Pooled nasopharyngeal and oropharyngeal samples for the identification of respiratory viruses in adults

Evaluation of the influenza and respiratory syncytial virus (RSV) targets in the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay: sample pooling increases testing throughput

During the COVID-19 pandemic, sample pooling has proven an effective strategy to overcome the limitations of reagent shortages and expand laboratory testing capacity. The inclusion of influenza and respiratory syncytial virus (RSV) in a multiplex tandem PCR platform with SARS-CoV-2 provides useful diagnostic and infection control information. This study aimed to evaluate the performance of the influenza and RSV targets in the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay, including the effect of pooling samples on target detection. RSV target detection in clinical samples was compared to the Cepheid Xpert Xpress Flu/RSV assay as a reference standard. Samples were then tested in pools of four and detection rates were compared. Owing to the unavailability of clinical samples for influenza, only the effect of sample pooling on simulated samples was evaluated for these targets. RSV was detected in neat clinical samples with a positive percent agreement (PPA) of 100% and negative percent agreement (NPA) of 99.5% compared to the reference standard, demonstrating 99.7% agreement. This study demonstrates that sample pooling by four increases the average Ct value by 2.24, 2.29, 2.20 and 1.91 cycles for the target's influenza A, influenza A typing, influenza B and RSV, respectively. The commercial AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay was able to detect influenza and RSV at an intermediate concentration within the limit of detection of the assay. Further studies to explore the applicability of sample pooling at the lower limit of detection of the assay is needed. Nevertheless, sample pooling has shown to be a viable strategy to increase testing throughput and reduce reagent usage. In addition, the multiplexed platform targeting various respiratory viruses assists with public health and infection control responses, clinical care, and patient management.

The etiologic, microbiologic, clinical and outcome characteristics of immunocompetent young children <2 years of age hospitalized with acute neutropenia

BACKGROUND

To describe the etiologic, microbiologic, clinical and outcome characteristics of acute neutropenia (absolute neutrophil count, ANC, <1.5 × 10⁹/L) in hospitalized immunocompetent children.

METHODS

Serious bacterial infections (SBI) were defined as culture-positive blood, urine, cerebrospinal fluid, articular fluid or stool infections, alveolar pneumonia, Brucellosis and Rickettsiosis.

RESULTS

431/671 (64.2%) healthy infants and children hospitalized with acute neutropenia were <2 years of age; 176 (40.8%), 167 (38.8%) and 88 (20.4%) patients were aged 0-3, 4-12 and 13-24 months, respectively. There were 19 (4.4%), 53 (12.3%), 140 (32.5%) and 209 (50.8%) patients with ANC count <200, 200-500, 501-1000 and 1001-1500 × 10⁹ cells/L, respectively. Severe neutropenia (<500 × 10⁹/L) was recorded in 72 (16.7%) patients. Fever >38 °C was present in 208/431 (48.3%) patients. Blood cultures were positive in 10 (2.3%), with Brucella melitensis, Staphylococcus aureus and Enterobacter spp. identified in 4, 3 and 2 patients, respectively; 5/10 patients with positive blood cultures were <3 months of age. Overall, 55/431 (12.7%) and 65/431 (15.1%) patients were diagnosed with SBIs and bacterial infections, respectively. Nasal washings-PCR for respiratory viruses was positive in 139/293 (47.4%) patients tested. An infectious etiology (bacterial and/or viral) was diagnosed in 190/431 (44.1%) patients. Three patients were diagnosed with acute lymphocytic leukemia. Resolution of neutropenia was achieved in 111/208 (53.4%) evaluable patients (63%, 50.6% and 48% of patients aged 0-3, 4-12 and >12 months, respectively and 56.8%, 53.5% and 52% of patients with severe, moderate and mild neutropenia, respectively).

CONCLUSION

Acute neutropenia is common in immunocompetent children <2 years of age and is frequently associated with viral infections. We showed a substantial involvement of bacterial infections and particularly SBIs in the etiology of acute neutropenia. After a 1-month follow-up, resolution of neutropenia occurred in half of the patients, without association with age subgroups and with neutropenia severity.

Diagnosis of COVID-19 Infection in Pregnancy

This chapter describes the diagnosis of COVID-19 infection in the general population with special consideration to diagnosis in pregnant women. Diagnosis includes the clinical characteristics including symptoms and signs of infection, similarities and differences between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and other viral infections particularly influenza, and diagnostic investigations including nucleic acid amplification test, SARS-CoV-2 virus antigen detection, and antibodies against the virus testing. WHO recommendations for testing were discussed. The value of different laboratory investigations in diagnosis and prognosis was highlighted. Explanation of data related to chest imaging and discussion of indications of imaging and different findings were assessed.

A combination of naso- and oropharyngeal swabs improves the diagnostic yield of respiratory viruses in adult emergency department patients

BACKGROUND

Along with the current development of molecular diagnostic methods of respiratory viruses, the bedside patient sampling techniques need to be evaluated. We here asked the question whether the addition of an oropharynx swab to the traditional nasopharynx swab might improve the diagnostic yield of multiplex PCR analysis. Ct values from the two sampling sites were compared as well as patient tolerability.

METHODS

In an emergency department in Malmö, Sweden, 98 adult patients with respiratory disease were sampled both from the nasopharynx and oropharynx for virus diagnostics by PCR.

RESULTS

Influenza (AH1, AH3, B), human metapneumovirus (hMPV) or respiratory syncytial virus (RSV) were detected by PCR in 58 subjects. The diagnostic yield was improved by combining nasopharyngeal and oropharyngeal sampling - a virus was detected in another 6 patients compared to traditional nasopharyngeal sampling (p = .031, McNemar's test). In 38/55 subjects viral load was higher in the nasopharynx than in the oropharynx. Self-reported discomfort was significantly lower from oropharyngeal sampling than from nasopharyngeal sampling.

CONCLUSIONS

Adding an oropharynx sample to a nasopharynx sample increased the diagnostic yield of respiratory viruses. Oropharyngeal sampling was well tolerated.

Mixed viral infections of the respiratory tract; an epidemiological study during consecutive winter seasons

The current study aimed to describe the molecular epidemiology of mixed respiratory viral infections during consecutive winter seasons in a tertiary care hospital. Patients with symptoms of respiratory tract infection were evaluated during the 2009‐2011 and 2013‐15 winter seasons. A clinical microarray technique was used for viral detection. Clinical and epidemiological data were correlated with mixed viral detection and the need for hospitalization. In 332 out of 604 (54.4%) evaluated patients (17.6% children) a respiratory virus was identified. Mixed viral infections were diagnosed in 68/332 (20.5%) patients with virus detection (66.2% mixed Influenza‐RSV infections). Mixed viral infections were more commonly detected in children (OR 3.7; 95%CI 1.9‐5.6, P < 0.01) and patients with comorbidities. In logistic regression analyses, mixed viral infections were associated with younger age (mean age 30.4 years vs. 41.8 years, P ≤ 0.001) and increased rates of fever (OR: 2.7; 95%CI 1.04‐7.2, P < 0.05) but no adverse outcomes or increased rates of hospitalization. High rates of mixed viral infections were noted during all winter seasons (especially Influenza and RSV) and were more common in younger patients. The clinical significance of mixed respiratory viral infection needs further elucidation.

Epidemiology of Respiratory Pathogens among Elderly Nursing Home Residents with Acute Respiratory Infections in Corsica, France, 2013-2017

Background

The current study aims to describe the demographical and clinical characteristics of elderly nursing home (NH) residents with acute respiratory infections (ARIs) during four winter seasons (2013/2014–2016/2017), as well as the microbiological etiology of these infections.

Methods

Seventeen NHs with at least one ARI resident in Corsica, France, were included. An ARI resident was defined as a resident developing a sudden onset of any constitutional symptoms in addition to any respiratory signs. Nasopharyngeal swabs from ARI residents were screened for the presence of 21 respiratory agents, including seasonal influenza viruses.

Results

Of the 107 ARI residents enrolled from NHs, 61 (57%) were positive for at least one of the 21 respiratory pathogens. Forty-one (38.3%) of the 107 ARI residents had influenza: 38 (92%) were positive for influenza A (100% A(H3N2)) and three (8%) for influenza B/Victoria. Axillary fever (≥38°C) was significantly more common among patients infected with influenza A(H3N2).

Conclusion

The circulation of seasonal respiratory viruses other than influenza A(H3N2) seems to be sporadic among elderly NH residents. Investigating the circulation of respiratory viruses in nonwinter seasons seems to be important in order to understand better the dynamic of their year-round circulation in NHs.

Sensitive Molecular Diagnostics for Cutaneous Leishmaniasis

BACKGROUND

Rapid diagnosis of cutaneous leishmaniasis (CL) and identification of Leishmania species is highly important for the disease management. In Israel, CL is caused mainly by Leishmania major and Leishmania tropica species.

METHODS

We established an easy to handle point of care lesion-swabbing, combined with a highly sensitive multiplex real time PCR (multiplex qPCR) for accurate and rapid diagnosis of Leishmania species.

RESULTS

Using three probes: one general for: Leishmania species, and two specific for L major, and L tropica, we screened 1783 clinical samples collected during two years. Leishmania species was found in 1086 individuals, 1008 L major, and 70 L tropica. Eight samples positive for Leishmania species only, were further tested using a second set of multiplex qPCR developed, and were found positive for Leishmania braziliensis and Leishmania infantum/donovani (2 and 6 samples, concomitantly).

CONCLUSIONS

Taken together, the test enabled diagnostics and better treatment of Leishmania infections from the Old World (1078 samples) and the New World (8 samples), and the subtyping of the dominant strains in the region, as well as in returning travelers'.

Expression of NKp46 Splice Variants in Nasal Lavage Following Respiratory Viral Infection: Domain 1-Negative Isoforms Predominate and Manifest Higher Activity

The natural killer (NK) cell activating receptor NKp46/NCR1 plays a critical role in elimination of virus-infected and tumor cells. The NCR1 gene can be transcribed into five different splice variants, but the functional importance and physiological distribution of NKp46 isoforms are not yet fully understood. Here, we shed light on differential expression of NKp46 splice variants in viral respiratory tract infections and their functional difference at the cellular level. NKp46 was the most predominantly expressed natural cytotoxicity receptor in the nasal lavage of patients infected with four respiratory viruses: respiratory syncytia virus, adenovirus, human metapneumovirus, or influenza A. Expression of NKp30 was far lower and NKp44 was absent in all patients. Domain 1-negative NKp46 splice variants (i.e., NKp46 isoform d) were the predominantly expressed isoform in nasal lavage following viral infections. Using our unique anti-NKp46 mAb, D2-9A5, which recognizes the D2 extracellular domain, and a commercial anti-NKp46 mAb, 9E2, which recognizes D1 domain, allowed us to identify a small subset of NKp46 D1-negative splice variant-expressing cells within cultured human primary NK cells. This NKp46 D1-negative subset also showed higher degranulation efficiency in term of CD107a surface expression. NK-92 cell lines expressing NKp46 D1-negative and NKp46 D1-positive splice variants also showed functional differences when interacting with targets. A NKp46 D1-negative isoform-expressing NK-92 cell line showed enhanced degranulation activity. To our knowledge, we provide the first evidence showing the physiological distribution and functional importance of human NKp46 splice variants under pathological conditions.

Molecular detection of human metapneumovirus and human bocavirus on oropharyngeal swabs collected from young children with acute respiratory tract infections from rural and peri-urban communities in South India

Background

Acute respiratory tract infections (ARTIs) are one of the major causes of morbidity and mortality among young children in developing countries. Information on the incidence of human metapneumovirus (hMPV) and human bocavirus (HBoV) infections in developing countries, especially among rural children, is very limited.

Objectives

This study was conducted to identify whether these viruses were associated with ARTI among children ≤5 years of age in rural and peri-urban populations in South India.

Methods

The study was cross-sectional with prospective sample collection. Oropharyngeal swabs were collected from children ≤5 years of age presenting with ARTI. None of the children in this study were known to have any immunosuppressive conditions. The two viruses, hMPV and HBoV, were identified using semi-nested polymerase chain reaction (PCR) assays and one-step PCR assays, respectively. The lower limits of detection of hMPV and HBoV were 6.69 × 10⁵ plasmid copies and 5.77 × 10³ plasmid copies, respectively, per 5 μL PCR reaction input.

Results

The frequency of hMPV infection in children was higher than that of HBoV infection. The different frequencies of hMPV in patients in various age groups with upper and lower respiratory tract infections were compared, and the variance was found to be insignificant. In the 38 children who were hMPV positive, the majority (73.7 %) were from rural communities. The overall hMPV-positive rate was higher in the rural population than in the peri-urban population, but the difference was statistically insignificant. The youngest age at which hMPV-positive status was recorded was 5 months.

Conclusion

This study demonstrated that hMPV was associated with a significant number (i.e. >10 %) of ARTIs in children in South India, whereas a relatively smaller number of HBoV infections was observed.

Specimen collection for the diagnosis of pediatric pneumonia

Diagnosing the etiologic agent of pneumonia has an essential role in ensuring the most appropriate and effective therapy for individual patients and is critical to guiding the development of treatment and prevention strategies. However, establishing the etiology of pneumonia remains challenging because of the relative inaccessibility of the infected tissue and the difficulty in obtaining samples without contamination by upper respiratory tract secretions. Here, we review the published and unpublished literature on various specimens available for the diagnosis of pediatric pneumonia. We discuss the advantages and limitations of each specimen, and discuss the rationale for the specimens to be collected for the Pneumonia Etiology Research for Child Health study.

Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children

Background

The detection of viral respiratory tract infections has evolved greatly with the development of PCR based commercial systems capable of simultaneously detecting a wide variety of pathogens.

Objectives

Evaluate the relative performance of two commercial broad range systems for the detection of viral agents in clinical respiratory tract specimens from immunocompromised children.

Study design

A total of 176 patient samples were included in the analysis, representing only the first sample collected for each patient, and excluding failed reactions. Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray^® Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Method comparison was based upon pair-wise concordance of results according to patient age, viral target and number of targets detected.

Results

The two systems showed an overall concordance, by patient, of 83.8% (p = 0.0001). FilmArray detected at least one target in 68.8% of samples, while ResPlex detected at least one target in 56.8%. ResPlex failed to detect 20.7% of FilmArray positives, and FilmArray failed to detect 4% of ResPlex positives. The relative performance of each system (including which system detected a higher number of positive samples) varied when stratified by target viral pathogen.

Conclusions

Broadly multiplexed PCR is an effective means of detecting large numbers of clinically relevant respiratory viral pathogens.

Added value of an oropharyngeal swab in detection of viruses in children hospitalized with lower respiratory tract infection

Paired nasopharyngeal and oropharyngeal swabs collected from 533 children hospitalized with lower respiratory tract infection were assessed by multiplex reverse transcription-PCR. Oropharyngeal swabs increased the number of viral infections detected by 15%, compared to collection of a nasopharyngeal swab alone. This advantage was most pronounced for detection of influenza, parainfluenza, and adenovirus.