Influenza A, like Omicron SARS-CoV-2, Is Similarly Detected in Saliva or Nasopharyngeal Samples via RT-qPCR.

After the Coronavirus pandemic, the importance of virus surveillance was highlighted, reinforcing the constant necessity of discussing and updating the methods for collection and diagnoses, including for other respiratory viruses. Although the nasopharyngeal swab is the gold-standard sample for detecting and genotyping SARS-CoV-2 and Influenza viruses, its collection is uncomfortable and requires specialized teams, which can be costly. During the pandemic, non-invasive saliva samples proved to be a suitable alternative for SARS-CoV-2 diagnosis, but for Influenza virus the use of this sample source is not recognized yet. In addition, most SARS-CoV-2 comparisons were conducted before the Omicron variant emerged. Here, we aimed to compare Influenza A and Omicron RT-qPCR analysis of nasopharyngeal swabs and saliva self-collection in paired samples from 663 individuals. We found that both nasopharyngeal swab and saliva collection are efficient for the diagnosis of Omicron (including sub-lineages) and for Influenza A, with high sensitivity and accuracy (>90%). The kappa index is 0.938 for Influenza A and 0.905 for SARS-CoV-2. These results showed excellent agreement between the two samples reinforcing saliva samples as a reliable source for detecting Omicron and highlighting saliva as a valid sample source for Influenza detection, considering this cheaper and more comfortable alternative.

IgA antibody dynamics in healthcare workers after CoronaVac® vaccination and heterologous Comirnaty® booster dose.

BACKGROUND: This study is aimed at calculating the IgA antibody dynamic range in healthcare workers (HCWs) after immunization with CoronaVac® and Comirnaty® booster dose. METHODS: A total of 118 HCW serum samples from Southern Brazil were collected the day before the first vaccine dose (day 0) and + 20, + 40, + 110, + 200 days following the vaccine's first dose, and + 15 days after a Comirnaty® booster dose. Immunoglobulin A (IgA) was quantified using immunoassays for anti-S1 (spike) protein antibodies (Euroimmun, Lübeck, Germany). RESULTS: Seroconversion for the S1 protein occurred in 75 (63.56%) and 115 (97.47%) HCWs by day + 40 and day + 15 after the booster dose, respectively. There was an absence of IgA antibodies after the booster dose in two (1.69%) HCWs undergoing biannual rituximab administration and one (0.85%) HCW for no apparent reason. CONCLUSION: Complete vaccination showed a significant IgA antibody production response, and the booster dose considerably increased this response.

Antibody response following a Comirnaty booster dose in CoronaVac vaccinated individuals.

Serum samples from 106 health care workers were analyzed by enzyme-linked immunosorbent assay (ELISA) test 15 days after a booster dose. A total of 99% of the participants showed a significant increase in the anti-S1 IgG index. The significant humoral response was observed 15 days after the heterologous dose of Comirnaty in most the subjects, regardless of having comorbidities. The administration of a third booster dose is suggested 5 months after the second vaccine dose of the initial vaccine.

SARS-CoV-2 Delta and Omicron Variants Surge in Curitiba, Southern Brazil, and Its Impact on Overall COVID-19 Lethality.

Screening efforts and genomic surveillance are essential tools to evaluate the course of the COVID-19 pandemic and assist the public healthcare system in dealing with an increasing number of infections. For the analysis of COVID-19 cases scenarios in Curitiba, Paraná, Brazil, we performed a diagnosis of positive cases, coupled with genotyping, for symptomatic and asymptomatic members of the Federal University of Paraná. We achieved over 1000 samples using RT-qPCR for diagnosis. The posterior genotyping allowed us to observe differences in the spread of strains in Curitiba, Brazil. The Delta variant was not associated with an infection wave, whereas the rapid Omicron variant spread became dominant in less than one month. We also evaluated the general vaccination coverage in the state, observing a striking reduction in lethality correlated to the vaccinated fraction of the population; although lower lethality rates were not much affected by the Omicron variant wave, the same effect was not translated in the number of infections. In summary, our results provide a general overview of the pandemic's course in Paraná State and how there was reduction in lethality after a combination of multiple infection waves and a large-scale vaccination program.

Comparison of SARS-CoV-2 molecular detection in nasopharyngeal swab, saliva, and gargle samples.

The nasopharyngeal swab is a gold standard for detecting SARS-CoV-2. However, the inconvenience of this method compelled us to compare its efficiency with saliva and gargle samples, which we collected sequentially from 229 individuals. Saliva outperformed gargle samples, constituting a reliable RNA viral source with similar performance to nasopharyngeal samples.

Severe acute respiratory syndrome coronavirus 2 infection among healthcare workers in a tertiary public hospital in Curitiba, Brazil.

BACKGROUND: We aimed to describe the clinical characteristics of coronavirus disease 2019 (COVID-19) among healthcare workers (HCWs) in Curitiba, Brazil. METHODS: Upper respiratory samples from 1077 HCWs were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using reverse transcription polymerase chain reaction from June 16, 2020 to December 9, 2020. RESULTS: Overall, 32.7% of HCWs were infected. The positivity rates in symptomatic and asymptomatic HCWs were 39.2% and 15.9%, respectively. Hospital departments categorized as high-risk for exposure had the highest number of infected HCWs. CONCLUSIONS: Early diagnosis and isolation of infected HCWs remain key in controlling SARS-CoV-2 transmission because HCWs in close contact with COVID-19 patients are more likely to be infected than those who are not.

Dynamic of humoral response to SARS-CoV-2 anti-Nucleocapsid and Spike proteins after CoronaVac vaccination.

This study aimed to calculate the seroconversion rate and IgG antibody dynamic range of the CoronaVac vaccine in healthcare workers (HCWs) after immunization. Serum samples from 133 HCWs from Southern Brazil were collected 1 day before (Day 0) and +10, +20, +40, + 60, +110 days after administering the vaccine's first dose. Immunoglobulin G (IgG) was quantified using immunoassays for anti-N-protein (nucleocapsid) antibodies (Abbott, Sligo, Ireland) and for anti-S1 (spike) protein antibodies (Euroimmun, Lübeck, Germany). Seroconversion by day 40 occurred in 129 (97%) HCWs for the S1 protein, and in 69 (51.87%) HCWs for the N protein. An absence of IgG antibodies (by both methodologies), occurred in 2 (1.5%) HCWs undergoing semiannual rituximab administration, and also in another 2 (1.5%) HCWs with no apparent reason. This study showed that CoronaVac has a high seroconversion rate when evaluated in an HCW population.

Severe acute respiratory syndrome coronavirus 2 infection among healthcare workers in a tertiary public hospital in Curitiba, Brazil

ABSTRACT BACKGROUND: We aimed to describe the clinical characteristics of coronavirus disease 2019 (COVID-19) among healthcare workers (HCWs) in Curitiba, Brazil. METHODS: Upper respiratory samples from 1077 HCWs were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using reverse transcription polymerase chain reaction from June 16, 2020 to December 9, 2020. RESULTS: Overall, 32.7% of HCWs were infected. The positivity rates in symptomatic and asymptomatic HCWs were 39.2% and 15.9%, respectively. Hospital departments categorized as high-risk for exposure had the highest number of infected HCWs. CONCLUSIONS: Early diagnosis and isolation of infected HCWs remain key in controlling SARS-CoV-2 transmission because HCWs in close contact with COVID-19 patients are more likely to be infected than those who are not.

Large-Scale Screening of Asymptomatic Persons for SARS-CoV-2 Variants of Concern and Gamma Takeover, Brazil.

We performed a large-scale severe acute respiratory syndrome coronavirus 2 screening campaign using 2 PCR-based approaches, coupled with variant genotyping, aiming to provide a safer environment for employees of Federal University in Curitiba, Brazil. We observed the rapid spread of the Gamma variant of concern, which replaced other variants in <3 months.

NEAT1 and MALAT1 are highly expressed in saliva and nasopharyngeal swab samples of COVID-19 patients.

COVID-19, caused by the SARS-CoV-2 virus, has become a significant global public health problem, with a wide variety of clinical manifestations and disease progression outcomes. LncRNAs are key regulators of the immune response and have been associated with COVID-19 risk infection. Previous studies focused mainly on in-silico analysis of lncRNA expression in the lungs or peripheral blood cells. We evaluated the expression of lncRNAs NEAT1, MALAT1, and MIR3142 in saliva and nasopharyngeal swab from SARS-CoV-2 positive (n = 34) and negative patients (n = 46). A higher expression of the lncRNAs NEAT1 and MALAT1 (p < 0.05) were found in positive samples. NEAT1 had a higher expression mainly in saliva samples (p < 0.001), and MALAT1 was upregulated in nasopharyngeal samples (p < 0.05). Area under the ROC curve for NEAT1 in saliva was 0.8067. This study was the first to investigate the expression of lncRNAs in saliva and nasopharyngeal samples of COVID-19 patients, which gives new insights into the initial response to infection and infectivity and may provide new biomarkers for severity and targets for therapy.

Association Between COVID-19 Pregnant Women Symptoms Severity and Placental Morphologic Features.

Since the beginning of the pandemic, few papers describe the placenta's morphological and morphometrical features in SARS-CoV-2-positive pregnant women. Alterations, such as low placental weight, accelerated villous maturation, decidual vasculopathy, infarcts, thrombosis of fetal placental vessels, and chronic histiocytic intervillositis (CHI), have been described. Objective: To analyze clinical data and the placental morphological and morphometric changes of pregnant women infected with SARS-CoV-2 (COVID-19 group) in comparison with the placentas of non-infected pregnant women, matched for maternal age and comorbidities, besides gestational age of delivery (Control group). Method: The patients in the COVID-19 and the Control group were matched for maternal age, gestational age, and comorbidities. The morphological analysis of placentas was performed using Amsterdam Placental Workshop Group Consensus Statement. The quantitative morphometric evaluation included perimeter diameter and number of tertiary villi, number of sprouts and knots, evaluation of deposition of villous fibrin, and deposition of intra-villous collagen I and III by Sirius Red. Additionally, Hofbauer cells (HC) were counted within villi by immunohistochemistry with CD68 marker. Results: Compared to controls, symptomatic women in the COVID-19 group were more likely to have at least one comorbidity, to evolve to preterm labor and infant death, and to have positive SARS-CoV-2 RNA testing in their concepts. Compared to controls, placentas in the COVID-19 group were more likely to show features of maternal and fetal vascular malperfusion. In the COVID-19 group, placentas of symptomatic women were more likely to show CHI. No significant results were found after morphometric analysis. Conclusion: Pregnant women with symptomatic SARS-CoV-2 infection, particularly with the severe course, are more likely to exhibit an adverse fetal outcome, with slightly more frequent histopathologic findings of maternal and fetal vascular malperfusion, and CHI. The morphometric changes found in the placentas of the COVID-19 group do not seem to be different from those observed in the Control group, as far as maternal age, gestational age, and comorbidities are paired. Only the deposition of villous fibrin could be more accentuated in the COVID-19 group (p = 0.08 borderline). The number of HC/villous evaluated with CD68 immunohistochemistry did not show a difference between both groups.

SARS-CoV-2 in asymptomatic pregnant women in South Brazil: RT-PCR and serological detection.

OBJECTIVES: This study aims to detect the SARS-CoV-2 infection prevalence in asymptomatic pregnant women. METHODS: A group of 195 asymptomatic pregnant women who attended the prenatal care outclinic and to the obstetric emergency department was tested concomitantly for SARS-CoV-2 by RT-PCR and serological tests. RESULTS: The virus was detected by RT-PCR in two (1.02%) cases and 17 (8.71%) patients had antibodies detected by immunochromatographic tests. CONCLUSIONS: Due to the high risk of this emerging infection in the health of pregnant women, fetuses and newborns, we suggest the universal screening of all pregnant women admitted to hospital through the combined method RT-PCR and serological.

Clinical performance of amperometry compared with enzymatic ultra violet method for lactate quantification in cerebrospinal fluid.

OBJECTIVES: The differential diagnosis between acute bacterial meningitis (BM) and viral meningitis (VM) is crucial for treatment and prognosis. Cerebrospinal fluid (CSF) lactate (LA) is considered a good biomarker for differentiating BM from VM. The objective of this study was to compare the clinical performance of amperometry, which is not validated for measurement of LA in CSF samples, with a validated method (enzymatic ultra violet), for their ability to discriminate between acute BM and VM. METHODS: It was a retrospective, descriptive comparative study, 320 CSF reports were included; LA was quantified in CSF using either Dimension AR machine (Dade Behring) or amperometry (RAPID Point 500, Siemens). All samples with bacteria (n=54) or virus (n=139) identified, compared with a control with normal CSF (n=127). RESULTS: CSF LA levels were comparable for amperometry or enzymatic methods on each group studied, in a wide range of LA levels; it was capable to distinguish BM from VM independent of the method used to quantify. CONCLUSIONS: The findings support the use of the amperometric method in measuring LA concentrations in CSF in a wide range of values. Amperometry is a less expensive method, validated for blood, easily available in small laboratories including in limited resources countries.

Intrauterine Transmission of SARS-CoV-2.

We documented fetal death associated with intrauterine transmission of severe acute respiratory syndrome coronavirus 2. We found chronic histiocytic intervillositis, maternal and fetal vascular malperfusion, microglial hyperplasia, and lymphocytic infiltrate in muscle in the placenta and fetal tissue. Placenta and umbilical cord blood tested positive for the virus by PCR, confirming transplacental transmission.

Comparison of Cerebrospinal Fluid Biomarkers for Differential Diagnosis of Acute Bacterial and Viral Meningitis with Atypical Cerebrospinal Fluid Characteristics.

OBJECTIVE: Several cerebrospinal fluid (CSF) biomarkers are used to distinguish between acute bacterial meningitis (BM) and viral meningitis (VM). We compared the ability of lactate and glucose (GL) in CSF and the CSF/blood GL ratio to distinguish between acute BM and VM with typical and atypical CSF characteristics. METHODS: Three hundred and twenty-four CSF reports were included, which were distributed as the acute BM, VM, and normal control groups (n = 63, 139, and 122, respectively). RESULTS: Lactate level in the CSF of acute BM group was 4-fold higher than that in the acute VM and control groups (p < 0.0001). CSF lactate presented higher specificity (92%) and negative predictive value (94%) compared to CSF GL and CSF/blood GL ratio in distinguishing acute BM and VM. Definitive acute BM or VM with atypical CSF cell characteristics was observed in 23.2 and 21.6% of samples, respectively, and these groups showed reduced performance of characteristics of all CSF biomarkers. CSF lactate showed better operational characteristics than those of CSF GL and CSF/blood GL ratio, presenting the highest positive likelihood ratio, and thus aided in the differential diagnosis of VM with atypical CSF. CONCLUSION: The CSF lactate assay can be routinely used in laboratories as a rapid, automated, and easy method that is independent of lactate blood levels.

Influenza Sentinel Surveillance and Severe Acute Respiratory Infection in a Reference Hospital in Southern Brazil

Abstract INTRODUCTION: We report the results of the active surveillance of influenza infections in hospitalized patients and the evaluation of the seasonality and correlation with temperature and rainfall data. METHODS: During the 2-year study period, 775 patients were tested for 15 respiratory viruses (RVs). RESULTS: Most of the 57% of (n=444) virus-positive samples were human rhinovirus and respiratory syncytial virus. However, 10.4% (n=46) were influenza virus (80% FluA; 20% FluB). Age and SARI were significantly associated with influenza. FluB circulation was higher is 2013. CONCLUSIONS: In the post-epidemic period, influenza remains an important cause of hospitalization in SARI patients.

Influenza Sentinel Surveillance and Severe Acute Respiratory Infection in a Reference Hospital in Southern Brazil.

INTRODUCTION: We report the results of the active surveillance of influenza infections in hospitalized patients and the evaluation of the seasonality and correlation with temperature and rainfall data. METHODS: During the 2-year study period, 775 patients were tested for 15 respiratory viruses (RVs). RESULTS: Most of the 57% of (n=444) virus-positive samples were human rhinovirus and respiratory syncytial virus. However, 10.4% (n=46) were influenza virus (80% FluA; 20% FluB). Age and SARI were significantly associated with influenza. FluB circulation was higher is 2013. CONCLUSIONS: In the post-epidemic period, influenza remains an important cause of hospitalization in SARI patients.

Human adenovirus meningoencephalitis: a 3-years' overview.

Human adenovirus (HAdV) has been recognized as a significant viral pathogen implicated in neurological diseases, particularly in immunocompromised patients. However, its involvement in meningoencephalitis remains unclear. The aim of this study was to investigate HAdV and other viral co-infections in the cerebrospinal fluid (CSF) of patients suspected of having either meningoencephalitis or encephalitis. A total of 373 CSF samples from patients under clinical suspicion of neurological viral infection were included in this study. HAdV was investigated by conventional or multiplex real-time PCR, for different time periods. The frequency of HAdV central nervous system (CNS) infection was 1.08%, predominating in female patients with a predisposing condition, and presented with HAdV encephalitis. HAdV CNS infection was found to occur during the months of autumn and winter. The frequency of HAdV detected in CSF positive samples increased after the change in the diagnostic method from conventional to multiplex real-time PCR. There were no specific NMRI or EEG characteristics and two CSF samples with HAdV encephalitis had normal CSF WBC count. There were two cases of co-infection with HIV; no other co-infections with enterovirus or herpes family viruses were detected. All patients had good outcome. Although HAdV is rarely observable in CNS infectious syndromes, it must be investigated particularly in immunocompromised patients.

High frequency of multiple HPV types detection in Fanconi anemia patients oral swabs.

BACKGROUND: Fanconi anemia (FA) is a rare genetic disease usually characterized by bone marrow failure and congenital malformations. The risk of development of malignancies in the oral cavity of FA patients, such as squamous cell carcinoma (SCC), increases significantly after a hematopoietic stem cells transplant (HSCT), and may also be linked with the presence of human papillomavirus (HPV) infections in the oral cavity. We investigated the prevalence and the HPV genotypes in oral mucosa of Brazilian FA patients. METHODS AND RESULTS: Oral swabs of 49 FA patients were collected. The median age of patients was 20 years (range 5-44) and 57% were over 18 years. Oral lesions were present in 20% of all patients, being 90% leukoplakia. HPV DNA was detected in 28% (14/49) of patients, and one of them also reported genital HPV lesions. Sixty-seven percent of all patients had undergone HSCT, including 12 patients (86%) of those with HPV results. Multiple HPV types were detected in 78% and 71% of HPV samples by Sanger sequencing and reverse hybridization methods, respectively. The most prevalent HPV types detected were 6, 11, 18, and 68. CONCLUSIONS: HPV prevalence in the oral mucosa of the assessed FA patients was higher than reported in the general population. Additional studies with collection of sequential samples are needed to know the natural history of the presence of multiple HPV types in these individuals and its association with the development of tumors, to evaluate the implementation of preventive measures, such as vaccination, and to guide early treatment.