine both peripheral cytokine levels, by ELISA sandwich, and viral load, by RT-PCR. RESULTS: the results showed that the lymphoproliferative response was smaller in cultures obtained from HIV-1-infected women than in control cultures [4.2±0.37 vs 2.4±0.56 (x 10(6) cell/mL), p<0.005]. In both control and infected pregnant women who had low plasma viral load, the level of IL-10 was higher than in those with high viral replication (9.790±3.224 vs 1.256±350 pg/mL, p=0.002). The elevated TNF-alpha production detected in serum (7.200±2.440 pg/mL) and supernatants (21.350±15.230 pg/mL) was associated with higher plasma viral loads and vertical infection. The IL-10 blockade by anti-IL-10 antibodies augmented viral replication in the cell cultures. CONCLUSION: these results indicate that IL-10 production exerts a negative influence on virus replication, diminishing the probability of intrauterine HIV-1 infection.