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.

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. .

Comparison of a rapid cytomegalovirus pp65 antigenemia assay revealed by immunofluorescence to an in-house assay revealed by immunoperoxidase for diagnosis in solid organ transplant recipient patients

Cytomegalovirus (CMV) antigenemia is still one of the two major assays available for diagnosis and monitoring of CMV infections. A commercial rapid test recently available in Brazil for quantification of human cytomegalovirus pp65 antigenemia revealed by immunofluorescence technique was compared with the original in-house method revealed by immunoperoxidase in patients receiving solid organ transplants. Of 80 blood samples tested for CMV antigenemia, 34 (42.5 percent) were positive: commercial assay detected 33 (97 percent) and in-house assay detected 20 (58.8 percent) samples. The numbers of positive cells in the two assays were different, with a median of 4.5 and 12 positive cells obtained by in-house and commercial kit, respectively. Discrepancies between assays occurred in 15 specimens from patients with low-grade antigenemia (median 6 positive cells). The assay-time was reduced in approximately 50 percent compared to in-house methodology. In conclusion, besides comparable results obtained for both assays, the commercial antigenemia assay provides more rapid and sensitive results.

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 percent) samples. The annual prevalence was 19.8 percent in 2003, 21.7 percent in 2004, and 18.7 percent in 2005. Rotavirus was detected every month during the period of the study, with peak of positivity between June and August (>35 percent). The prevalence in hospitalized patients was 26.1 percent (352/1,350) and in outpatients was 16.7 percent (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 percent, 295/534). Overall positivity was up to 30 percent in patients between six months and five years of age (67 percent of all positive patients), all other age groups had at least 10 percent positive tests. Rotavirus infection is common in Sao Paulo, and besides the expected higher frequency in children it is also frequent in adults.

Avaliação de quatro kits comerciais para detecção rápida de antígenos de Rotavírus em amostras de fezes / Four kits evaluation for Rotavirus rapid antigen detection in stool samples

O Rotavírus é um dos principais agentes causadores de diarréia, sendo desejável o diagnóstico laboratorial de maior rapidez e acurácia para evitar a complicação por essa infecção. Nesse estudo, foram comparados os resultados obtidos por 4 diferentes kits comerciais para pesquisa de antígenos de rotavírus em 42 amostras de fezes: dois kits com metodologia de aglutinação em látexe dois kits de detecção combinada de Rotavírus e Adenovírus por imunocromatografia. A concordância entre os kits testados foi de 88%, sendo 16 amostras positivas e 21 negativas em todos os testes. Nas cinco amostras com resultados discordantes apenas um kit obteve resultado diferente dos demais, sendo estes, repetidos por outro executor. Essa repetição demonstrou interpretação diferenteem duas amostras por um dos testes de aglutinação de látex. As taxas de detecção pelos kits imunocormatográficos foi de 66% (18/42) e para os kits de aglutinação de látex foi de 38-40% (16 e 17/42). Os kits imunocromatográficos demonstraram total concordância coma maioria dos demais kits testados. Conclui-se que, apesar da boa concordância entre os kits avaliados, algumas metodologias podem apresentar problemas na aplicação prática, principalmente com a interpretação da aglutinação de látex.

A total of 42 stool specimens were tested for the presence of antigen rotavirus by two distinct enzyme immunoassays (EIA) and two latex agglutination tests (LAT). Overall concordance was 88%, with 16 positive and 21 negative results by all tests. Discordant results occurred when one test differed from the others and was repeated by other technician. These procedures change the interpretation of latex agglutination. Detection rate for two immunocromatographic tests were 66% (18/42) and two latex agglutination tests were 40% and 38% (17 and 16/42). The results show that each of the commercial assays evaluated could accurately detect rotavirus in the stools specimens. Comparative results demonstrate that sensitivity of latex agglutination tests was lower than immunocromatographic tests. In conclusion, those rapid tests could be detect differently antigen rotavirus, the latex agglutination methodology could be difficult interpretation and immunochromatographic technique do not require specialized equipment, showed higher sensitivity and was rapid and easy to perform in the routine clinical laboratory.

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 percent, 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 percent) 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.