Epidemiologic, clinical, and serum markers may improve discrimination between bacterial and viral etiologies of childhood pneumonia.

Background: Discrimination of bacterial and viral etiologies of childhood community-acquired pneumonia (CAP) is often challenging. Unnecessary antibiotic administration exposes patients to undue risks and may engender antimicrobial resistance. This study aimed to develop a prediction model using epidemiological, clinical and laboratory data to differentiate between bacterial and viral CAP. Methods: Data from 155 children with confirmed bacterial or mixed bacterial and viral infection (N = 124) and viral infection (N = 31) were derived from a comprehensive assessment of causative pathogens [Partnerships for Enhanced Engagement in Research-Pneumonia in Pediatrics (PEER-PePPeS)] conducted in Indonesia. Epidemiologic, clinical and biomarker profiles (hematology and inflammatory markers) were compared between groups. The area under the receiver operating characteristic curve (AUROC) for varying biomarker levels was used to characterize performance and determine cut-off values for discrimination of bacterial and mixed CAP versus viral CAP. Diagnostic predictors of bacterial and mixed CAP were assessed by multivariate logistic regression. Results: Diarrhea was more frequently reported in bacterial and mixed CAP, while viral infections more frequently occurred during Indonesia's rainy season. White blood cell counts (WBC), absolute neutrophil counts (ANC), neutrophil-lymphocyte ratio (NLR), C-reactive protein (CRP), and procalcitonin (PCT) were significantly higher in bacterial and mixed cases. After adjusting for covariates, the following were the most important predictors of bacterial or mixed CAP: rainy season (aOR 0.26; 95% CI 0.08-0.90; p = 0.033), CRP ≥5.70 mg/L (aOR 4.71; 95% CI 1.18-18.74; p = 0.028), and presence of fever (aOR 5.26; 95% CI 1.07-25.91; p = 0.041). The model assessed had a low R-squared (Nagelkerke R2 = 0.490) but good calibration (p = 0.610 for Hosmer Lemeshow test). The combination of CRP and fever had moderate predictive value with sensitivity and specificity of 62.28 and 65.52%, respectively. Conclusion: Combining clinical and laboratory profiles is potentially valuable for discriminating bacterial and mixed from viral pediatric CAP and may guide antibiotic use. Further studies with a larger sample size should be performed to validate this model.

Performance and correlation of ten commercial immunoassays for the detection of SARS-CoV-2 antibodies.

Accurate immunoassays with a good correlation to neutralizing antibodies are required to support SARS-CoV-2 diagnosis, management, vaccine deployment, and epidemiological investigation. We conducted a study to evaluate the performance and correlation of the surrogate virus neutralization test (sVNT) and other commercial immunoassays. We tested 107 sera of COVID-19 confirmed cases from three different time points, 58 confirmed non-COVID-19 sera, and 52 sera collected before the pandemic with two sVNTs, seven chemiluminescent assays, and one fluorescein assay. All assays achieved excellent sensitivity (95%-100%, ≥15 days after onset of illness), specificity (95.5%-100%), and showed moderate to high correlation with GenScript sVNT (r = 0.58 to r = 0.98), except Roche total antibodies (r = 0.48). Vazyme sVNT and Siemens total antibodies showed the highest correlation with GenScript sVNT (r = 0.98 and 0.88, respectively). Median indexes that may be used to estimate sera with the highest ability to inhibit SARS-CoV-2 and ACE-2 receptor attachment (GenScript sVNT inhibition 90%-100%) were 6.9 S/C (Abbott IgG), 161.9 COI (FREND™ IgG), 16.8 AU/ml (Snibe IgG), 40.1 S/CO (Beckman IgG), 281.9 U/ml (Mindray IgG), 712.2 U/ml (Mindray total antibodies), >10 index (Siemens total antibodies), and 95.3% inhibition (Vazyme sVNT). All ten commercial COVID-19 serology assays, with different targeting antigens, demonstrated a reliable performance, supporting the utility of those assays in clinical and research settings. However, further studies using more samples are needed to refine the results of evaluating the performances of these marketed serological assays. Reliable serological assays would be useful for clinicians, researchers and epidemiologists in confirming SARS-CoV-2 infections, observing SARS-CoV-2 transmission, and immune response post infection and vaccination, leading to better management and control of the disease.

Mild reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant: First case report from Indonesia.

Background: Reinfection with SARS-CoV-2 has been well documented, yet little is known about the degree of protection a previous infection provides against reinfection, especially against Variants of Concern (VOC). Case presentation: Here we describe a case of an unvaccinated 49-year-old man who experienced two sequential SARS-CoV-2 infections with two different variants, as evidenced by genomic sequencing. The first episode was caused by the Pango lineage B.1.466.2 and resulted in severe COVID-19 with 5 days in an intensive care unit (ICU). The second episode occurred approximately 6 months later, during the Delta surge in Indonesia. Genomic analysis showed that the second infection was caused by the Delta variant (Pango lineage B.1.617.2) and resulted in mild disease that did not require hospitalization. No SARS-CoV-2 nucleic acid was detected between the two episodes, but both binding and neutralizing antibodies to SARS-CoV-2 were detected prior to the reinfection, with the second infection leading to an increase in the levels of antibody. Conclusion: We confirmed that the patient experienced a reinfection instead of persistent viral shedding from the first infection based on epidemiological, clinical, serological, and genomic analyses. Our case supports the hypothesis that SARS-CoV-2 reinfection may occur once antibody titers decrease or following the emergence of a new variant. The milder presentation in the patient's second infection deserves further investigation to provide a clear picture of the role of post-infection immunity in altering the course of subsequent disease.

Diagnosis of COVID-19 in a Dengue-Endemic Area.

Emergence of SARS-CoV-2 in dengue virus (DENV)-endemic areas complicates the diagnosis of both infections. COVID-19 cases may be misdiagnosed as dengue, particularly when relying on DENV IgM, which can remain positive months after infection. To estimate the extent of this problem, we evaluated sera from 42 confirmed COVID-19 patients for evidence of DENV infection. No cases of SARS-CoV-2 and DENV coinfection were identified. However, recent DENV infection, indicated by the presence of DENV IgM and/or high level of IgG antibodies, was found in seven patients. Dengue virus IgM and/or high IgG titer should not exclude COVID-19. SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) testing is appropriate when dengue nonstructural protein 1 (NS1) or RT-PCR is negative. Given the possibility of coinfection, testing for both DENV and SARS-CoV-2 is merited in the setting of the current pandemic.

Leptospirosis in Indonesia: diagnostic challenges associated with atypical clinical manifestations and limited laboratory capacity.

BACKGROUND: The burden of leptospirosis in Indonesia is poorly understood. Data from an observational study conducted from 2013 to 2016 in seven cities across Indonesia was used to estimate the incidence of leptospirosis and document its clinical manifestations in patients requiring hospitalization. METHODS: Specimens from patients hospitalized with acute fever were collected at enrollment, 14-28 days, and 3 months. Demographic and clinical information were collected during study visits and/or retrieved from medical records and double-entered into clinical report forms. After initially screening for dengue virus and other pathogens, specimens were tested at a central Reference Laboratory for anti-Leptospira IgM using commercial ELISA kits and for Leptospira DNA using an in-house quantitative real-time PCR assay. RESULTS: Of 1464 patients enrolled, 45 (3.1%) confirmed cases (by PCR and/or sero-coversion or four-fold increase of IgM) and 6 (0.4%) probable cases (by high titer IgM) of leptospirosis were identified by the Reference Laboratory. Disease incidence at sites ranged from 0 (0%) cases in Denpasar to 17 (8.9%) cases in Semarang. The median age of patients was 41.2 years (range of 5.3 to 85.0 years), and 67% of patients were male. Twenty-two patients (43.1%) were accurately diagnosed at sites, and 29 patients (56.9%) were clinically misdiagnosed as having another infection, most commonly dengue fever (11, 37.9%). Clinically, 20 patients (39.2%) did not present with hyperbilirubinemia or increased creatinine levels. Two patients (3.9%) died, both from respiratory failure. Fifteen patients (29.4%) clinically diagnosed with leptospirosis at sites were negative based on IgM ELISA and/or PCR at the Reference Laboratory. CONCLUSIONS: Leptospirosis remains an important cause of hospitalization in Indonesia. It can have diverse clinical presentations, making it difficult to differentiate from other common tropical infections. PCR combined with ELISA is a powerful alternative to the cumbersome gold-standard microscopic agglutination test, particularly in resource-limited settings.

Comparison of Commercial Enzyme-Linked Immunosorbent Assay and Immunofluorescence Assay for Diagnosis of Acute Rickettsia typhi Infections.

Murine typhus is a tropical disease caused by Rickettsia typhi and is endemic in resource-limited settings such as Southeast Asian countries. Early diagnosis of R. typhi infection facilitates appropriate management and reduces the risk of severe disease. However, molecular detection of R. typhi in blood is insensitive due to low rickettsemia. Furthermore, the gold standard of sero-diagnosis by immunofluorescence assay (IFA) is cumbersome, subjective, impractical, and unavailable in many endemic areas. In an attempt to identify a practical diagnostic approach that can be applied in Indonesia, we evaluated the performance of commercial R. typhi IgM and IgG enzyme-linked immunosorbent assay (ELISA) and IFA using paired plasma from previously studied R. typhi PCR-positive cases and controls with other known infections. Sensitivity and specificity of combined ELISA IgM and IgG anti-R. typhi using paired specimens were excellent (95.0% and 98.3%, respectively), comparable to combined IFA IgM and IgG (97.5% and 100%, respectively); sensitivity of ELISA IgM from acute specimens only was poor (45.0%), but specificity was excellent (98.3%). IFA IgM was more sensitive (77.5%), but less specific (89.7%) for single specimens.

Comparison of the Hemagglutination Inhibition Test and IgG ELISA in Categorizing Primary and Secondary Dengue Infections Based on the Plaque Reduction Neutralization Test.

Secondary dengue infection by heterotypic serotypes is associated with severe manifestations of disease, that is, dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). The World Health Organization (WHO) has recommended criteria based on the hemagglutination inhibition (HI) test to distinguish between primary and secondary dengue infections. Since the HI test has practical limitations and disadvantages, we evaluated the accuracy of WHO HI criteria and compared it with criteria based on an IgG enzyme-linked immunosorbent assay (ELISA) using a plaque reduction neutralization test (PRNT) as the gold standard. Both WHO HI criteria and IgG ELISA criteria performed strongly (16/16) in determining primary infection. However, to determine secondary infection, the IgG ELISA criteria performed better (72/73) compared to the WHO HI criteria (23/73).