Betacoronavirus Infection Outbreak, São Paulo, Brazil, Fall 2023.

We report a human coronavirus OC43 infection outbreak in hospitalized patients and healthcare workers in São Paulo, Brazil, occurring after SARS-CoV-2 cases disappeared. Infection was associated with healthcare workers in 5 (29.4%) patients. Routine surveillance including a respiratory virus panel can improve coronavirus detection in both healthcare professionals and patients.

Comparison of viral load between saliva and nasopharyngeal swabs for SARS-CoV2: the role of days of symptoms onset on diagnosis.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is highly infectious causing millions of deaths worldwide. Nasopharyngeal swabs are the primary sample of choice for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), thus, to decrease the exposure to potentially infected samples through the collection is a key point to reduce the risk of infection in healthcare workers. OBJECTIVES: This study aimed to evaluate the sensitivity and viral load of saliva specimens by days of symptoms onset comparing to nasopharyngeal swabs in subjects with mild symptoms. METHODS: Saliva and nasopharyngeal swabs samples were collected from São Paulo Hospital workers presenting mild symptoms, such as fever, cough, sore throat, rhinorrhea, myalgia, headaches, anosmia, ageusia, and fatigue. To understand the positivity and viral load, reverse transcription-polymerase chain reaction (RT-PCR) was performed. FINDINGS: Saliva specimens presented a sensitivity of 98.6% compared to nasopharyngeal swabs. Overall, saliva showed lower viral load compared to nasopharyngeal swabs, regarding days of symptoms onset on diagnosis, the first four days had significant changes in viral load and no significant difference was reported in the days five to nine. MAIN CONCLUSIONS: Although RT-PCR of saliva has presented a lower viral load compared to nasopharyngeal swabs, saliva specimens are a potential and reliable candidate for COVID-19 diagnosis through RT-PCR.

Influenza B viral load analysis in patients with acute respiratory infection from a tertiary hospital in Brazil.

Currently, 2 genotypes of Influenza B viruses (IFB) are cocirculating in humans: Victoria (VIC) and Yamagata (YAM). Infection and viral load (VL) were analyzed in 105 genotyped IFB (59 VIC and 46 YAM) out of 3452 respiratory samples from immunodepressed (ID), immunocompetent (IC) including outpatients (OP) and hospitalized patients (HP) attended during 2001-2013 at São Paulo Hospital. VL (Log10 RNA copies/mL) calculation was possible in 78 samples (47 VIC, 31 YAM). The age group of 12 to 18 years presented the highest detection (14.13%). Rates of infection among groups were of 3.67% (IC), 1.68% (ID), 3.50% (OP), 0.6% (HP), and VLs varied from 2.8 to 10.13 with no difference regarding age, immune status, and disease severity. From 10 OP vaccinated against influenza, 8 (7 children, 1 ID) received a matching strain shot (VIC), and 2 a monovalent influenza A H1N1pdm09. Those patients presented a VL of 6.31 ± 1.62 (mean ± SD). IFB infection rates follow an age pattern, but VL seems not to be related to frequency or clinical outcome. IFB patients with previous immunization could point to some protection for VIC infections since there was no HP. Other immunological aspects, such as lineage infection immune priming, previous infections, and vaccinations, should be further investigated.

Influenza A(H1N1)pdm09 infection and viral load analysis in patients with different clinical presentations.

BACKGROUND Influenza viral load (VL) can be a decisive factor in determining the antiviral efficacy in viral clearance. OBJECTIVE This study aimed to evaluate the rate of infection and the role of influenza VL on the clinical spectrum of illnesses among different patient groups attended at a tertiary hospital in Brazil. METHODS Samples were collected from patients presenting acute respiratory infection from 2009 to 2013. Overall, 2262 samples were analysed and distributed into three groups: (i) asymptomatic (AS); (ii) symptomatic outpatients (OP); and (iii) hospitalised patients (HP). VL (expressed in Log10 RNA copies/mL) was calculated through a quantitative real-time one-step reverse transcription-polymerase chain reaction (RT-PCR) assay aimed at the M gene, with human RNAseP target as internal control and normalising gene of threshold cycle values. FINDINGS A total of 162 (7.16%) H1N1pdm09 positive samples were analysed. Patients aged from 0.08 to 77 years old [median ± standard deviation (SD): 12.5 ± 20.54]. Children with 5 to 11 years old presented the highest detection (p < 0.0001). AS patients had the lowest VL, with a significant difference when compared with symptomatic patients (p = 0.0003). A higher VL was observed within two days of disease onset. Ten patients (HP group) received antiviral treatment and were followed up and presented a mean initial VL of 6.64 ± 1.82. A complete viral clearance for 50% of these patients was reached after 12 days of treatment. MAIN CONCLUSIONS It is important to evaluate AS patients as potential spreaders, as viral shedding was still present, even at lower VL. Our results suggest that patients with underlying diseases and severe clinical symptoms may be considered for prolonged viral treatment.

Detection of influenza B lineages from 2001 to 2013 in a tertiary hospital in the city of São Paulo, Brazil.

Two antigenically distinct lineages of influenza B viruses, the Victoria-like and Yamagata-like strains, currently circulate among humans. Surveillance from United States of America and Europe over the last 10 years showed that the chance of a correct matching between vaccine and the circulating lineage had been 50%. We investigated influenza B infection in different patient groups (asymptomatic, general community, with comorbidities and hospitalised) attended at a tertiary hospital in the city of São Paulo, Brazil between 2001-2013. All samples were screened for influenza B virus by one-step real-time reverse transcription-polymerase chain reaction. From 2,992 respiratory samples collected, 114 (3.8%) tested positive for influenza B. Teenagers (13-18 years) presented the highest rate of 18.5% (odds ratio 22.87, 95% confidence interval 2.90-180.66, p < 0.001). One hundred nine samples could be characterised: 50 were Yamagata-like and 59 were Victoria-like strains. Mismatching between the vaccine and predominant circulating strain was observed in 2002 and 2013 seasons. Based on data collected during a period of 12 years, we found that influenza B was more frequent in teenagers. Co-circulation of both lineages and mismatch with the vaccine strain can occur. Our data highlighted the importance of quadrivalent vaccines and future analysis of the age groups included in vaccination programs.

Household transmission of COVID-19 according to index case: children, parents, and healthcare workers.

The first SARS-CoV-2 intrafamilial transmission was investigated in China. We evaluated the dynamics of SARS-CoV-2 transmission in 242 individuals from 60 family clusters, including 30 healthcare workers (HCW) and 30 patients, in São Paulo city. Sixty index cases with COVID-19 were selected, being 30 HCW index cases from Hospital São Paulo (HSP) and its 93 household contacts and 30 index case patients from Hospital Infantil Sabará (HIS) and its 89 household contacts. Asymptomatic and symptomatic individuals participating were tested for COVID-19. The secondary attack rates in the family clusters of HCW and HIS patients were 37.63% and 68.54%, respectively. Considering all households, the transmission from adults to children was 55.4%, while the transmission from children to children was 37.5%. Children were more infected if the index case was an adult, suggesting that children were less competent to transmit. The average time for a household to be COVID-19 positive was 4 and 3 days for HCW and HIS patients. Although HCW have a higher risk of infection and social vulnerability, the secondary attack rate was lower than that observed for HIS patients, possibly because HCW are more aware of transmission risks than the general community.

Comparative analysis of three point-of-care lateral flow immunoassays for detection of anti-SARS-CoV-2 antibodies: data from 100 healthcare workers in Brazil.

Since the coronavirus disease 2019 (COVID-19) pandemic, Brazil has the third-highest number of confirmed cases and the second-highest number of recovered patients. SARS-CoV-2 detection by real-time RT-PCR is the gold standard but requires a certified laboratory infrastructure with high-cost equipment and trained personnel. However, for large-scale testing, diagnostics should be fast, cost-effective, widely available, and deployed for the community, such as serological tests based on lateral flow immunoassay (LFIA) for IgM/IgG detection. We evaluated three different commercial point-of-care (POC) LFIAs for anti-SARS-CoV-2 IgM and IgG detection in capillary whole blood of 100 healthcare workers (HCW) from São Paulo university hospital previously tested by RT-PCR: (1) COVID-19 IgG/IgM BIO (Bioclin, Brazil), (2) Diagnostic Kit for IgM/IgG Antibody to Coronavirus (SARS-CoV-2) (Livzon, China), and (3) SARS-CoV-2 Antibody Test (Wondfo, China). A total of 84 positives and 16 negatives HCW were tested. The data was also analyzed by the number of days post symptoms (DPS) in three groups: <30 (n=26), 30-59 (n=42), and >59 (n=16). The observed sensibility was 85.71%, 47.62%, and 44.05% for Bioclin, Wondfo, and Livzon, respectively, with a specificity of 100% for all LFIA. Bioclin was more sensitive (p<0.01), regardless of the DPS. Thus, the Bioclin may be used as a POC test to monitor SARS-CoV-2 seroconversion in HCW.

Asymptomatic COVID-19 in hospital visitors: The underestimated potential of viral shedding.

In a single day, six of 150 (4%) asymptomatic visitors were diagnosed with COVID-19 at a hospital with a universal masking policy. Two inpatients (contacts) subsequently developed symptoms. More rigorous protective measures during visitation periods may need to be included in infection control practices to reduce nosocomial transmissions.

Detected SARS-CoV-2 in Ascitic Fluid Followed by Cryptococcemia: a Case Report.

SARS coronavirus-2 (SARS-CoV-2) detection in different clinical specimens has raised important insights about its pathogenesis, but some details remain to be understood. In that respect, disrupt viral control seen in solid organ transplant patients on chronic immunosuppression can help unveil pathogenic mechanisms and characterize new coronavirus disease-19 (COVID-19) immunological and clinical aspects, as well as secondary complications. We herein report a case of SARS-CoV-2 detection in ascitic fluid from a kidney transplant patient with decompensated cirrhosis and COVID-19 and then discuss about immune, cellular, and virological aspects of such clinical presentation of the disease, which also included a disseminated infection, demonstrated by viral detection in his blood sample. We subsequently discuss about the fatal outcome caused by a secondary bloodstream infection by Cryptococcus neoformans. This unprecedented case report presents ascitic fluid as a novel specimen in which SARS-CoV-2 can be detected. Immune dysregulation and cumulative risk factors may lead to secondary infections by opportunistic agents, including Cryptococcus neoformans.

No benefit of hydroxychloroquine on SARS-CoV-2 viral load reduction in non-critical hospitalized patients with COVID-19.

BACKGROUND: Some studies have shown that hydroxychloroquine (HCQ) is an effective drug in reducing the in vitro replication of SARS-CoV-2. However, the in vivo effect of HCQ still unclear. OBJECTIVES: This study aims to evaluate viral load clearance in patients with COVID-19 who underwent HCQ treatment in comparison with a control group that did not receive the drug. STUDY DESIGN: This prospective study comprised consecutive viral load measurements in patients with COVID-19 hospitalized with a moderate illness. Patients received 400 mg of HCQ every 12 h for 10 days according to the medical decision. Nasal swab samples were collected from patients during early, intermediary, and final clinical stage of COVID-19. RESULTS: A total of 155 samples were collected from 66 patients with COVID-19 (60% female), with a median age of 58 years. The viral load between studied groups, assumed as a semiquantitative measure of cycle threshold (Ct) values, presented no significant difference within the three consecutive measures (ΔCt) (p > 0.05). We also analyzed the ΔCt viral load at different intervals of sample collection (Δt < 7; 7-12; and > 12 days) without significant differences at any ΔCt (p > 0.05). CONCLUSION: In this study, we did not observe any change in viral load reduction in vivo with the use of HCQ.

The occurrence of polyomaviruses WUPyV and KIPyV among patients with severe respiratory infections.

In 2007, the new polyomaviruses WUPyV and KIPyV were identified in patients with acute respiratory infections. The aim of this study was to investigate these viruses in hospitalized patients with severe acute respiratory infection (SARI). A retrospective study was conducted with 251 patients, from April 2009 to November 2010, using nasopharyngeal aspirates, naso- and oropharyngeal swab samples from hospitalized patients (children < 12 years and adults) who had SARI within 7 days of the onset of symptoms, including fever (> 38.8 °C), dyspnea, and cough. Clinical and epidemiological information was obtained through standardized questionnaire. Enrolled patients were initially suspected to have influenza A(H1N1)pdm09 infections. WUPyV and KIPyV were detected by real-time PCR. Samples were also tested for influenza A and B viruses, human respiratory syncytial virus, rhinovirus, metapneumovirus, coronavirus, adenovirus, and parainfluenza viruses. WUPyV and KIPyV were detected in 6.77% (4.78% and 1.99%, respectively) of hospitalized patients with SARI. All samples from children showed coinfections (rhinovirus was the most commonly detected). Six adults had polyomavirus infection and four (1.6%) had monoinfection. Of them, 3 reported comorbidities including immunosuppression and 1 patient had worse outcome, requiring ICU admission. These preliminary data may suggest a possible role of polyomaviruses in SARI among immunocompromised adult patients.

Acute respiratory infection and influenza-like illness viral etiologies in Brazilian adults.

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.

Patterns of influenza infections among different risk groups in Brazil.

Influenza virus infections are associated with high morbidity and mortality. Influenza activity varies worldwide, and regional detection is influenced by geographic conditions, demographic and patient-risk factors. We assessed influenza activity and patterns of seasonality during three consecutive years (2001-2003) in three risk groups in São Paulo city. Four-hundred-twelve outpatients with acute respiratory infection were subjected to epidemiological, clinical and laboratory investigations; these included community population (N=140), health-care workers (N=203), and renal-transplanted patients (N=69). Nasal wash samples were tested by direct fluorescent assay for influenza, parainfluenza, adenovirus, and respiratory syncytial virus. Overall Influenza positivity was 21%, and a progressive decline was observed in all groups over time. Influenza A and B co-circulated at the same time in 2001 and 2002, but not in 2003. Low influenza-vaccination rates (19%) were reported by health-care workers. Unexpected low levels of etiological agents were detected in renal-transplanted patients, and infected cases were less symptomatic than immunocompetent patients. Based on this study, we conclude that health-care worker-immunization programs should be implemented and the clinical patterns of infected influenza patients should be used as a guide for better case-definition criteria for adequate influenza surveillance, particularly for renal-transplant patients.

Comparison of viral load between saliva and nasopharyngeal swabs for SARS-CoV2: the role of days of symptoms onset on diagnosis

BACKGROUND Coronavirus disease 2019 (COVID-19) is highly infectious causing millions of deaths worldwide. Nasopharyngeal swabs are the primary sample of choice for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), thus, to decrease the exposure to potentially infected samples through the collection is a key point to reduce the risk of infection in healthcare workers. OBJECTIVES This study aimed to evaluate the sensitivity and viral load of saliva specimens by days of symptoms onset comparing to nasopharyngeal swabs in subjects with mild symptoms. METHODS Saliva and nasopharyngeal swabs samples were collected from São Paulo Hospital workers presenting mild symptoms, such as fever, cough, sore throat, rhinorrhea, myalgia, headaches, anosmia, ageusia, and fatigue. To understand the positivity and viral load, reverse transcription-polymerase chain reaction (RT-PCR) was performed. FINDINGS Saliva specimens presented a sensitivity of 98.6% compared to nasopharyngeal swabs. Overall, saliva showed lower viral load compared to nasopharyngeal swabs, regarding days of symptoms onset on diagnosis, the first four days had significant changes in viral load and no significant difference was reported in the days five to nine. MAIN CONCLUSIONS Although RT-PCR of saliva has presented a lower viral load compared to nasopharyngeal swabs, saliva specimens are a potential and reliable candidate for COVID-19 diagnosis through RT-PCR.