The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations.

BackgroundEpidemiological and clinical data of human coronaviruses (HCoVs) infections are restricted to span 1–3 years at most. We conducted a comprehensive 9‐year study on HCoVs by analyzing 1137 respiratory samples from four subsets of patients (asymptomatic, general community, with comorbidities, and hospitalized) in São Paulo, Brazil.MethodsA pan‐coronavirus RT‐PCR screening assay was performed, followed by species‐specific real‐time RT‐PCR monoplex assays.ResultsHuman coronaviruses were detected in 88 of 1137 (7.7%) of the samples. The most frequently detected HCoV species were NL63 (50.0%) and OC43 (27.3%). Patients with comorbidities presented the highest risk of acquiring coronavirus infection (odds ratio = 4.17; 95% confidence interval = 1.9–9.3), and children with heart diseases revealed a significant HCoV infection presence. Dyspnea was more associated with HCoV‐229E infections (66.6%), and cyanosis was reported only in HCoV‐OC43 infections. There were interseasonal differences in the detection frequencies, with HCoV‐229E being predominant in the year 2004 (61.5%) and HCoV‐NL63 (70.8%) in 2008.ConclusionsOur data provide a novel insight into the epidemiology and clinical knowledge of HCoVs among different subsets of patients, revealing that these viruses may cause more than mild respiratory tract disease.

Influenza-like illness (ILI) definitions have been used worldwide for influenza surveillance. These different case definitions can vary with regard to sensitivity and predictive values for laboratory confirmed influenza. The literature has indicated the inclusion of other viruses may be the cause of these variable results. The objective of the study was to evaluate ILI national sentinel criteria and viral etiologies in adults diagnosed with acute respiratory infection (ARI) and/or ILI from 2001 to 2003 in Sao Paulo, Brazil. Clinical and laboratory evaluations were observed from 420 adults and collected on a daily basis from outpatient care units at University Hospital. The ILI definition included: fever plus at least one respiratory symptom (cough and/or sore throat) and one constitutional symptom (headache, malaise, myalgia, sweat or chills, or fatigue). DFA and RT-PCR for influenza, parainfluenza, respiratory syncytial virus, adenovirus, enterovirus, coronavirus, rhinovirus, and metapneumovirus were performed on nasal washes and 61.8% resulted positive. The respiratory viruses detected most often were influenza and rhinovirus. ILI was reported for 240/420 patients (57.1%), with influenza and rhinovirus etiologies accounting for 30.9% and 19.6%, respectively. Rhinovirus peak activity was concurrent with the influenza season. These findings highlight the implications of other viruses in ILI etiology and suggest that during the influenza season, this clinical overlap must be considered in the diagnosis and clinical management of patients.

This suggests that the use of sirolimus plus ganciclovir therapy could be useful in ganciclovir-resistant CMV infections.

Helicobacter pylori and immune thrombocytopenic purpura (ITP) association is not well established in chronic ITP (cITP) in children, although the cure of thrombocytopenia in approximately half of H. pylori eradicated adult patients has been described. The aim of this study was to investigate the effect of H. pylori eradication on platelet (PLT) recovery in cITP children and adolescents through a randomized, controlled trial. A total of 85 children (mean age 11.4 years) with cITP were prospectively enrolled. Diagnosis of H. pylori was established by two locally validated tests, (13)C-urea breath test and monoclonal stool antigen test. Twenty-two infected patients were identified, and randomly allocated into two groups: H. pylori treatment group (n = 11) and the non-intervention control group (n = 11). The control group was offered treatment if the thrombocytopenia persisted after the follow-up. At baseline, there were no differences regarding age, sex, duration of disease, and PLT count between groups. Sixty three of 85 patients were uninfected. PLT response was classified as complete response: PLT > 150 × 10(9 )l(-1); partial response: PLT 50-150 × 10(9 )l(-1), or an increase of 20-30 × 10(9 )l(-1); no response: PLT < 50 × 10(9 )l(-1) or an increase of <20 × 10(9 )l(-1) after at least 6 months of follow-up. Complete response was observed in 60.0% (6/10, one excluded) H. pylori eradicated patients vs. 18.2% (2/11) in non-eradicated patients (p = 0.08; OR = 6.75) after 6-9 months of follow-up. Among uninfected patients, only 13.8% (8/58) presented complete response. Two non-treated controls were treated after 6-12 months of follow-up, and PLT response was observed in 61.5% (8/13) of H. pylori eradicated patients, and in 19.0% (11/58) of uninfected patients (p = 0.004). Cytotoxin associated gene A and vacuolating cytotoxin gene A IgG antibodies were present in almost all infected patients. Therefore, the study suggests that H. pylori eradication plays a role in the management of H. pylori infected cITP children and adolescents.

The aims of this study were to (i) evaluate the prevalence and the incidence of hepatitis C virus (HCV) infection in hemodialysis patients in two different centers in São Paulo (Brazil), (ii) determine the time required to detect HCV infection among these patients by serology or PCR, (iii) establish the importance of alanine aminotransferase determination as a marker of HCV infection, and (iv) identify the HCV genotypes in this population. Serum samples were collected monthly for 1 year from 281 patients admitted to hospital for hemodialysis. Out of 281 patients, 41 patients (14.6%) were HCV positive; six patients seroconverted during this study (incidence = 3.1/1000 person-month). In 1.8% (5/281) of cases, RNA was detected before the appearance of antibodies (up to 5 months), and in 1.1% (3/281) of cases, RNA was the unique marker of HCV infection. The genotypes found were 1a, 1b, 3a, and 4a. The presence of genotype 4a is noteworthy, since it is a rare genotype in Brazil. These data pointed out the high prevalence and incidence of HCV infection at hemodialysis centers in Brazil and showed that routine PCR is fundamental for improving the detection of HCV carriers among patients undergoing hemodialysis.

Hepatitis E virus (HEV) causes acute and chronic hepatitis in organ transplant recipients. Serological evidence for HEV infection has been discovered in various population groups in Brazil, and a single acute case has been confirmed. To date, however, no cases of HEV infection in immunocompromised patients have been reported in Brazil. This study aimed to identify and characterize hepatitis E cases in renal transplant recipients in Brazil. A retrospective study was performed on 96 serum samples from renal transplant recipients with unexplained liver enzymes elevation. Three confirmed cases of HEV infection were identified that lacked seroconversion to HEV IgG antibodies. The prevalence of HEV in these patients was 3.1%. Using a sequence analysis of a 304-nucleotide fragment within ORF2, the strains were classified as genotype 3 with a low percent identity to previously characterized strains. This is the first report of hepatitis E infection in renal transplant recipients in Brazil, and the data indicate that a novel genotype 3 subvariant may be present and that further investigation is necessary to characterize the circulating HEV strains. In this setting, HEV infection should be considered as a potential cause of abnormal liver tests of unknown origin.

The chronic course of hepatitis E virus infection in immunosuppressed patients has been recently documented; however, clinical features and factors associated with this occurrence are not well known. The aim of this study was to evaluate the prevalence of previous or current HEV infection in renal transplant patients. One hundred ninety-two kidney transplant patients were studied and classified in three groups: G1-infected with hepatitis B and/or C virus; G2-patients with elevated ALT; G3-patients with normal ALT and no hepatotropic virus infection. Demographic, epidemiologic and clinical characteristics were compared between the groups. Patients with HEV infection (previous or current) were also compared to those who tested negative for HEV. HEV infection was detected using serologic (anti-HEV IgG) and molecular (HEV RNA) methods. Anti-HEV IgG was positive in 28 (15%) while HEV RNA was positive in 20 (10%). When both markers were considered, 44 (23%) patients showed evidence of previous or current HEV infection. However, both markers were concomitantly positive in only four cases (2%). In the comparative analysis, patients infected with HBV and/or HCV showed lower frequency of anti-HEV IgG (P = 0.009). There was no difference regarding demographic, epidemiologic and laboratory variable between viremic and non-viremic patients. In conclusion, past and current infection with HEV was a frequent finding among renal transplant recipients. Actively infected patients (HEV RNA positive) did not present distinct demographic and epidemiological characteristics or laboratory alterations suggestive of underlying liver damage. Therefore, infection with HEV can only be detected in immunosuppressed patients by systematic investigation of HEV RNA.