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 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.

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.

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 virus prevalence in asymptomatic and symptomatic subjects during pandemic and postpandemic periods.

BACKGROUND: In 2009, Influenza A(H1N1)pdm09 had a major effect on global health, causing thousands of deaths. However, the results of asymptomatic infection in transmission has not been well studied. We analyzed asymptomatic influenza infection in individuals with different risk factors for acquiring influenza in a university hospital. METHODS: Respiratory samples from 100 children with respiratory symptoms, their asymptomatic caregivers, 100 asymptomatic HIV-infected patients, and 100 health care workers collected during 2009-2011 were tested for influenza by real time real-time polymerase chain reaction. RESULTS: Influenza infection rate in symptomatic children was 44% and in asymptomatic adults it was 8.3% (P < .01). Children older than age 5 years had a 3.4 times greater chance of being infected during influenza season than younger children. Among the asymptomatic group, influenza was more frequent in caregivers (14%; P = .032) and a higher rate (31.8%) was observed if a child was infected during the 2009 pandemic. Contact with an infected child was an important risk factor for influenza acquisition (odds ratio, 3.8; 95% confidence interval, 1.1-13.2) among caregivers. The mean cluster of differentiation 4 T-cell count of HIV-positive patients infected with influenza was not statistically different from uninfected patients (P = .29). CONCLUSIONS: Asymptomatic household contacts of symptomatic children may play an important role in community transmission and a more proactive intervention should be considered during future pandemics.

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.

Influenza virus surveillance among young children in São Paulo, Brazil: the impact of vaccination.

This study assessed the presence of influenza virus among young children and the coverage of vaccination from 2010 to 2012 in São Paulo, Brazil. Our results demonstrated a lower rate of influenza detection and a predominance of influenza B. A decrease of coverage vaccination through the surveillance periods was observed.

Comparison of the direct fluorescence assay and real-time polymerase chain reaction for the detection of influenza virus A and B in immunocompromised patients.

OBJECTIVE: This study evaluated the diagnostic performance of two methods for the detection of influenza virus in immunocompromised transplant patients. METHODS: A total of 475 respiratory samples, 236 from patients in a hematopoietic stem cell transplantation program and 239 from kidney transplant patients, were analyzed by a direct fluorescence assay and the Centers for Disease Control real-time polymerase chain reaction protocol for influenza A and B detection. RESULTS: Influenza detection using either method was 7.6% in the hematopoietic stem cell transplant group and 30.5% in the kidney transplant patient group. Influenza detection by real-time polymerase chain reaction yielded a higher positive rate compared with fluorescence than that reported by other studies, and this difference was more pronounced for influenza A. The fluorescence assay sensitivity, specificity, positive and negative predictive values, and kappa coefficient were 17.6%, 100%, 1, 0.83, and 0.256, respectively, and lower detection rates occurred in the kidney transplant patients. CONCLUSIONS: The real-time polymerase chain reaction performance and the associated turnaround time for a large number of samples support the choice of this method for use in different routine diagnostic settings and influenza surveillance in high-risk patients.

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.

Influenza virus surveillance among young children in São Paulo, Brazil: the impact of vaccination

This study assessed the presence of influenza virus among young children and the coverage of vaccination from 2010 to 2012 in São Paulo, Brazil. Our results demonstrated a lower rate of influenza detection and a predominance of influenza B. A decrease of coverage vaccination through the surveillance periods was observed.

Rotavirus infection in children and adult patients attending in a tertiary Hospital of São Paulo, Brazil.

During the period of January 2003 to December 2005, 3,768 stool samples were received in the Microbiology Laboratory for rotavirus antigen detection from outpatients and inpatients of Albert Einstein Hospital, SP. Fresh stool samples from children and adults were analyzed by two methodologies: during 2003 and 2004 by latex agglutination (Slidex Rotavirus, Biomerieux) and 2005 by an immunochromatographic assay for the combined detection of rotavirus and adenovirus (Vikia Rota-Adeno, Biomerieux). Rotavirus group A was detected in 755 (20%) samples. The annual prevalence was 19.8% in 2003, 21.7% in 2004, and 18.7% in 2005. Rotavirus was detected every month during the period of the study, with peak of positivity between June and August (>35%). The prevalence in hospitalized patients was 26.1% (352/1,350) and in outpatients was 16.7% (403/2,418). For hospitalized patients most of the rotavirus infections were diagnosed in Pediatric setting, age range of 0 to 10 years (prevalence of 55.3%, 295/534). Overall positivity was up to 30% in patients between six months and five years of age (67% of all positive patients), all other age groups had at least 10% positive tests. Rotavirus infection is common in Sao Paulo, and besides the expected higher frequency in children it is also frequent in adults.

Comparison of the direct fluorescence assay and real-time polymerase chain reaction for the detection of influenza virus A and B in immunocompromised patients

OBJECTIVE: This study evaluated the diagnostic performance of two methods for the detection of influenza virus in immunocompromised transplant patients. METHODS: A total of 475 respiratory samples, 236 from patients in a hematopoietic stem cell transplantation program and 239 from kidney transplant patients, were analyzed by a direct fluorescence assay and the Centers for Disease Control real-time polymerase chain reaction protocol for influenza A and B detection. RESULTS: Influenza detection using either method was 7.6% in the hematopoietic stem cell transplant group and 30.5% in the kidney transplant patient group. Influenza detection by real-time polymerase chain reaction yielded a higher positive rate compared with fluorescence than that reported by other studies, and this difference was more pronounced for influenza A. The fluorescence assay sensitivity, specificity, positive and negative predictive values, and kappa coefficient were 17.6%, 100%, 1, 0.83, and 0.256, respectively, and lower detection rates occurred in the kidney transplant patients. CONCLUSIONS: The real-time polymerase chain reaction performance and the associated turnaround time for a large number of samples support the choice of this method for use in different routine diagnostic settings and influenza surveillance in high-risk patients. .

Influenza and rhinovirus infections among health-care workers.

BACKGROUND AND OBJECTIVE: Health-care workers (HCWs) are at higher risk of acquisition and transmission of respiratory virus infections. Nosocomial transmission of influenza has been documented but whether this is so for other respiratory viruses has not been assessed. METHODS: Epidemiological, clinical and viral laboratory surveillance was carried out on HCWs presenting with acute respiratory infection in a university hospital. RESULTS: Over a 2-year period, 203 subjects were recruited: rhinovirus was the most frequently detected virus (37.7% in flu negative samples) and influenza A/B was positive in only 12.3% of subjects. Only 19.7% of HCWs were immunized against influenza. High detection of rhinovirus occurred even during the peak of the influenza season and half of the infected subjects reported an influenza-like illness. CONCLUSION: Rhinovirus infection occurred frequently in this study population and probably contributes to influenza misdiagnosis. Educational interventions about different viruses causing respiratory symptoms and an increase in standards of infection control besides influenza immunization among HCWs is needed.