Human bocavirus 1 epidemiology in children in relation to virus load and codetection.

AIM: Human bocavirus 1 (HBoV1) has been associated with respiratory tract infections in children. We aimed at retrospectively describing patient characteristics, seasonality, pre-existing medical conditions, codetections, clinical manifestations and complications of HBoV1 infection in relation to viral load in the child population in Stockholm, with the overarching aim of elucidating the clinical significance of HBoV1. METHODS: We included all hospitalised children 0-17 years testing positive for HBoV1 by real-time polymerase chain reaction on nasopharyngeal aspirates 1 July 2008-30 June 2019. Patients with HBoV1 single detection, high viral load expressed as an HBoV1-DNA cycle threshold (Ct) < 25, or both, were separately analysed. We retrieved information on pre-existing conditions and clinical course from the medical records. RESULTS: We found 768 episodes in 727 children, 496 (64.6%) male and 441 (60.7%) previously healthy. The median age was 17.6 months. Most (476/768, 62.0%) episodes occurred during December-March. HBoV1 was in 549 episodes (71.5%) codetected with other viruses. Ct < 25 was independently associated with young age, single detection of HBoV1 and presentation early in the epidemic season. We saw few differences in clinical manifestations between the subgroups. CONCLUSION: Our findings are consistent with primary HBoV1 infection causing mild-to-severe respiratory tract manifestations in young children.

Duration of clinical symptoms in children with acute respiratory infection.

AIM: To investigate duration of clinical symptoms associated with various respiratory viruses and with the co-detection of respiratory viral and bacterial pathogens. METHODS: This prospective cohort study included 737 acutely ill children treated in a paediatric emergency department prior to the COVID-19 pandemic. Nasal swab samples were analysed with multiplex PCR panels for 16 viral and 7 bacterial respiratory pathogens. Parents filled in a questionnaire about the symptoms at the time of the visit and 14 days afterwards. RESULTS: Persistent symptoms 2 weeks after the onset of acute illness were common: 32% of the patients with a coronavirus 229 E, NL63 or OC43 finding, 31% of those with human metapneumovirus and 25% of those with rhinovirus reported ongoing symptoms. At least one symptom lasting more than 4 weeks was observed in 3-4% of the children. Children with viral and bacterial co-detection had a longer duration of fever than those with only viral detection (3.3 days [SD 2.8] vs. 1.6 days [SD 2.4], p < 0.001). CONCLUSION: Symptoms lasting for more than 2 to 4 weeks appear to be relatively frequent in all respiratory viral infections in children. Viral and bacterial co-detection may increase the duration of illness.

Characteristics of hospitalized COVID-19 patients with other respiratory pathogens identified by rapid diagnostic test.

Rapid diagnostic tests (RDTs) significantly impact disease treatment strategy. In Japan, information on the use of RDTs for patients with COVID-19 is limited. Here, we aimed to investigate the RDT implementation rate, pathogen detection rate, and clinical characteristics of patients positive for other pathogens by using COVIREGI-JP, a national registry of hospitalized patients with COVID-19. A total of 42,309 COVID-19 patients were included. For immunochromatographic testing, influenza was the most common (n = 2881 [6.8%]), followed by Mycoplasma pneumoniae (n = 2129 [5%]) and group A streptococcus (GAS) (n = 372 [0.9%]). Urine antigen testing was performed for 5524 (13.1%) patients for S. pneumoniae and for 5326 patients (12.6%) for L. pneumophila. The completion rate of M. pneumonia loop-mediated isothermal amplification (LAMP) testing was low (n = 97 [0.2%]). FilmArray RP was performed in 372 (0.9%) patients; 1.2% (36/2881) of patients were positive for influenza, 0.9% (2/223) for the respiratory syncytial virus (RSV), 9.6% (205/2129) for M. pneumoniae, and 7.3% (27/372) for GAS. The positivity rate for urine antigen testing was 3.3% (183/5524) for S. pneumoniae and 0.2% (13/5326) for L. pneumophila. The positivity rate for LAMP test was 5.2% (5/97) for M. pneumoniae. Five of 372 patients (1.3%) had positive FilmArray RP, with human enterovirus being the most frequently detected (1.3%, 5/372). The characteristics of patients with and without RDTs submission and positive and negative results differed for each pathogen. RDTs remain an important diagnostic tool in patients with COVID-19 in whom coinfection with other pathogens needs to be tested based on clinical evaluation.

Navigating the cellular landscape in tissue: Recent advances in defining the pathogenesis of human disease.

Over the past decade, our understanding of human diseases has rapidly grown from the rise of single-cell spatial biology. While conventional tissue imaging has focused on visualizing morphological features, the development of multiplex tissue imaging from fluorescence-based methods to DNA- and mass cytometry-based methods has allowed visualization of over 60 markers on a single tissue section. The advancement of spatial biology with a single-cell resolution has enabled the visualization of cell-cell interactions and the tissue microenvironment, a crucial part to understanding the mechanisms underlying pathogenesis. Alongside the development of extensive marker panels which can distinguish distinct cell phenotypes, multiplex tissue imaging has facilitated the analysis of high dimensional data to identify novel biomarkers and therapeutic targets, while considering the spatial context of the cellular environment. This mini-review provides an overview of the recent advancements in multiplex imaging technologies and examines how these methods have been used in exploring pathogenesis and biomarker discovery in cancer, autoimmune and infectious diseases.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Codetection With Influenza A and Other Respiratory Viruses Among School-Aged Children and Their Household Members-12 March 2020 to 22 February 2022, Dane County, Wisconsin.

BACKGROUND: Concurrent detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and another respiratory virus in individuals can document contemporaneous circulation. We used an ongoing, community-based study of school-aged children and their households to evaluate SARS-CoV-2 codetections with other respiratory viruses in a non-medically attended population over a 2-year period. METHODS: Household enrollment was predicated on an acute respiratory illness in a child residing in that household who was also a kindergarten through 12th-grade student in the participating school district. Demographic, symptom, and household composition data and self-collected nasal specimens were obtained on the recruitment day, and 7 and 14 days later, from the index child and all other household members. All specimens were tested for SARS-CoV-2 and influenza A/B by reverse-transcription polymerase chain reaction. Day 0 specimens from the index children were simultaneously tested for 16 pathogens using a commercial respiratory pathogen panel (RPP). To assess viral codetections involving SARS-CoV-2, all household specimens were tested via RPP if the index child's day 0 specimen tested positive to any of the 16 pathogen targets in RPP and any household member tested positive for SARS-CoV-2. RESULTS: Of 2109 participants (497 index children in 497 households with 1612 additional household members), 2 (0.1%) were positive for both SARS-CoV-2 and influenza A; an additional 11 (0.5%) were positive for SARS-CoV-2 and another RPP-covered respiratory virus. Codetections predominantly affected school-aged children (12 of 13 total) and were noted in 11 of 497 households. CONCLUSIONS: SARS-CoV-2 codetections with other respiratory viruses were uncommon and predominated in school-aged children.

Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has infected almost 200 million people worldwide by July 2021 and the pandemic has been characterized by infection waves of viral lineages showing distinct fitness profiles. The simultaneous infection of a single individual by two distinct SARS-CoV-2 lineages may impact COVID-19 disease progression and provides a window of opportunity for viral recombination and the emergence of new lineages with differential phenotype. Several hundred SARS-CoV-2 lineages are currently well phylogenetically defined, but two main factors have precluded major coinfection/codetection and recombination analysis thus far: (i) the low diversity of SARS-CoV-2 lineages during the first year of the pandemic, which limited the identification of lineage defining mutations necessary to distinguish coinfecting/recombining viral lineages; and the (ii) limited availability of raw sequencing data where abundance and distribution of intrasample/intrahost variability can be accessed. Here, we assembled a large sequencing dataset from Brazilian samples covering a period of 18 May 2020 to 30 April 2021 and probed it for unexpected patterns of high intrasample/intrahost variability. This approach enabled us to detect nine cases of SARS-CoV-2 coinfection with well characterized lineage-defining mutations, representing 0.61 % of all samples investigated. In addition, we matched these SARS-CoV-2 coinfections with spatio-temporal epidemiological data confirming its plausibility with the cocirculating lineages at the timeframe investigated. Our data suggests that coinfection with distinct SARS-CoV-2 lineages is a rare phenomenon, although it is certainly a lower bound estimate considering the difficulty to detect coinfections with very similar SARS-CoV-2 lineages and the low number of samples sequenced from the total number of infections.

Frequency of respiratory pathogens other than SARS-CoV-2 detected during COVID-19 testing.

The frequencies of 19 respiratory pathogens other than SARS-CoV-2 were assessed in 6,"?>235 Brazilian individuals tested for COVID-19. Overall, only 83 individuals who tested positive for SARS-CoV-2 had codetection of other pathogens. Individuals infected with Rhinovirus/Enterovirus, Human Coronavirus (HCoV)-HKU1, HCoV-NL63, HPIV-4, Influenza A (-H1N1 and other subtypes), Influenza B, Human Respiratory Syncytial Virus and Human Metapneumovirus were less likely to test positive for SARS-CoV-2. Infection with Streptococcys pyogenes, Chlamydophila pneumoniae, Mycoplasma pneumoniae, and Bordetella pertussis were more frequent in individuals who tested negative for SARS-CoV-2, but without significancy. We found 150 individuals infected with ≥2 pathogens other than SARS-CoV-2, only 3 out of whom tested positive for COVID-19. The codetection frequency was low in individuals diagnosed with COVID-19. Other viral infections may provide a cross-reactive, protective immune response against SARS-CoV-2. Screening for bacterial respiratory infections upon COVID-19 testing is important to drive suitable therapeutic approaches and avoid unnecessary antibiotic prescription.

One-pot pre-coated interface proximity extension assay for ultrasensitive co-detection of anti-SARS-CoV-2 antibodies and viral RNA.

In the field of in vitro diagnostics, detection of nucleic acids and proteins from biological samples is typically performed with independent platforms; however, co-detection remains a major technical challenge. Specifically, during the coronavirus disease 2019 (COVID-19) pandemic, the ability to simultaneously detect viral RNA and human antibodies would prove highly useful for efficient diagnosis and disease course management. Herein, we present a multiplex one-pot pre-coated interface proximity extension (OPIPE) assay that facilitates the simultaneous recognition of antibodies using a pre-coated antigen interface and a pair of anti-antibodies labeled with oligonucleotides. Following anti-antibody-bound nucleic acid chain extension to form templates in proximity, antibody signals can be amplified, together with that of targeted RNA, via a reverse transcription-polymerase chain reaction. Using four-color fluorescent TaqMan probes, we demonstrate the co-detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies and viral nucleic acids in a single bio-complex sample, including nucleocapsid protein-specific IgG and IgM, and the RNA fragments of RdRp and E genes. The serum detection limit for this platform is 100 fg/mL (0.67 fM) for the anti-SARS-CoV-2 antibody and 10 copies/µL for viral RNA. The OPIPE assay offers a practical and affordable solution for ultrasensitive co-detection of nucleic acids and antibodies from the same trace biological sample without the additional requirement of complicated equipment.

Distribution of spreading viruses during COVID-19 pandemic: Effect of mitigation strategies.

BACKGROUND: The study aimed to evaluate the distribution of circulating respiratory viral pathogens other than severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) during the first year of the coronavirus disease-2019 (COVID-19) pandemic with especially focusing on the effects of the national-based mitigation strategies. METHODS: This single-center study was conducted between March 11, 2020-March 11, 2021. All children who were tested by polymerase chain reaction on nasopharyngeal swabs for SARS-CoV-2 and other common respiratory viral pathogens were included in the study. RESULTS: A total of 995 children with suspected COVID-19 admitted to the study center. Of these, 513 patients who were tested by polymerase chain reaction for both SARS-CoV-2 and common respiratory viral pathogens were included in the final analysis. Two hundred ninety-five patients were (57.5%) male. The median age was 3 years of age (27 days-17 years). A total of 321 viral pathogens identified in 310 (n: 310/513, 60.4%) patients, and 11 of them (n: 11/310, 3.5%) had co-detection with more than 1 virus. The most common detected virus was rhinovirus (n: 156/513, 30.4%), and SARS-CoV-2 (n: 122/513, 23.8%) followed by respiratory syncytial virus (n: 18/513, 3.5%). The influenza virus was detected in 2 patients (0.4%). A total of 193 patients were negative for both SARS-CoV-2 and other pathogens. CONCLUSIONS: There is a decline in the frequency of all viral pathogens like SARS-CoV-2 in correlation with the national-based mitigation strategies against COVID-19 during the pandemic.

Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia, China.

We report co-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus in a patient with pneumonia in China. The case highlights possible co-detection of known respiratory viruses. We noted low sensitivity of upper respiratory specimens for SARS-CoV-2, which could further complicate recognition of the full extent of disease.