Optimization and evaluation of a novel real-time RT-PCR test for detection of parechovirus in cerebrospinal fluid

Epidemiology of respiratory pathogens in patients with acute respiratory infections during the COVID-19 pandemic and after easing of COVID-19 restrictions

We aimed to investigate the epidemiological characteristics of non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory pathogens among patients with acute respiratory infections (ARIs) in Shijiazhuang, China, during the coronavirus disease 2019 (COVID-19) pandemic (January 2021--December 2022) and after the relaxation of COVID-19 restrictive measures (January 2022--December 2023). This retrospective study enrolled 6,633 ARIs patients who visited the Hebei General Hospital between 2021- and 2023. Nasopharyngeal swabs samples were collected for multiplex PCR detection of 13 common respiratory pathogens. Respiratory pathogens were detected in 31.58% of individuals diagnosed with ARIs, whileereas a co-infection with multiple pathogens was observed in 8.5% of the ARI patients. In the years 2021 and 2022, 326 (27.63%) and 283 (24.38%) respiratory pathogens were found to be positive, respectively, during the COVID-19 pandemic. However, in 2023, subsequent to the easing of COVID-19 restrictions, the positivity rate significantly rose to 34.62%, with 4,292 cases identified. The majority of positive cases over the last three3 years were concentrated in patients under 14 years old. The predominant pathogens identified were human rhinovirus (HRVs) (15.08%) in 2021, mycoplasma pneumonia (MP) (6.46%) in 2022, and influenza A virus (FluA) (11.35%) in 2023. Seasonal prevalence patterns of most pathogens were affected, except for parainfluenza virus (PIV). There was a simultaneous increase in the positive cases and positivity rates of FluA and adenovirus (ADV) Iin 2023, compared to 2021 and 2022. Additionally, the infection rates of respiratory syncytial virus (RSV), MP, and coronavirus (CoV) in 2023 either exceeded or were comparable to those in 2021 and 2022. Conversely, the positivity rates of PIV, RVs, metapneumovirus (MPV), and influenza B virus (FluB) were lower in 2023 compared to 2021 or 2022.

IMPORTANCE

The implementation of strict non-pharmaceutical interventions (NPIs) during the coronavirus disease 2019 (COVID-19) pandemic may lead to changes in the epidemiological features of respiratory pathogens, as well as the occurrence of immune debt, potentially causing a resurgence in respiratory pathogen activity following the easing of strict NPIs measures. There are limited reports on the epidemiological characteristics of respiratory pathogens among patients of all ages with acute respiratory infections (ARIs) during the COVID-19 pandemic and after the easing of COVID-19 restrictions. Our study investigated the epidemiology of 13 respiratory pathogens in Shijiazhuang, China, from January 2021 to December 2023. Thisese data isare crucial for the ongoing surveillance of epidemiological shifts in respiratory pathogens during and post the -COVID-19 pandemic, and serves as a scientific foundation for the prevention and management of ARIs.

Dynamic changes in the circulation of respiratory pathogens in children during and after the containment of the 2019 coronavirus disease pandemic in Kunming, China

PURPOSE

We aimed to determine the changes in the frequency of respiratory pathogens and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during containment of the 2019 coronavirus disease pandemic and elucidate the epidemiological interference that may have occurred after lifting pandemic measures.

METHODS

A total of 4,770 Nasopharyngeal swab samples were collected from children with ARTIs from the First People's Hospital of Yunnan Province between January 2022 and December 2023 and subjected to nucleic acid testing for 13 types of respiratory pathogens and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

RESULTS

The frequency of pathogens among children from 2020 to 2022 was in the following order: HRV > Mp > HADV > H3N2 > HMPV and HRV > HRSV > HPIV > H1N1 > H3N2. In weeks 1 to 3 of 2023, the frequency of pathogens significantly declined, and then H1N1 rebounded significantly in 2023. HRV, HRSV, and H3N2 showed a shift in the season of high frequency. Patterns of multi-pathogen infections were more complex in 2023 than in 2022, with HRV having a higher frequency and co-infection rate than other pathogens. These changes may have been associated with interference caused by the resurgence of SARS-CoV-2 prevalence, in addition to being influenced by changes in pandemic containment and lifting measures.

CONCLUSIONS

The frequency rate of common respiratory pathogens among children was not significantly different and remained high. The study findings help elucidate the aforementioned unique historical period and effectively control respiratory tract infections to reduce the harm to pediatric health caused by respiratory pathogens.

The impact of optimizing microbial diagnosis processes on clinical and healthcare economic outcomes in hospitalized patients with bloodstream infections

PURPOSE

Bloodstream infections (BSIs) are associated with significant morbidity, mortality and costs, while prolonged blood culture (BC) diagnosis may delay the initiation of targeted therapy. This study evaluates the impact of an optimized microbiology laboratory process on turnaround times, antibiotic use, clinical outcomes and economics for hospitalized BSI patients.

METHODS

A pre-post study was conducted in a Chinese hospital in which BSI derived BC results before (Oct. 2020- Sep. 2021) and after (Oct. 2021- Sep. 2022) newly implemented microbiology diagnostics and workflow changes were analyzed. Turnaround times, antibiotic initiation, length of stay and in-hospital costs were compared.

RESULTS

From 213 included patients, 134 were pre-optimization (pre-op) and 79 were post-optimization (post-op) cases. The median time from blood sample collection (BSC) to pathogen identification (ID) decreased from 70.12 to 47.43 h post-op (P < 0.001). The median time from BSC to the first ID report related initiation of pathogen-directed antibiotic use decreased from 88.48 to 47.85 h post-op (P < 0.001). The average hospital stay decreased from 19.54 to 16.79 days and 30-day readmissions declined from 18.7 to 13.9%, while the mean total antimicrobial drug usage costs decreased by 3,889 CNY per patient (P = 0.022) after optimization.

CONCLUSIONS

Implementing new diagnostics technologies and optimizing laboratory workflows significantly reduced antimicrobial drug usage costs, shortened the time to ID results and improved the timeliness of appropriate antibiotic choices to treat BSIs. Investments in faster testing and process improvements were clearly beneficial for patient outcomes and healthcare economics.

Clinical characteristics and logistic regression analysis of macrolide-resistant Mycoplasma pneumoniae pneumonia in children

PURPOSE

To investigate macrolide-resistant Mycobacterium pneumoniae (MRMP) pneumonia in children and construct a logistic regression model for mutations in the Mycoplasma pneumoniae drug-resistant gene.

METHODS

Clinical data of 281 children were analyzed. Sequencing confirmed a mutation at the A2063G locus of the 23 S rRNA gene in 227 children (A2063G group); 54 children showed no mutations (non-MRMP [NMRMP] group). We compared clinical features, laboratory tests, imaging, and bronchoscopy results and constructed a multifactorial logistic regression model to analyze risk and protective factors.

RESULTS

The A2063G group had longer durations of fever and hospitalization before admission, a higher proportion of treatment with sodium methylprednisolone succinate (MPS)/dexamethasone, longer time to discontinue hormones, and higher probability of combined infections. Monocyte percentage was significantly higher in the A2063G group. Imaging suggested a higher incidence of infections in the right lung compared to both lungs. Univariate analysis revealed fever duration before admission, hormone dose and duration, monocyte percentage, and mixed infections as risk factors for Mycoplasma pneumoniae infection with the A2063G mutation. The logistic regression model showed that mixed infections were an independent risk factor for the A2063G locus mutation, whereas hormone dose was a protective factor.

CONCLUSION

A prevalence of macrolide resistance of 80.8% among children was observed in the region. Logistic regression analysis revealed that co-infection with other respiratory pathogens is an independent risk factor for the development of resistance genes, while the use of hormone dosage acts as a protective factor.

Development and validation of nomogram for predicting the risk of transferring to the ICU for children with influenza

OBJECTIVE

Development of a nomogram model for predicting the magnitude of risk of transferring hospitalized children with influenza to the ICU.

METHODS

In a single-center retrospective study, 318 children with influenza who were hospitalized in our hospital from January 2018 to August 2023 were collected as study subjects. Children with influenza were randomly assigned to the training set and validation set in a ratio of 4:1. In the training set, risk factors were identified using univariate and multivariate logistic regression analyses, and a nomogram model was created on this basis. The validation set was used to evaluate the predictive power of the model.

RESULTS

Multifactorial logistic regression analysis revealed six independent risk factors for transfer to the ICU in hospitalized children with influenza, including elevated peripheral white blood cell counts, elevated large platelet ratios, reduced mean platelet width, reduced complement C3, elevated serum globulin levels, and reduced total immunoglobulin M levels. Using these six metrics as predictors to construct a nomogram graphical model, the C-index was 0.970 (95% Cl: 0.953-0.988). The areas under the curve for the training and validation sets were 0.966 (95%Cl 0.947-0.985) and 0.919 (95%Cl 0.851-0.986), respectively.

CONCLUSION

A nomogram for predicting the risk of transferring to the ICU for children with influenza was developed and validated, which demonstrates good calibration and clinical benefits.

Epidemiologic trends and changes in humoral immunity and lymphocyte subsets levels among hospitalized children with Mycoplasma pneumoniae infection during 2019-2023

PURPOSE

To understand the changes in humoral immunity and lymphocyte subsets levels among hospitalized children with Mycoplasma pneumoniae (MP) infection from 2019 to 2023.

METHODS

This study retrospectively analyzed inpatients aged 0-14 years who were diagnosed with MP infection or MP pneumonia in a tertiary hospital from January 2019 to December 2023. The children were divided into three groups: before the implementation of nonpharmaceutical interventions (NPIs), during the implementation of NPIs, and after the NPIs being lifted.

RESULTS

A total of 4103 patients were enrolled in this study, of whom 2125 were diagnosed with MP infection and 1978 were diagnosed with MP pneumonia. The number of MP infection cases dramatically decreased early during the implementation of NPIs, and the previous epidemic trend resumed after the NPIs were lifted, with the number of cases during the period 2019-2023 peaked in November 2023. In children aged < 5 years, the levels of IgA and IgM and the percentages of total T cells and cytotoxic T cells in the "before the implementation of NPIs" group were greater than those in the other groups, and the percentage of total B cells was lower than that in the other groups. In children aged ≥ 5 years, the IgM level in the "before the implementation of NPIs" group was greater than that in the other groups.

CONCLUSION

The number of MP-infected hospitalized children decreased significantly after NPI implementation and reached its highest peak during 2019-2023 in November 2023. After the NPIs were lifted, the level of humoral immunity was decreased and balance lymphocyte subsets were disrupted, especially in children aged < 5 years. We should pay close attention to and prevent MP infection in a timely manner after epidemics caused by large respiratory pathogens.

Molecular surveillance of influenza A virus in Saudi Arabia: whole-genome sequencing and metagenomic approaches

Outbreaks of influenza A viruses are generally seasonal and cause annual epidemics worldwide. Due to their frequent reassortment and evolution, annual surveillance is of paramount importance to guide vaccine strategies. The aim of this study was to explore the molecular epidemiology of influenza A virus and nasopharyngeal microbiota composition in infected patients in Saudi Arabia. A total of 103 nasopharyngeal samples from 2015 and 12 samples from 2022 were collected from patients positive for influenza A. Sequencing of influenza A as well as metatranscriptomic analysis of the nasopharyngeal microbiota was conducted using Oxford Nanopore sequencing. Phylogenetic analysis of hemagglutinin, neuraminidase segments, and concatenated influenza A genomes was performed using MEGA7. Whole-genome sequencing analysis revealed changing clades of influenza A virus: from 6B.1 in 2015 to 5a.2a in 2022. One sample containing the antiviral resistance-mediating mutation S247N toward oseltamivir and zanamivir was found. Phylogenetic analysis showed the clustering of influenza A strains with the corresponding vaccine strains in each period, thus suggesting vaccine effectiveness. Principal component analysis and alpha diversity revealed the absence of a relationship between hospital admission status, age, or gender of infected patients and the nasopharyngeal microbial composition, except for the infecting clade 5a.2a. The opportunistic pathogens Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis were the most common species detected. The molecular epidemiology appears to be changing in Saudi Arabia after the COVID-19 pandemic. Antiviral resistance should be carefully monitored in future studies. In addition, the disease severity of patients as well as the composition of the nasopharyngeal microbiota in patients infected with different clades should also be assessed.IMPORTANCEIn this work, we have found that the clade of influenza A virus circulating in Riyadh, KSA, has changed over the last few years from 6B.1 to 5a.2a. Influenza strains clustered with the corresponding vaccine strains in our population, thus emphasizing vaccine effectiveness. Metatranscriptomic analysis showed no correlation between the nasopharyngeal microbiome and the clinical and/or demographic characteristics of infected patients. This is except for the 5a.2a strains isolated post-COVID-19 pandemic. The influenza virus is among the continuously evolving viruses that can cause severe respiratory infections. Continuous surveillance of its molecular diversity and the monitoring of anti-viral-resistant strains are thus of vital importance. Furthermore, exploring potential microbial markers and/or dysbiosis of the nasopharyngeal microbiota during infection could assist in the better management of patients in severe cases.

Group A Streptococcal meningitis in children: a short case series and systematic review

BACKGROUND

Group A streptococcal(GAS) meningitis is a severe disease with a high case fatality rate. In the era of increasing GAS meningitis, our understanding about this disease is limited.

PURPOSE

To gain a better understanding about GAS meningitis.

METHODS

Five new cases with GAS meningitis were reported. GAS meningitis related literatures were searched for systematic review in PUBMED and EMBASE. Case reports and case series on paediatric cases were included. Information on demographics, risk factors, symptoms, treatments, outcomes, and emm types of GAS was summarized.

RESULTS

Totally 263 cases were included. Among 100 individuals, 9.9% (8/81) had prior varicella, 11.1% (9/81) had anatomical factors, and 53.2% (42/79) had extracranial infections. Soft tissue infections were common among infants (10/29, 34.5%), while ear/sinus infections were more prevalent in children ≥ 3 years (21/42, 50.0%). The overall case fatality rate (CFR) was 16.2% (12/74). High risk of death was found in patients with shock or systemic complications, young children(< 3 years) and cases related to hematogenic spread. The predominate cause of death was shock(6/8). Among the 163 patients included in case series studies, ear/sinus infections ranged from 21.4 to 62.5%, while STSS/shock ranged from 12.5 to 35.7%, and the CFR ranged from 5.9 to 42.9%.

CONCLUSIONS

A history of varicella, soft tissue infections, parameningeal infections and CSF leaks are important clinical clues to GAS in children with meningitis. Young children and hematogenic spread related cases need to be closely monitored for shock due to the high risk of death.

Risk factors for pneumonia among children with coinfection of influenza A virus and Mycoplasma pneumoniae

OBJECTIVE

To investigate the clinical characteristics and risk factors for pneumonia in children co-infected with influenza A virus (IAV) and Mycoplasma pneumoniae (MP).

METHODS

Children who were diagnosed with IAV and MP infection between January and December, 2023 were enrolled and divided into a non-pneumonia group and a pneumonia group. Univariate analysis and logistic regression analysis were used to evaluate each index, and the risk factors for pneumonia caused by coinfection in the two groups were explored.

RESULTS

A total of 209 patients were enrolled, of which 107 and 102 patients were in the pneumonia and non-pneumonia groups, respectively. The patients in the pneumonia group were older and had a longer duration of fever (P < 0.05). Univariate analysis revealed that the median age, duration of fever, and CD3+, CD4+, CD8+ and IL-10 levels were significantly correlated with pneumonia (P < 0.05). Multivariate logistic regression analysis revealed that the median age, duration of fever, and CD4+, CD8+ and IL-10 levels were independent risk factors for pneumonia. Area under the curve of the five combined indicators in the ROC (receiver operator characteristic) analysis was 0.883, was higher than single factor.

CONCLUSION

Children with IAV and MP infection whose age older than 6.08 years, had a fever longer than 4 days, had a CD4+ count < 22.12%, had a CD8+ count < 35.21%, had an IL-10 concentration > 22.08 ng/ml were more likely to develop pneumonia.

Application of MPBT Assay for Multiplex Determination of Infectious Titers and for Selection of the Optimal Formulation for the Trivalent Novel Oral Poliovirus Vaccine

Recently, a multiplex PCR-based titration (MPBT) assay was developed for simultaneous determination of infectious titers of all three Sabin strains of the oral poliovirus vaccine (OPV) to replace the conventional CCID50 assay, which is both time-consuming and laborious. The MPBT assay was shown to be reproducible, robust and sensitive. The conventional and MPBT assays showed similar results and sensitivity. The MPBT assay can be completed in two to three days, instead of ten days for the conventional assay. To prevent attenuated vaccine strains of poliovirus from reversion to virulence, a novel, genetically stable OPV (nOPV) was developed by modifying the genomes of conventional Sabin strains used in OPV. In this work, we evaluated the MPBT assay as a rapid screening tool to support trivalent nOPV (tnOPV) formulation development by simultaneous titration of the three nOPV strains to confirm stability as needed, for the selection of the lead tnOPV formulation candidate. We first assessed the ability of the MPBT assay to discriminate a 0.5 log10 titer difference by titrating the two tnOPV samples (undiluted and threefold-diluted) on the same plate. Once the assay was shown to be discriminating, we then tested different formulations of tnOPV drug products (DPs) that were subjected to different exposure times at 37 °C (untreated group and treated groups: 2 and 7 days at 37 °C), and to three freeze and thaw (FT) cycles. Final confirmation of the down selected formulation candidates was achieved by performing the conventional CCID50 assay, comparing the stability of untreated and treated groups and FT stability testing on the top three candidates. The results showed that the MPBT assay generates similar titers as the conventional assay. By testing two trivalent samples in the same plate, the assay can differentiate a 0.5 log10 difference between the titers of the tested nOPV samples. Also, the assay was able to detect the gradual degradation of nOPV viruses with different formulation compositions and under different time/temperature conditions and freeze/thaw cycles. We found that there were three tnOPV formulations which met the stability criteria of less than 0.5 log10 loss after 2 days' exposure to 37 ℃ and after three FT cycles, maintaining the potency of all three serotypes in these formulations. The ability of the MPBT assay to titrate two tnOPV lots (six viruses) in the same plate makes it cheaper and gives it a higher throughput for rapid screening. The assay detected the gradual degradation of the tnOPV and was successful in the selection of optimal formulations for the tnOPV. The results demonstrated that the MPBT method can be used as a stability indicating assay to assess the thermal stability of the nOPV. It can be used for rapid virus titer determination during the vaccine manufacturing process, and in clinical trials. The MPBT assay can be automated and applied for other viruses, including those with no cytopathic effect.

Development and validation of an online dynamic nomogram system for pulmonary consolidation in children with Mycoplasma pneumoniae pneumonia

INTRODUCTION

The occurrence of pulmonary consolidation in children with Mycoplasma pneumoniae pneumonia (MPP) can lead to exacerbation of the disease. Therefore, early identification of children with MPP in combination with pulmonary consolidation is critical. The purpose of this study was to develop a straightforward, easy-to-use online dynamic nomogram for the identification of children with MPP who are at high risk of developing pulmonary consolidation.

METHODS

491 MPP patients were chosen and divided randomly into a training cohort and an internal validation cohort at a 4:1 ratio. Multi-factor logistic regression was used to identify the risk variables for mixed pulmonary consolidation in children with Mycoplasma pneumoniae (MP). The selected variables were utilized to build the nomograms and validated using the C-index, decision curve analysis, calibration curves, and receiver operating characteristic (ROC) curves.

RESULTS

Seven variables were included in the Nomogram model: age, fever duration, lymphocyte count, C-reactive protein (CRP), ferritin, T8 lymphocyte percentage, and T4 lymphocyte percentage. We created a dynamic nomogram that is accessible online ( https://ertong.shinyapps.io/DynNomapp/ ). The C-index was 0.90. The nomogram calibration curves in the training and validation cohorts were highly comparable to the standard curves. The area under the curve (AUC) of the prediction model was, respectively, 0.902 and 0.883 in the training cohort and validation cohort. The decision curve analysis (DCA) curve shows that the model has a significant clinical benefit.

CONCLUSIONS

We developed a dynamic online nomogram for predicting combined pulmonary consolidation in children with MP based on 7 variables for the first time. The predictive value and clinical benefit of the nomogram model were acceptable.

Detection of intrathecal IgG antibody for varicella and measles diagnosis by evaluation and comparison of a commercial IgG chemiluminescent immunoassay with two ELISAs

OBJECTIVES

Analyse alternative methods of intrathecal antibody detection by comparing chemiluminescent immunoassay (CLIA) and enzyme-linked immunosorbent assay (ELISA) techniques to determine if CLIA can replace ELISA in the diagnosis of CNS infections.

METHODS

A panel of 280 paired samples-cerebrospinal fluid (CSF) and serum-with known antibody reactivities (Varicella, n = 60; Measles, n = 120) and negative samples (n = 100) were used to evaluate the performance of six serological test kits (Enzygnost, VirClia®, and Serion ELISA (Measles and Variella).

RESULTS

For Measles virus IgG, the VirClia® IgG monotest revealed 97% and 94% positive and negative agreement to the Enzygnost as reference test, respectively. In contrast, Serion ELISA kits yielded values of 18% and 90%. For the Varicella Zoster virus (VZV) IgG, the VirClia® IgG monotest showed 97% and 90% positive and negative agreement compared to Enzygnost. The Serion ELISA kits showed values of 55% and 86%, respectively. ROC analysis revealed that the areas under the curve for Measles and VZV IgGs were 0.7 and 0.852, respectively, using the Serion kit, and 0.963 and 0.955, for Vircell S.L CLIA technique. VirClia® monotest values were calculated using an antibody index cut-off of 1.3.

CONCLUSION

The findings indicate that CLIA testing can improve antibody detection in CSF samples, aiding the diagnosis of infectious neurological impairments.

Comparison of Mycoplasma pneumoniae infection in children admitted with community acquired pneumonia before and during the COVID-19 pandemic: a retrospective study at a tertiary hospital of southwest China

PURPOSE

The COVID-19 pandemic has notably altered the infection dynamics of various pathogens. This study aimed to evaluate the pandemic's impact on the infection spectrum of Mycoplasma pneumoniae (M. pneumoniae) among children with community acquired pneumonia (CAP).

METHODS

We enrolled pediatric CAP patients admitted to a tertiary hospital in southwest China to compare the prevalence and characteristics of M. pneumoniae infections before (2018-2019) and during (2020-2022) the COVID-19 pandemic. Detection of M. pneumoniae IgM antibodies in serum were conducted using either indirect immunofluorescence or passive agglutination methods.

RESULTS

The study included 1505 M. pneumoniae-positive and 3160 M. pneumoniae-negative CAP patients. Notable findings were the higher age and frequency of pneumonia-associated symptoms in M. pneumoniae-positive patients, alongside a lower male proportion and fewer respiratory co-infections. The year 2019 saw a notable increase in M. pneumoniae infections compared to 2018, followed by a decline from 2020 to 2022. The COVID-19 pandemic period witnessed significant alterations in age distribution, male proportion, and co-infections with specific pathogens in both M. pneumoniae-positive and negative patients. The M. pneumoniae infections were predominantly seasonal, peaking in autumn and winter during 2018 and 2019. Although there was a sharp drop in February 2020, the infection still peaked in cold months of 2020 and 2021. However, the typical seasonal pattern was nearly absent in 2022.

CONCLUSIONS

The COVID-19 pandemic has markedly changed the infection landscape of M. pneumoniae in pediatric CAP patients, with shifts observed in infection rates, demographic profiles, co-infections, and seasonal patterns.

Detection and genetic diversity of parechoviruses in children with acute flaccid paralysis in Cameroon

Human Parechoviruses (HPeVs) have rarely been considered in the virological investigation of Acute Flacid Paralysis (AFP) cases in Africa, where enteric infections are very common. This study investigated the prevalence and genetic diversity of HPeV in 200 children aged ≤ 15 years with AFP in Cameroon from 2018 to 2019. HPeVs were detected in their faecal RNA using 5'-untranslated real-time RT-PCR. Detected HPeVs were typed by phylogenetic comparison with homologous sequences from homotypic reference strains. Overall, HPeV RNA was detected in 11.0% (22/200) of the 200 stool samples tested. Twelve HPeVs were successfully sequenced and reliably assigned to HPeV-A1, A4, A5, A10, A14, A15, A17 and A18 genotypes. Phylogenetic analyses revealed a high genetic variability among the studied HPeVs, as well as between the studied HPeVs and their previously reported counterparts from Cameroon in 2014. These findings suggest that different HPeV genotypes co-circulate in Cameroon without documented epidemics.

Mpox (Monkeypox) Virus and Its Co-Infection with HIV, Sexually Transmitted Infections, or Bacterial Superinfections: Double Whammy or a New Prime Culprit?

Epidemiologic studies have established that mpox (formerly known as monkeypox) outbreaks worldwide in 2022-2023, due to Clade IIb mpox virus (MPXV), disproportionately affected gay, bisexual, and other men who have sex with men. More than 35% and 40% of the mpox cases suffer from co-infection with HIV and sexually transmitted infections (STIs) (e.g., Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, and herpes simplex virus), respectively. Bacterial superinfection can also occur. Co-infection of MPXV and other infectious agents may enhance disease severity, deteriorate outcomes, elongate the recovery process, and potentially contribute to the morbidity and mortality of the ensuing diseases. However, the interplays between MPXV and HIV, bacteria, other STI pathogens and host cells are poorly studied. There are many open questions regarding the impact of co-infections with HIV, STIs, or bacterial superinfections on the diagnosis and treatment of MPXV infections, including clinical and laboratory-confirmed mpox diagnosis, suboptimal treatment effectiveness, and induction of antiviral drug resistance. In this review article, we will discuss the progress and knowledge gaps in MPXV biology, antiviral therapy, pathogenesis of human MPXV and its co-infection with HIV, STIs, or bacterial superinfections, and the impact of the co-infections on the diagnosis and treatment of mpox disease. This review not only sheds light on the MPXV infection and co-infection of other etiologies but also calls for more research on MPXV life cycles and the molecular mechanisms of pathogenesis of co-infection of MPXV and other infectious agents, as well as research and development of a novel multiplex molecular testing panel for the detection of MPXV and other STI co-infections.

Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities

Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at the Prince Mohammed Bin Abdulaziz Hospital Riyadh. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that Streptococcus spp including Streptococcus pneumoniae and Streptococcus thermophilus were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus Staphylococcus was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of Leptotrichia was significantly higher in healthy subjects compared to recovered patients. Corynebacterium on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.IMPORTANCEIn this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia, Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.

Key roles for phosphorylation and the Coiled-coil domain in TRIM56-mediated positive regulation of TLR3-TRIF-dependent innate immunity

Tripartite-motif protein-56 (TRIM56) positively regulates the induction of type I interferon response via the TLR3 pathway by enhancing IRF3 activation and depends on its C-terminal residues 621-750 for interacting with the adaptor TRIF. However, the precise underlying mechanism and detailed TRIM56 determinants remain unclear. Herein, we show ectopic expression of murine TRIM56 also enhances TLR3-dependent interferon-β promoter activation, suggesting functional conservation. We found that endogenous TRIM56 and TRIF formed a complex early (0.5-2 h) after poly-I:C stimulation and that TRIM56 overexpression also promoted activation of NF-κB by poly-I:C but not that by TNF-α or IL-1β, consistent with a specific effect on TRIF prior to the bifurcation of NF-κB and IRF3. Using transient transfection and Tet-regulated cell lines expressing various TRIM56 mutants, we demonstrated the Coiled-coil domain and a segment spanning residues ∼434-610, but not the B-box or residues 355-433, were required for TRIM56 augmentation of TLR3 signaling. Moreover, alanine substitution at each putative phosphorylation site, Ser471, Ser475, and Ser710, abrogated TRIM56 function. Concordantly, mutants bearing Ser471Ala, Ser475Ala, or Ser710Ala, or lacking the Coiled-coil domain, all lost the capacity to enhance poly-I:C-induced establishment of an antiviral state. Furthermore, the Ser710Ala mutation disrupted the TRIM56-TRIF association. Using phospho-specific antibodies, we detected biphasic phosphorylation of TRIM56 at Ser471 and Ser475 following TLR3 stimulation, with the early phase occurring at ∼0.5 to 1 h, prior to IRF3 phosphorylation. Together, these data reveal novel molecular details critical for the TRIM56 augmentation of TLR3-dependent antiviral response and highlight important roles for TRIM56 scaffolding and phosphorylation.

Hybrid capture shotgun sequencing detected unexpected viruses in the cerebrospinal fluid of children with acute meningitis and encephalitis

PURPOSE

Investigation of undiagnosed cases of infectious neurological diseases, especially in the paediatric population, remains a challenge. This study aimed to enhance understanding of viruses in CSF from children with clinically diagnosed meningitis and/or encephalitis (M/ME) of unknown aetiology using shotgun sequencing enhanced by hybrid capture (HCSS).

METHODS

A single-centre prospective study was conducted at Sant Joan de Déu University Hospital, Barcelona, involving 40 M/ME episodes of unknown aetiology, recruited from May 2021 to July 2022. All participants had previously tested negative with the FilmArray Meningitis/Encephalitis Panel. HCSS was used to detect viral nucleic acid in the patients' CSF. Sequencing was performed on Illumina NovaSeq platform. Raw sequence data were analysed using CZ ID metagenomics and PikaVirus bioinformatics pipelines.

RESULTS

Forty episodes of M/ME of unknown aetiology in 39 children were analysed by HCSS. A significant viral detection in 30 CSF samples was obtained, including six parechovirus A, three enterovirus ACD, four polyomavirus 5, three HHV-7, two BKV, one HSV-1, one VZV, two CMV, one EBV, one influenza A virus, one rhinovirus, and 13 HERV-K113 detections. Of these, one sample with BKV, three with HHV-7, one with EBV, and all HERV-K113 were confirmed by specific PCR. The requirement for Intensive Care Unit admission was associated with HCSS detections.

CONCLUSION

This study highlights HCSS as a powerful tool for the investigation of undiagnosed cases of M/ME. Data generated must be carefully analysed and reasonable precautions must be taken before establishing association of clinical features with unexpected or novel virus findings.

Quantitation of Enterovirus A71 Empty and Full Particles by Sedimentation Velocity Analytical Ultracentrifugation

The enterovirus A71 (EV71) inactivated vaccine is an effective intervention to control the spread of the virus and prevent EV71-associated hand, foot, and mouth disease (HFMD). It is widely administered to infants and children in China. The empty particles (EPs) and full particles (FPs) generated during production have different antigenic and immunogenic properties. However, the antigen detection methods currently used were established without considering the differences in antigenicity between EPs and FPs. There is also a lack of other effective analytical methods for detecting the different particle forms, which hinders the consistency between batches of products. In this study, we analyzed the application of sedimentation velocity analytical ultracentrifugation (SV-AUC) in characterizing the EPs and FPs of EV71. Our results showed that the proportions of the two forms could be quantified simultaneously by SV-AUC. We also determined the repeatability and accuracy of this method and found that both parameters were satisfactory. We assessed SV-AUC for bulk vaccine quality control, and our findings indicated that SV-AUC can be used effectively to analyze the percentage of EPs and FPs and monitor the consistency of the process to ensure the quality of the vaccine.

Molecular Epidemiology and Clinical Characteristics of an Outbreak on Respiratory Virus Coinfection in Gansu, China

This study aims to analyze the epidemiological and pathogenic characteristics of an outbreak primarily caused by respiratory syncytial virus (RSV), human rhinovirus (HRV), and human metapneumovirus (HMPV) in a kindergarten and primary school. The outbreak was investigated by field epidemiological investigation, and the common respiratory pathogens were screened by RT-PCR detection technology. The attack rate of this outbreak was 63.95% (110/172). Main symptoms included cough (85.45%), sore throat (60.91%), and sneezing (60.00%). Multifactorial logistic regression analysis revealed that continuous handwashing and mouth and nose covering when sneezing were protective factors. All 15 collected throat swab specimens tested positive for viruses, with HMPV as the predominant pathogen (80.00%), followed by HRV (53.33%), and two cases of positive respiratory syncytial virus (13.33%). Among them, six samples showed coinfections of HMPV and HRV, and one had coinfections of HMPV and RSV, resulting in a coinfection rate of 46.67%. Genetic sequencing indicated that the HMPV genotype in this outbreak was A2c, and the HRV genotype was type A, resulting in a coinfection outbreak of HMPV, HRV, and RSV in schools and kindergartens, suggesting that multi-pathogen surveillance of respiratory tract infections should be strengthened.

A multicenter evaluation of the QIAstat-Dx meningitis-encephalitis syndromic test kit as compared to the conventional diagnostic microbiology workflow

PURPOSE

Rapid diagnosis and treatment of infectious meningitis and encephalitis (ME) is critical to minimize morbidity and mortality. Recently, Qiagen introduced the CE-IVD QIAstat-Dx ME panel (QS-ME) for syndromic diagnostic testing of meningitis and encephalitis. Some data on the performance of the QS-ME in comparison to the BioFire FilmArray ME panel are available. In this study, the performance of the QS-ME is compared to the current diagnostic workflow in two academic medical centers in the Netherlands.

METHODS

A total of 110 cerebrospinal fluid samples were retrospectively tested with the QS-ME. The results obtained were compared to the results of laboratory-developed real-time PCR assays (LDTs), IS-pro, bacterial culture, and cryptococcal antigen (CrAg) testing. In addition, the accuracy of the QS-ME was also investigated using an external quality assessment (EQA) panel consisting of ten samples.

RESULTS

Four of the 110 samples tested failed to produce a valid QS-ME result. In the remaining 106 samples, the QS-ME detected 53/53 viral targets, 38/40 bacterial targets, and 7/13 Cryptococcus neoformans targets. The discrepant bacterial results consisted of two samples that were previously tested positive for Listeria monocytogenes (CT 35.8) and Streptococcus pneumoniae (CT 40), respectively. The QS-ME detected one additional result, consisting of a varicella-zoster virus signal (CT 35.9), in a sample in which both techniques detected Streptococcus pyogenes. Finally, 100% concordance was achieved in testing a blinded bacterial ME EQA panel.

CONCLUSION

The QS-ME is a relevant addition to the syndromic testing landscape to assist in diagnosing infectious ME.

Molecular Amplification and Cell Culturing Efficiency for Enteroviruses' Detection in Cerebrospinal Fluids of Algerian Patients Suffering from Meningitis

Enteroviruses (EVs) represent a major cause of viral meningitis, being responsible for nearly 1 billion infections each year worldwide. Several techniques were developed to obtain better diagnostic results of EV infections. Herein, we evaluated the efficiency of EV detection through isolation on both Rhabdomyosarcoma (RD) and Vero cell line cultures, conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR. Thus, 50 cerebrospinal fluid (CSF) samples belonging to patients suspected to have viral meningitis in northern Algeria were collected, anonymously numbered from 1 to 50 and subjected to the above-mentioned techniques for EV detection. Using real-time RT-PCR, 34 CSF samples were revealed to be positive for viral origin of meningitis (68%). Thirteen of them were positive when the conventional RT-PCR was used (26%), and only three samples gave positive results when the cell culture technique was used (6%). Surprisingly, two cell culture-positive CSF samples, namely, 31 and 39, were negative using RT-PCR directly on the original samples. However, they turned to be positive when amplification was carried out on their corresponding cell culture supernatant. The cell-cultured viral isolates were then identified by sequencing their viral genome's VP1 regions. All of them were revealed to belong to the echovirus 27 strain. This investigation demonstrates that RT-PCR techniques are often more sensitive, accurate and much faster, providing reliable results within a clinically acceptable timeframe. However, viral isolation on cell cultures remains crucial to obtain enough viral load for serological tests or even to avoid the rare, but existing, false negative PCR.

Evaluation of Stability, Inactivation, and Disinfection Effectiveness of Mpox Virus

BACKGROUND

Mpox virus (MPXV) infections have increased in many countries since May 2022, increasing demand for diagnostic tests and research on the virus. To ensure personnel safety, appropriate and reliable measures are needed to disinfect and inactivate infectious samples; Methods: We evaluated the stability of infectious MPXV cultures stored at different temperatures and through freeze-thaw cycles. Heat physical treatment (56 °C, 70 °C, 95 °C), chemical treatment (beta-propiolactone (BPL)) and two commercialized disinfectants (Micro-Chem Plus (MCP) and ethanol) were tested against infectious MPXV cultures; Results: The results indicated that MPXV stability increases with lower temperatures. The MPXV titer was stable within three freeze-thaw cycles and only decreased by 1.04 log10 (lg) 50% cell culture infective dose (CCID50) per milliliter (12.44%) after twelve cycles. MPXV could be effectively inactivated at 56 °C for 40 min, 70 °C for 10 min, and 95 °C for 5 min. For BPL inactivation, a 1:1000 volume ratio (BPL:virus) could also effectively inactivate MPXV. A total of 2% or 5% MCP and 75% ethanol treated with MPXV for at least 1 min could reduce >4.25 lg; Conclusions: MPXV shows high stability to temperature and freeze-thaw. Heat and BPL treatments are effective for the inactivation of MPXV, while MCP and ethanol are effective for disinfection, which could help laboratory staff operate the MPXV under safer conditions and improve operational protocols.

Urine: A Pitfall for Molecular Detection of Toscana Virus? An Analytical Proof-of-Concept Study

Toscana virus (TOSV), a sandfly-borne virus, is an important etiological agent in human acute meningitis and meningoencephalitis in the Mediterranean area during the summer. However, the actual number of TOSV infections is underestimated. Laboratory confirmation is necessary because TOSV infection has overlapping clinical features with other neuro-invasive viral infections. Nowadays, the reference test for direct diagnosis in the acute phase of TOSV infection is the PCR based method for detecting TOSV in cerebrospinal fluid and/or plasma, serum, or blood. Although poorly employed, urine is another helpful biological matrix for TOSV detection. Urine is a matrix rich in PCR inhibitors that affect PCR efficiency; consequently, false negatives could be generated. To investigate the potential effect of urine PCR inhibitors on TOSV detection, we compared undiluted and diluted urine using 10-fold series of spiked TOSV. The results showed a significant improvement in TOSV detection performance in diluted urine (1 TCID50 vs. 1 × 104 TCID50 limit of detection and 101.35% vs. 129.62% efficiency, respectively, in diluted and undiluted urine). In conclusion, our data provide preliminary important insights into the use of diluted urine to limit the impact of the inhibitory effects of urine on the detection of TOSV in RT-PCR-based approaches.

Laboratory diagnosis of CNS infections in children due to emerging and re-emerging neurotropic viruses

Recent decades have witnessed the emergence and re-emergence of numerous medically important viruses that cause central nervous system (CNS) infections in children, e.g., Zika, West Nile, and enterovirus/parechovirus. Children with immature immune defenses and blood-brain barrier are more vulnerable to viral CNS infections and meningitis than adults. Viral invasion into the CNS causes meningitis, encephalitis, brain imaging abnormalities, and long-term neurodevelopmental sequelae. Rapid and accurate detection of neurotropic viral infections is essential for diagnosing CNS diseases and setting up an appropriate patient management plan. The addition of new molecular assays and next-generation sequencing has broadened diagnostic capabilities for identifying infectious meningitis/encephalitis. However, the expansion of test menu has led to new challenges in selecting appropriate tests and making accurate interpretation of test results. There are unmet gaps in development of rapid, sensitive and specific molecular assays for a growing list of emerging and re-emerging neurotropic viruses. Herein we will discuss the advances and challenges in the laboratory diagnosis of viral CNS infections in children. This review not only sheds light on selection and interpretation of a suitable diagnostic test for emerging/re-emerging neurotropic viruses, but also calls for more research on development and clinical utility study of novel molecular assays. IMPACT: Children with immature immune defenses and blood-brain barrier, especially neonates and infants, are more vulnerable to viral central nervous system infections and meningitis than adults. The addition of new molecular assays and next-generation sequencing has broadened diagnostic capabilities for identifying infectious meningitis and encephalitis. There are unmet gaps in the development of rapid, sensitive and specific molecular assays for a growing list of emerging and re-emerging neurotropic viruses.

Shotgun metagenomics to investigate unknown viral etiologies of pediatric meningoencephalitis

INTRODUCTION

Meningoencephalitis in children poses a diagnostic challenge, as etiology remains unknown for most of patients. Viral metagenomics by shotgun sequencing represents a powerful tool for investigating unknown viral infections related to these cases.

PATIENTS AND METHODS

In a two-year, reference-centre, retrospective study, we investigated the usefulness of viral metagenomics of cerebrospinal fluid (CSF) for the diagnosis of viral infectious meningoencephalitis in forty seven pediatric patients, forty of them previously tested negative with a routine neurologic panel of viral targets that included herpesvirus 1-3 and enterovirus. We enhanced the detection by targeting viral sequences by hybrid capture. Raw sequence data was analysed using three bioinformatics pipelines.

RESULTS

Out of forty remaining children with meningoencephalitis of unknown viral etiology, a significant detection of viral nucleic acid by shotgun sequencing was found in twenty one, which was confirmed in ten of them by specific PCR: seven human endogenous retrovirus K113 (HER K113), one parechovirus 3, one human herpesvirus 5 (HHV5); one enterovirus B (Echovirus 9). The remaining eleven CSF were not confirmed by PCR: three rotavirus, one human herpesvirus 7 (HHV7), one influenza A, one mastadenovirus C, one sindbis virus, one torque teno virus, one human immunodeficiency virus 1 (HIV-1), one human alphaherpesvirus 3 (HHV3), one human alphaherpesvirus 2 (HHV2).

CONCLUSIONS

Underutilization of currently available meningitis-encephalitis diagnostic techniques such as BioFire® FilmArray® is the main cause of undiagnosed cases of meningoencephalitis. However, in this study we detected uncommon viruses that should be considered, including virus, rotavirus, sindbis virus, influenza A virus and HHV7. No other viral sequences that could be readily linked to CNS inflammation were detected. Some findings may stem from reagent or sample contamination, as seen with papillomavirus; for others, the clinical relevance of the virus remains uncertain and should be substantiated by further studies, as is the case with endogenous retrovirus K113 virus. Online bioinformatics pipeline CZID represents a valuable tool for analysing shotgun sequencing data in cases of neurological conditions with unknown etiology. Altogether, this study highlights the potential of shotgun sequencing in identifying previously unknown viral neuropathogens and sheds light on the interpretation issues related to its application in clinical microbiology.

Clinical indicators combined with S100A12/TLR2 signaling molecules to establish a new scoring model for coronary artery lesions in Kawasaki disease

Coronary artery lesions (CALs) are the most common and serious complication of Kawasaki disease (KD), and the pathogenesis is unknown. Exploring KD-specific biomarkers and related risk factors is significant for clinical diagnosis and treatment. This study aimed to explore the feasibility of combining clinical indicators with S100A12/TLR2-associated signaling molecules for the predictive modeling of CALs in KD. A total of 346 patients (224 males and 122 females) with KD who visited the rheumatology department of Wuhan Children's Hospital between April 2022 and March 2025 were enrolled and divided into two groups according to the presence or absence of CALS (292 patients had CALs and 54 patients did not). Forty-one variables were collected from the two groups, including demographic characteristics, clinical manifestations, and laboratory data. Single nucleated cells from each patient were extracted, and the expression of the S100A12/TLR2 signal transduction-related molecules S100A12, TLR2, MYD88, and NF-κB were detected by real-time fluorescent quantitative polymerase chain reaction. Statistically significant variables were subjected to logistic regression analysis to determine the independent risk factors for KD with CALs, and a new risk score model was established to assess the predictive efficacy based on receiver operating characteristic curves. Sixteen variables significantly differed between the no-CALs and CALs groups: gender, fever duration, white blood cells (WBC), hemoglobin (HGB), Ce reactive protein (CRP), procalcitonin, serum ferritin (SF), erythrocyte sedimentation rate (ESR), fibrinogen (FIB), aspartate aminotransferase-to-alanine aminotransferase ratio (AST/ALT), serum albumin (ALB), sodium (Na), Interleukin (IL-10), tumor necrosis factor (TNF-α), S100 calcium binding protein A12 (S100A12), and Myeloid Differentiation Factor 88 (MYD88) (p < 0.05). After performing a univariate analysis, 12 variables (gender, fever duration, WBC, HGB, CRP, SF, ESR, FIB, AST/ALT, ALB, Na, and S100A12) were included in the multifactorial binary logistic regression, which showed that fever duration ≥ 6.5 days, ESR ≥ 46.5 mm/h, AST/ALT ≤ 1.51, and S100A12 ≥ 10.02 were independent risk factors for KD with CALs and were assigned scores of 3, 2, 1, and 2, respectively, according to the odds ratio (OR). The total score of each patient was counted, and a new prediction model for KD combined with CALs was established, where < 3.5 was considered low risk and ≥ 3.5 was regarded as high risk; the sensitivity, specificity, Jorden index, and area under the curve of this scoring system were 0.667, 0.836, 0.502, and 0.838, respectively. This new scoring model has good efficacy for predicting the occurrence of KD with CALs. The expression of S100A12 was significantly increased in the CALs group and was an independent risk factor for the occurrence of CALs, and has the potential as a biomarker for predicting KD with CALs.

A Patent Review on the Therapeutic Application of Monoclonal Antibodies in COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains spike proteins that assist the virus in entering host cells. In the absence of a specific intervention, efforts are afoot throughout the world to find an effective treatment for SARS-CoV-2. Through innovative techniques, monoclonal antibodies (MAbs) are being designed and developed to block a particular pathway of SARS-CoV-2 infection. More than 100 patent applications describing the development of MAbs and their application against SARS-CoV-2 have been registered. Most of them target the receptor binding protein so that the interaction between virus and host cell can be prevented. A few monoclonal antibodies are also being patented for the diagnosis of SARS-CoV-2. Some of them, like Regeneron^® have already received emergency use authorization. These protein molecules are currently preferred for high-risk patients such as those over 65 years old with compromised immunity and those with metabolic disorders such as obesity. Being highly specific in action, monoclonal antibodies offer one of the most appropriate interventions for both the prevention and treatment of SARS-CoV-2. Technological advancement has helped in producing highly efficacious MAbs. However, these agents are known to induce immunogenic and non-immunogenic reactions. More research and testing are required to establish the suitability of administering MAbs to all patients at risk of developing a severe illness. This patent study is focused on MAbs as a therapeutic option for treating COVID-19, as well as their invention, patenting information, and key characteristics.

Infection Spread, Recovery, and Fatality from Coronavirus in Different Provinces of Saudi Arabia

The World Health Organization (WHO) announced COVID-19, a novel coronavirus outbreak, as a pandemic in 2020. In the month of February 2020, the disease began to spread through the Middle East. The first case of COVID-19 in the Kingdom of Saudi Arabia was identified in March 2020, and it is now one of the region’s most affected countries. Analyzing the disease’s propagation pattern may aid in the development of pandemic-fighting strategies. This study aims to analyze the trend of COVID-19’s spread, its recovery, and mortality in the Kingdom of Saudi Arabia (KSA). Two to three major cities from the 13 provinces of the country were chosen, and the rate of infection recovery was recorded from the first month until the number of confirmed cases showed a decline. The data published on the official Ministry of Health website were recorded on an Excel sheet, graphically represented as figures to indicate the pattern of spread. According to the study’s findings, COVID-19 positive cases were discovered in the majority of provinces as early as March 2020. The province of Makkah had the largest number of COVID-19 positive cases (30.7%), followed by Riyadh (23%). The province of Al Jowf had the lowest number of COVID-19 cases (0.3%). Tabuk province had the highest rate of recovery (97.8%), followed by the Northern Border Province (96.7%). Makkah province had the highest mortality rate (2.6%), followed by Al Jawf province (2.4%). The peak case–fatality ratio was recorded in August and September. The highest number of tests to detect the COVID-19 was performed in the month of July, and the highest percentage of positive cases was detected in June (19.55%). All the provinces from the month of September 2020 showed a progressive decline in the number of confirmed COVID-19 cases. According to this study, COVID-19 infection was found in the majority of Saudi Arabian provinces in March 2020, with a peak in June–July 2020. Considering the climatic and demographic characteristics of the region, specific modalities need to be adopted in collaboration with international guidelines to defeat the COVID-19 pandemic.

Knowledge, attitude and practices of healthcare professionals of Riyadh, Saudi Arabia towards covid-19: A cross-sectional study

Background & objectives

COVID-19 is an emerging pandemic that necessitates the implementation of effective infection prevention and control steps. The knowledge, attitudes, and practices (KAP) of healthcare professionals toward COVID-19 affect their compliance to prevention and control initiatives. During the evolving pandemic, we examined the KAP among healthcare professionals against COVID-19 in this research.

Materials and methods

This was a cross-sectional study conducted among Riyadh region health care professionals from the beginning of December 2020 to the end of February 2021 using a validated self-administered questionnaire. The knowledge questionnaire contained questions about COVID-19 clinical characteristics, prevention, and management. The evaluation of attitudes and practices included questions regarding actions and adjustments in COVID-19 response activities. Knowledge scores were measured and compared using demographic characteristics, as well as attitudes and practices toward COVID-19. Using SPSS-IBM 25, bivariate statistics were done to analyze the data.

Results

146 healthcare professionals completed the survey. Physicians were the most prominent party in the survey, accounting for 74 (51 percent), followed by nurses 44 (30 percent) and pharmacists 28 (19 percent). The participants' average age was 39.69 ± 8.48 years. The participant's mean knowledge, attitude, and practice scores were 11.43 ± 1.34, 3.89 ± 0.93, and 3.85 ± 0.81, respectively. With a positive attitude, the mean knowledge score was 11.52, and with proper practice, it was 11.32. With an improvement in knowledge, the attitude score increased significantly (r = 0.172, P = 0.001). Besides, there was a greater association between attitudes and practices (r = 0.170, P = 0.029). A significant enhancement in the practice score of the professionals was noted with an increase in knowledge score (r = 0.095, P = 0.010), an indicator for a positive correlation between practice and knowledge scores.

Interpretation & conclusion

Healthcare practitioners have a good understanding of COVID-19. Improved knowledge and a positive attitude toward COVID-19 infection are linked to appropriate practice. There is a need for more manpower, better COVID-19 management training, and strategies to reduce anxiety among healthcare professionals.

Development and Evaluation of a Fully Automated Molecular Assay Targeting the Mitochondrial Small Subunit rRNA Gene for the Detection of Pneumocystis jirovecii in Bronchoalveolar Lavage Fluid Specimens

The fungal pathogen Pneumocystis jirovecii causes Pneumocystis pneumonia. Although the mitochondrial large subunit rRNA gene (mtLSU) is commonly used as a PCR target, a mitochondrial small subunit rRNA gene (mtSSU)-targeted MultiCode PCR assay was developed on the fully automated ARIES platform for detection of P. jirovecii in bronchoalveolar lavage fluid specimens in 2.5 hours. The assay showed a limit of detection of 800 copies/mL (approximately equal to 22 organisms/mL), with no cross-reactivity with other respiratory pathogens. Compared with the reference Pneumocystis-specific direct fluorescent antibody assay (DFA) and mtLSU-targeted PCR assay, the new assay demonstrated sensitivity of 96.9% (31/32) and specificity of 94.6% (139/147) in detecting P. jirovecii in 180 clinical bronchoalveolar lavage fluid specimens. This assay was concordant with all DFA-positive samples and all but one mtLSU PCR-positive sample, and detected eight positive samples that were negative by DFA and mtLSU PCR. Receiver operating characteristic curve analysis revealed an area under the curve of 0.98 and a threshold cycle (C_T) cutoff of 39.1 with sensitivity of 90.9% and specificity of 99.3%. The detection of 39.1 <C_T < 40.0 indicates the presence of a low load of the organism and needs further determination of either colonization or probable/possible Pneumocystis pneumonia. Overall, the new assay demonstrates excellent analytical and clinical performance and may be more sensitive than mtLSU PCR target for the detection of P. jirovecii.