Clinical Relevance of Absolute BK Polyoma Viral Load Kinetics in Patients With Biopsy Proven BK Polyomavirus Associated Nephropathy

Introduction: The absolute BK viral load is an important diagnostic surrogate for BK polyomavirus associated nephropathy (PyVAN) after renal transplant (KTX) and serial assessment of BK viremia is recommended. However, there is no data indicating which particular viral load change, i.e., absolute vs. relative viral load changes (copies/ml; percentage of the preceding viremia) is associated with worse renal graft outcomes.Materials and Methods: In this retrospective study of 91 biopsy proven PyVAN, we analyzed the interplay of exposure time, absolute and relative viral load kinetics, baseline risk, and treatment strategies as risk factors for graft loss after 2 years using a multivariable Poisson-model.Results: We compared two major treatment strategies: standardized immunosuppression (IS) reduction (n = 53) and leflunomide (n = 30). The median viral load at the index biopsy was 2.15E+04 copies/ml (interquartile range [IQR] 1.70E+03–1.77E+05) and median peak viremia was 3.6E+04 copies/ml (IQR 2.7E+03–3.3E+05). Treatment strategies and IS-levels were not related to graft loss. After correction for baseline viral load and estimated glomerular filtration rate (eGFR), absolute viral load decrease/unit remained an independent risk factor for graft loss [incidence rate ratios [IRR] = 0.77, (95% CI 0.61–0.96), p = 0.02].Conclusion: This study provides evidence for the prognostic importance of absolute BK viremia kinetics as a dynamic parameter indicating short-term graft survival independently of other established risk factors.

Viral loads in nasopharyngeal aspirates and tracheal aspirates among children hospitalized with invasive ventilation for human adenovirus pneumonia

Purpose To evaluate viral loads in children with human adenovirus (HAdV) pneumonia at different stages of disease and compare the viral load between upper and lower respiratory tract samples. Methods We prospectively enrolled children who required invasive ventilation for HAdV pneumonia. Nasopharyngeal aspirate (NPA) and tracheal aspirate (TA) samples were collected throughout the entire period of invasive ventilation. Viral detection and quantification were performed using quantitative real-time polymerase chain reaction. Results Ninety-four children were enrolled. The median age of the children was 12.0 months (IQR: 11.0–24.0), and > ninety percent of patients were aged between 6 and 59 months. Seven hundred and nine paired NPA-TA samples were collected. The median viral loads of the NPA and TA samples were 7.31 log10 and 7.50 log10 copies/mL, respectively. Viral loads generally decreased steadily over time. The median viral load after 1, 2, 3, and > 3 weeks of the disease course was 8.65, 7.70, 6.69, and 5.09 log10 copies/mL, respectively, in NPA samples and 8.67, 7.79, 7.08, and 5.53 log10 copies/mL, respectively, in TA samples. Viral load showed a significant negative correlation with time since symptom onset in both NPA samples (Spearman r = − 0.607, P = 0.000) and TA samples (Spearman r = − 0.544, P = 0.000). The predicted duration of HAdV shedding was 60.17 days in the NPA group and 65.81 days in the TA group. Viral loads in NPA and TA from the same subjects correlated well with each other (R2 = 0.694). HAdV loads in NPA and TA were most comparable during the early phase of infection (95% limits of agreement, − 1.36 to 1.30 log10 copies/mL, R2 = 0.746). Variation increased during the late phase of infection (i.e., in follow-up samples), with viral loads remaining significantly higher in TA than NPA. Conclusions In children with HAdV pneumonia, viral loads in both NPA and TA steadily decreased during the course of the disease, and the predicted duration of viral shedding was more than 2 months. The HAdV DNA load of NPA is highly correlated with that of TA, especially in the initial phase of infection.

Predictors of SARS-CoV-2 Infection in Youth at a Large, Urban Healthcare Center in California, March–September 2020

Objective: To understand which social, epidemiologic, and clinical risk factors are associated with SARS-CoV-2 infection in youth accessing care in a large, urban academic institution.Methods: We conducted a prospective cohort study with case–control analyses in youth who received testing for SARS-CoV-2 at our academic institution in Los Angeles during the first wave of the COVID-19 pandemic (March–September 2020).Results: A total of 27,976 SARS-CoV-2 assays among 11,922 youth aged 0–24 years were performed, including 475 youth with positive SARS-CoV-2 results. Positivity rate was higher among older, African American, and Hispanic/Latinx youth. Cases were more likely to be from non-English-speaking households and have safety-net insurance. Zip codes with higher proportion of Hispanic/Latinx and residents living under the poverty line were associated with increased SARS-CoV-2 cases. Youth were more likely to have positive results if tested for exposure (OR 21.5, 95% CI 14.6–32.1) or recent travel (OR 1.5, 95% CI 1.0–2.3). Students were less likely to have positive results than essential worker youth (OR 0.5, 95% CI 0.3–0.8). Patterns of symptom presentation varied significantly by age group; number of symptoms correlated significantly with age in SARS-CoV-2 cases (r = 0.030, p < 0.001). SARS-CoV-2 viral load did not vary by symptom severity, but asymptomatic youth had lower median viral load than those with symptoms (21.5 vs. 26.7, p = 0.009).Conclusions: Socioeconomic factors are important drivers of SARS-CoV-2 infection in youth. Presence of symptoms, exposure, and travel can be used to drive testing in older youth. Policies for school reopening and infection prevention should be tailored differently for elementary schools and universities.

Evaluation of the SARS-CoV-2 positivity ratio and upper respiratory tract viral load among asymptomatic individuals screened before hospitalization or surgery in Flanders, Belgium

Introduction The incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in the Belgian community is mainly estimated based on test results of patients with coronavirus disease (COVID-19)-like symptoms. The aim of this study was to investigate the evolution of the SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) positivity ratio and distribution of viral loads within a cohort of asymptomatic patients screened prior hospitalization or surgery, stratified by age category. Materials/Methods We retrospectively studied data on SARS-CoV-2 real-time RT-PCR detection in respiratory tract samples of asymptomatic patients screened pre-hospitalization or pre-surgery in nine Belgian hospitals located in Flanders over a 12-month period (1 April 2020–31 March 2021). Results In total, 255925 SARS-CoV-2 RT-PCR test results and 2421 positive results for which a viral load was reported, were included in this study. An unweighted overall SARS-CoV-2 real-time RT-PCR positivity ratio of 1.27% was observed with strong spatiotemporal differences. SARS-CoV-2 circulated predominantly in 80+ year old individuals across all time periods except between the first and second COVID-19 wave and in 20–30 year old individuals before the second COVID-19 wave. In contrast to the first wave, a significantly higher positivity ratio was observed for the 20–40 age group in addition to the 80+ age group compared to the other age groups during the second wave. The median viral load follows a similar temporal evolution as the positivity rate with an increase ahead of the second wave and highest viral loads observed for 80+ year old individuals. Conclusion There was a high SARS-CoV-2 circulation among asymptomatic patients with a predominance and highest viral loads observed in the elderly. Moreover, ahead of the second COVID-19 wave an increase in median viral load was noted with the highest overall positivity ratio observed in 20–30 year old individuals, indicating they could have been the hidden drivers of this wave.

The Unmet Needs of Hepatitis E Virus Diagnosis in Suspected Drug-Induced Liver Injury in Limited Resource Setting

Background: Currently, there are no specific biomarkers for drug-induced liver injury (DILI), and the diagnosis of DILI is based mainly on the exclusion of other causes of liver dysfunction and the recognition of potential causative drugs. Hepatitis E virus (HEV) diagnosis is not routinely enrolled in many countries, and HEV infection could be misdiagnosed as DILI.Methodology: We retrospectively analyzed plasma samples (n = 80) collected from suspected DILI for HEV markers such as anti-HEV IgM, anti-HEV IgG, and HEV RNA. Anti-HEV antibodies were assessed using commercial ELISA kits. HEV RNA was tested by RT-qPCR targeting HEV ORF2/3, the receiver operating characteristic (ROC) curve was plotted, and a putative threshold for liver function parameters was determined.Results: Out of 80 samples, 12 samples were positive for anti-HEV IgM and anti-HEV IgG, and HEV RNA was detected in seven samples. The median viral load was 3.46 × 103 IU/ml, and the isolated viruses belonged to HEV genotype 1. The level of liver enzymes such as alanine transaminase (ALT) and aspartate transaminase (AST), but not alkaline phosphatase (ALP), was significantly higher in HEV confirmed cases than in non-HEV confirmed cases. We identified a plasma ALT level of at least 415.5 U/L and AST level of at least 332 U/L; ALT/ALP ratio of at least 5.08 could be used as a guide for the patients diagnosed as DILI to be tested for HEV infection. The previous liver function parameters showed high sensitivity and good specificity.Conclusion: Hepatitis E virus was detected in suspected DILI cases. The diagnosis of DILI is not secure until HEV testing is done. Liver function parameters can be used as a guide for HEV testing in suspected DILI cases in countries with limited resources.

The contemporary study of acute myocarditis in South Africa – CAMISA

Introduction The aetiology and estimated incidence of acute myocarditis (AM) remains undefined in Africa. Whilst cardiac magnetic resonance (CMR) provides for a provisional non-invasive diagnosis, endomyocardial biopsy (EMB), which is infrequently clinically sought, remains the gold standard. The developed world has experienced a shift in the viral epidemiology of AM and the ESC's most recent position statement on myocarditis recommends both CMR and EMB as the standard of care in suspected cases. We report on the interim results of the study. Purpose To determine the nature of presentation, underlying aetiology, and outcomes of patients presenting with AM to a single tertiary centre in South Africa. Methods A cohort of patients from a single tertiary centre in South Africa will be recruited from January 2018 to December 2022. All patients presenting or referred to the centre with clinically suspected AM that are investigated according to the ESC recommendations on myocarditis, which includes blood tests (CRP, hsTNT, HIV and Hepatitis C serology, ANA), a standard twelve-lead ECG, TTE, coronary angiography, CMR and EMB, will be included. Enrolment is ongoing. Results A total of 102 (mean age 42.2±13 years, 64.7% male) cases of clinically suspected AM were identified between January 2018 and January 2021. AM was confirmed in 41 (40.2%) cases on CMR only, while 41 (40.2%) were also confirmed on EMB. 4 cases of sarcoidosis, 1 case each of eosinophilic myocarditis, amyloidosis and primary cardiac lymphoma were diagnosed. Viral genome was isolated by PCR in 60 (59.8%) patients. PVB19 (73.5%) was the most commonly identified virus in those with confirmed AM followed by EBV (12.2%), HHV6 (4.1%) and Human Bocavirus (2%). 3 were coinfected with PVB19/EBV, and 1 with PVB19/EBV/HHV6. PVB19 was also isolated in 9 patients with no evidence of AM on CMR or EMB, but with lower median viral load compared to those with AM (198copies/ml IQR 113 – 282 vs 483copies/ml IQR 366 – 1460, p=0.005). The virus-positive patients with confirmed AM tended to be older (43.1±13.4 years vs 37.6±12.2 years, p=n/s), had higher median CRP (24mg/L vs 16mg/L, p=n/s) but lower median hsTnT (326.5ng/L vs 434.5ng/L, p=n/s) at presentation, and were more likely to be EMB positive (60% vs 37.5%, p=0.04) when compared to the virus-negative group. To date 6 patients have demised, of which 4 were related to AM. Conclusion To our knowledge, this is the first study to evaluate AM in Africa, and the biggest cohort of AM patients outside of the developed world. It demonstrates the heterogeneity in presentations and provides insight into the viral pathogens within our local setting, which appears similar to those reported in the developed world. We were also able to highlight some differences in demographic and clinical characteristics between those with virus-positive and virus-negative AM. The background prevalence and causal role of PVB19 in our setting will also need to be further explored. FUNDunding Acknowledgement Type of funding sources: None.

Clinical profile and mortality in patients with T. cruzi/HIV co-infection from the multicenter data base of the “Network for healthcare and study of Trypanosoma cruzi/HIV co-infection and other immunosuppression conditions”

Objective Chagas disease (CD) globalization facilitated the co-infection with Human Immunodeficiency Virus (HIV) in endemic and non-endemic areas. Considering the underestimation of Trypanosoma cruzi (T. cruzi)-HIV co-infection and the risk of life-threatening Chagas Disease Reactivation (CDR), this study aimed to analyze the major co-infection clinical characteristics and its mortality rates. Methods This is a cross-sectional retrospective multicenter study of patients with CD confirmed by two serological or one parasitological tests, and HIV infection confirmed by immunoblot. CDR was diagnosed by direct microscopy with detection of trypomastigote forms in the blood or other biological fluids and/or amastigote forms in inflammatory lesions. Results Out of 241 patients with co-infection, 86.7% were from Brazil, 47.5% had <200 CD4+ T cells/μL and median viral load was 17,000 copies/μL. Sixty CDR cases were observed. Death was more frequent in patients with reactivation and was mainly caused by CDR. Other causes of death unrelated to CDR were the manifestation of opportunistic infections in those with Acquired Immunodeficiency Syndrome. The time between the co-infection diagnosis to death was shorter in patients with CDR. Lower CD4+ cells count at co-infection diagnosis was independently associated with reactivation. Similarly, lower CD4+ cells numbers at co-infection diagnosis and male sex were associated with higher lethality in CDR. Additionally, CD4+ cells were lower in meningoencephalitis than in myocarditis and milder forms. Conclusion This study showed major features on T. cruzi-HIV co-infection and highlighted the prognostic role of CD4+ cells for reactivation and mortality. Since lethality was high in meningoencephalitis and all untreated patients died shortly after the diagnosis, early diagnosis, immediate antiparasitic treatment, patient follow-up and epidemiological surveillance are essentials in T. cruzi/HIV co-infection and CDR managements.

Virological and Serological Characterization of SARS-CoV-2 Infections Diagnosed After mRNA BNT162b2 Vaccination.

Coronavirus disease 2019 (COVID-19) vaccines are proving to be very effective in preventing severe illness; however, although rare, post-vaccine infections have been reported. The present study describes 94 infections (47.9% symptomatic, 52.1% asymptomatic), occurred in Lazio Region (Central Italy) in the first trimester 2021, after first or second dose of mRNA BNT162b2 vaccine. Median viral load at diagnosis was independent from number and time of vaccine dose administration, despite the higher proportion of samples with low viral load observed in fully vaccinated individuals. More importantly, infectious virus was cultured from NPS collected from both asymptomatic and symptomatic vaccinated individuals, suggesting that, at least in principle, they can transmit the infection to susceptible people. The majority of the post-vaccine infections here reported, showed pauci/asymptomatic clinical course, confirming the impact of vaccination on COVID-19 disease. Most cases (78%) showed infection in presence of neutralizing antibodies at the time of infection diagnosis, presumably attributable to vaccination, due to the concomitant absence of anti-N IgG in most cases. The proportion of post-vaccine infections attributed either to Alpha and Gamma VOCs was similar to the proportion observed in the contemporary unvaccinated population in Lazio region. In addition, mutational analysis did not suggest enrichment of a defined set of Spike protein substitutions depending on the vaccination status. Characterization of host and virus factors associated with vaccine breakthrough, coupled with intensive and continuous monitoring of involved viral strains, is crucial to adopt informed vaccination strategies.

Virological and Epidemiological Features of Norovirus Infections in Brazil, 2017–2018

Noroviruses are considered an important cause of acute gastroenteritis (AGE) across all age groups. Here, we investigated the incidence of norovirus, genotypes circulation, and norovirus shedding in AGE stool samples from outpatients in Brazil. During a two-year period, 1546 AGE stool samples from ten Brazilian states were analyzed by RT-qPCR to detect and quantify GI and GII noroviruses. Positive samples were genotyped by dual sequencing using the ORF1/2 junction region. Overall, we detected norovirus in 32.1% of samples, with a massive predominance of GII viruses (89.1%). We also observed a significant difference between the median viral load of norovirus GI (3.4×105 GC/g of stool) and GII (1.9×107 GC/g). The most affected age group was children aged between 6 and 24 m old, and norovirus infection was detected throughout the year without marked seasonality. Phylogenetic analysis of partial RdRp and VP1 regions identified six and 11 genotype combinations of GI and GII, respectively. GII.4 Sydney[P16] was by far the predominant genotype (47.6%), followed by GII.2[P16], GII.4 Sydney[P31], and GII.6[P7]. We detected, for the first time in Brazil, the intergenogroup recombinant genotype GIX.1[GII.P15]. Our study contributes to the knowledge of norovirus genotypes circulation at the national level, reinforcing the importance of molecular surveillance programs for future vaccine designs.

Use of prednisolone to prevent the development of immunity reconstitution syndrome in patients with multidrug-resistant tuberculosis

Inflammatory reconstitution of immune syndrome (IRIS) is an immunological reaction characterized by recurrent or new inflammatory signs of tuberculosis (TB) that occur shortly after antiretroviral therapy (ART) in 18 % of patients infected with human immunodeficiency virus (HIV). Features of the syndrome include recurrent symptoms: fever, lymphadenitis and the spread of pulmonary infiltrates on radiography. Low CD4 levels and a short interval between the onset of ART increase the risk of developing TB-associated immune system recovery syndrome. Clinical trials show that early onset of ART results in higher survival rates than ART initiated approximately 8 weeks after the start of TB treatment in patients with a CD4 count of 50 cells/μl. These findings are in line with the recommendations of the World Health Organization, which emphasize the acceleration of the onset of ART in patients with TB and low CD4 levels. However, despite the advantage of survival, early administration of ART more than increases the risk of developing IRIS associated with TB. There is no evidence-based strategy for the prevention of IRIS associated with TB. Studies evaluating adjuvant glucocorticoids for the treatment of various forms of TB have shown reduced mortality among TB patients and fewer complications among TB patients. The aim of the study was to evaluate the prophylactic use of prednisolone to safely reduce the incidence of TB-associated IRIS in patients with multidrug resistant TB (MDR TB) is at high risk of developing the syndrome. We observed HIV-infected patients who started ART (and had not previously received ART) and started TB treatment within 30 days before the start of ART and had a CD4 count of 50 cells/μl. Patients received either standard therapy with prednisolone (at a dose of 40 mg per day for 14 days, then 20 mg per day for 14 days) or only standard therapy without prednisolone. The main endpoint was the development of TB associated with TB within 12 weeks after the onset of ART. Among the 64 patients observed, the mean age was 36 years, 60 % were male, and 73 % had microbiologically confirmed TB; the median amount of CD4 was 49 cells/μl, and the median viral load was 5.5 log 10 copies/μl. Patients were divided into 2 groups. Each group included 32 patients with MDR TB / HIV co-infection. IRIS associated with TB was diagnosed in 10 patients (31.25 %) in the prednisolone group and in 17 (53.14 %) in the control group (p<001). Thus, prednisolone treatment of co-infected patients with MDR TB for the first 4 weeks after the onset of HIV-related ART resulted in a lower incidence of TB-associated IRIS than in the control group, with no evidence of an increased risk of severe infections or cancer.