Detection Of Other Respiratory Viruses Research Articles

The Impact of COVID-19 Public Health Measures on Detection of Other Respiratory Viruses in Children during the Winter of 2020–2021 in Hangzhou, China

Abstract Objective Acute respiratory tract infection (ARTI) is one of the main diseases in childhood. This study aimed to monitor the distribution of respiratory tract viruses in children with ARTI in the impact of coronavirus disease 2019 (COVID-19). Methods We conducted surveillance of 2019 novel coronavirus, human metapneumovirus, respiratory syncytial virus, human adenovirus, human parainfluenza virus 1–3, and influenza A and B virus by using quantitative real-time polymerase chain reaction. Results During the winter of 2020 to 2021, among the 1,442 throat swabs we collected, 937 (64.98%, 937/1,442) were positive for respiratory viruses. Respiratory syncytial virus was the most frequently detected respiratory virus (34.12%, 492/1,442) and 2019 novel coronavirus and influenza A and B virus were not detected in the study period. Coinfection was observed in 156 positive samples including 149 samples of double infection and 7 of triple infection. The positive rate of viral respiratory tract infection in infants less than 6 months was the highest (72.95%) in the study period. Conclusion There are some differences in the distribution of respiratory viruses in children after the outbreak of COVID-19 in Hangzhou, China.

Syndromic approach to SARS-CoV-2 detection using QIAstat-Dx SARS-CoV-2 panel from clinical samples

The QIAstat-Dx SARS-CoV-2 panel is a multiplex cartridge based assay based on real time PCR which can detect 17 respiratory viruses, including the novel coronavirus SARS-CoV-2. A syndromic approach is the need of the hour for COVID-19 diagnostics among patients presenting with respiratory symptoms. The present study was done to evaluate 120 archived respiratory clinical specimens for SARS-CoV-2 on the SARS-CoV-2 panel. Further, 27 specimens were tested for other respiratory viruses, in comparison with the BioFire RP1.7 platform. The sensitivity and specificity for SARS-CoV-2 on SARS panel was found to be 90.00 % and 100 % respectively, indicating good diagnostic accuracy. The positive predictive value was found to be 100 %, negative predictive value was found to be 99.93 % and accuracy was 99.93 %. Detection of other respiratory viruses observed a concordance of 77.7 %. Despite advantages of speed, minimal expertise and accurate results; significant costs and discrepancies at Ct >35 remain important limitations of the SARS panel.

Shifting Patterns of Respiratory Virus Activity Following Social Distancing Measures for Coronavirus Disease 2019 in South Korea.

BackgroundWe hypothesized that nationwide social distancing and other preventive measures for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were associated with reduced detection of other respiratory viruses in South Korea.MethodsWe analyzed national surveillance data to compare incidence of respiratory viruses during 2016-2019 vs. 2020. Results of multiplex reverse transcriptase–polymerase chain reaction assays for eight respiratory viruses were included: adenovirus (ADV), parainfluenza virus (PIV), respiratory syncytial virus (RSV), influenza virus (IFV), human coronavirus (HCoV; non-SARS-CoV-2), human rhinovirus (HRV), human bocavirus (HBoV), and human metapneumovirus (HMPV).ResultsDuring 2016-2019, rates of detection of respiratory viruses were relatively stable: ADV, 3.7%-9.2%; PIV, 1.4%-17.0%; RSV, 0.3%-15.3%; IFV, 0.4%-35.6%; HCoV, 1.5%-8.4%; HRV, 7.0%-25.1%; HBoV, 0.6%-6.3%; and HMPV, 0.7%-14.5%. Following implementation of social distancing in February 2020, rates of detection of enveloped viruses (HCoV, HMPV, IFV, PIV and RSV) were significantly reduced by up to 100%. However, non-enveloped viruses (ADV, HRV and HBoV) persisted throughout 2020, and HRV rates in hospitalized patients significantly increased.ConclusionsAfter implementation of social distancing for SARS-CoV-2 in South Korea, rates of detection of enveloped respiratory viruses decreased significantly, whereas non-enveloped viruses persisted, suggesting that enhanced infection prevention strategies are required to mitigate spread of these viruses.

A Longitudinal Study of the Epidemiology of Seasonal Coronaviruses in an African Birth Cohort.

Since non-epidemic, seasonal human coronaviruses (sHCoV) commonly infect children, an improved understanding of the epidemiology of these infections may offer insights into the context of severe acute respiratory syndrome (SARS)-CoV-2. We investigated the epidemiology of sHCoV infection during the first year of life, including risk factors and association with lower respiratory tract infection (LRTI). We conducted a nested case-control study of infants enrolled in a birth cohort near Cape Town, South Africa, from 2012 to 2015. LRTI surveillance was implemented, and nasopharyngeal swabs were collected fortnightly over infancy. Quantitative PCR detected respiratory pathogens, including coronaviruses-229E, -NL63, -OC43, and -HKU1. Swabs were tested from infants at the time of LRTI and from the 90 days prior as well as from age-matched control infants from the cohort over the equivalent period. In total, 885 infants were included, among whom 464 LRTI events occurred. Of the 4751 samples tested for sHCoV, 9% tested positive, with HCoV-NL63 the most common. Seasonal HCoV detection was associated with LRTI; this association was strongest for coronavirus-OC43, which was also found in all sHCoV-associated hospitalizations. Birth in winter was associated with sHCoV-LRTI, but there were no clear seasonal differences in detection. Co-detection of Streptococcus pneumoniae was weakly associated with sHCoV-LRTI (odds ratio: 1.8; 95% confidence interval: 0.9-3.6); detection of other respiratory viruses or bacteria was not associated with sHCoV status. Seasonal HCoV infections were common and associated with LRTI, particularly sHCoV-OC43, which is most closely related to the SARS group of coronaviruses. Interactions of coronaviruses with bacteria in the pathogenesis of LRTI require further study.

Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19

ObjectivesThis study was performed during the early outbreak period of coronavirus disease 2019 (COVID-19) and the seasonal epidemics of other respiratory viral infections, in order to describe the extent of co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with other respiratory viruses. It also compared the diagnostic performances of upper respiratory tract (URT) and lower respiratory tract (LRT) samples for SARS-CoV-2 infection. MethodsFrom 25 January to 29 March 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were simultaneously tested for SARS-CoV-2 and other respiratory viruses. ResultsA total of 1423 consecutive patients were tested: 677 (47.6%) males, 746 (52.4%) females, median age 50 (range, 1–103) years. Twenty-one (1.5%) patients were positive for both SARS-CoV-2 and other respiratory viruses. The detection rate of SARS-CoV-2 was significantly higher in LRT than in URT (53.6% vs. 13.4%; p<0.0001). The analysis of paired samples from 117 (8.2%) patients showed that SARS-CoV-2 load was lower in URT than in LRT samples in 65% of cases. ConclusionThe detection of other respiratory viruses in patients during this epidemic period could not rule out SARS-CoV-2 co-infection. Furthermore, LRT samples increased the accuracy of diagnosis of COVID-19.

Guidance for the management of adult patients with coronavirus disease 2019.

In December 2019, a novel coronavirus was identified in Wuhan City, Hubei Province, China and later the disease was named coronavirus disease 2019 (COVID-19). On March 11, 2020, the World Health Organization (WHO) officially announced that COVID-19 had reached global pandemic status. This article summarized the understanding of the etiology, pathogenesis, epidemiology, clinical characteristics, diagnosis, treatment, rehabilitation, and prevention and control measures of COVID-19 based on the available data and anti-epidemic experience in China.

HoBi-like pestivirus infection in an outbreak of bovine respiratory disease

HoBi-like is an emerging pestivirus of the family Flaviviridae detected in cattle herds and biological products of bovine origin in many parts of the world, causing disease similar to that observed in bovine viral diarrhea virus (BVDV) infections. In this study we reported the detection of HoBi-like pestivirus in an outbreak of respiratory disease in calves from Brazil, seropositive for viruses of the bovine respiratory disease complex (BRDC). Thus, serum samples and nasal swabs were collected from calves up to one year old, presenting or not clinical signs of respiratory disease. Serum samples were submitted to virus neutralization test (VNT) for BVDV-1, BVDV-2, bovine herpesvirus-1 (BoHV-1), bovine respiratory syncytial virus (BRSV) and bovine parainfluenza-3 (BPIV-3). These samples were also tested for the presence of pestiviruses (BVDV-1, BVDV-2 and HoBi-like) and BoHV-1 by RT-PCR and PCR, respectively. Nasal swabs were analyzed by RT-PCR for pestiviruses, BRSV and BPIV-3. VNT results showed high serological prevalence and a wide range of antibodies titers, for all viruses studied, in calves of different age groups. The RT-PCR amplified the 5′UTR and E2 regions of pestiviruses of four calves, from both nasal swabs and serum samples, which sequencing identified the HoBi-like pestivirus. This is the first detection of HoBi-like in nasal secretions of calves in an outbreak of respiratory disease in Brazil, along with the serological detection of other respiratory viruses. We concluded that HoBi-like pestivirus should be considered as part of the BRDC, as a differential diagnosis, to take correct measures of control and prophylaxis.

Outcome of children with rhinovirus detection prior to allogeneic hematopoietic cell transplant.

Rhinoviruses are commonly detected in symptomatic and asymptomatic children prior to HCT. Unlike pre‐HCT detection of other respiratory viruses, it is not known whether RV detection, with or without clinical symptoms, is associated with worse outcomes in children post‐HCT. In a retrospective study of children undergoing allogeneic HCT from January 2009 to February 2015, 91 children underwent allogeneic HCT, and 62 children had RPP testing within 30 days pre‐HCT. Fifty‐six (90%) children had either no pathogen (n = 34, 55%) or single RV detection (n = 22, 35%), which was the most common pathogen identified. Compared with virus negative children, children with pre‐HCT RV detection were not more likely to require ventilated support and did not have longer length of stay, higher mortality, or less days alive and out of the hospital within the first 100 days post‐HCT. In a secondary analysis of all 56 patients with RPP testing and no pathogen or RV alone detected, the seven children with LRTI had less days alive and out of the hospital within the first 100 days post‐HCT compared with the 49 children who were either asymptomatic or had URTI (10 vs 60 days, P = 0.002). In a bootstrapped regression model, presence of LRTI, not RV detection, was significantly associated with decreased days alive and out of the hospital within the first 100 days post‐HCT. Thus, pre‐HCT detection of RV, without associated LRTI, does not always warrant HCT delay.

Human Bocavirus Capsid Messenger RNA Detection in Children With Pneumonia.

The role of human bocavirus (HBoV) in respiratory illness is uncertain. HBoV genomic DNA is frequently detected in both ill and healthy children. We hypothesized that spliced viral capsid messenger RNA (mRNA) produced during active replication might be a better marker for acute infection. As part of the Etiology of Pneumonia in the Community (EPIC) study, children aged <18 years who were hospitalized with community-acquired pneumonia (CAP) and children asymptomatic at the time of elective outpatient surgery (controls) were enrolled. Nasopharyngeal/oropharyngeal specimens were tested for HBoV mRNA and genomic DNA by quantitative polymerase chain reaction. HBoV DNA was detected in 10.4% of 1295 patients with CAP and 7.5% of 721 controls (odds ratio [OR], 1.4 [95% confidence interval {CI}, 1.0-2.0]); HBoV mRNA was detected in 2.1% and 0.4%, respectively (OR, 5.1 [95% CI, 1.6-26]). When adjusted for age, enrollment month, and detection of other respiratory viruses, HBoV mRNA detection (adjusted OR, 7.6 [95% CI, 1.5-38.4]) but not DNA (adjusted OR, 1.2 [95% CI, .6-2.4]) was associated with CAP. Among children with no other pathogens detected, HBoV mRNA (OR, 9.6 [95% CI, 1.9-82]) was strongly associated with CAP. Detection of HBoV mRNA but not DNA was associated with CAP, supporting a pathogenic role for HBoV in CAP. HBoV mRNA could be a useful target for diagnostic testing.

Contribution of non- influenza respiratory viruses in causation of Influenza like Illness (ILI) during influenza epidemic: A laboratory based study

IntroductionAccording to CDC USA February 2016 document for outpatient illness surveillance, Influenza like illness (ILI) is defined as fever (temperature of 100°F [37.8°C] or greater) and a cough and/or a sore throat without a known cause other than influenza. Most of the laboratories do not test for other known causes of ILI, especially in situation like epidemics. ObjectiveIn the present study we detected Influenza and other respiratory viruses in the cases presenting as ILI during a flu epidemic in North India from January to April 2015. Materials and methodsTotal 200 cases, 50 from each month, that were negative for all types of influenza viruses, were randomly selected and tested by Multiplex Real- Time PCR for detection of other respiratory viruses; rhinovirus, adenovirus, Respiratory Syncitial virus (RSV), Human Boca virus (hBoV), Para Influenza viruses 1,2,3, and 4 (PIV 1, PIV 2, PIV 3, PIV 4), measles virus and human Meta Pneumo virus (hMPV). ResultsA total of 28/200 cases (14%) showed presence of other respiratory viruses. Rhinovirus was most commonly detected, (17/200; 8.5%) followed by adenovirus (7/200, 3.5%), RSV (5/200, 2.5%), hBoV (2/200, 1%), and PIV-3 (2/200, 1%). PIV 1, 2, 4, measles and hMPV were not detected in any of the samples. ConclusionEven during an epidemic other respiratory viruses contribute substantially to ILI

Concurrent detection of other respiratory viruses in children shedding viable human respiratory syncytial virus

Human respiratory syncytial virus (HRSV) is an important cause of respiratory disease. The majority of studies addressing the importance of virus co‐infections to the HRSV‐disease have been based on the detection of HRSV by RT‐PCR, which may not distinguish current replication from prolonged shedding of remnant RNA from previous HRSV infections. To assess whether co‐detections of other common respiratory viruses are associated with increased severity of HRSV illnesses from patients who were shedding viable‐HRSV, nasopharyngeal aspirates from children younger than 5 years who sought medical care for respiratory infections in Ribeirão Preto (Brazil) were tested for HRSV by immunofluorescence, RT‐PCR and virus isolation in cell culture. All samples with viable‐HRSV were tested further by PCR for other respiratory viruses. HRSV‐disease severity was assessed by a clinical score scale. A total of 266 samples from 247 children were collected and 111 (42%) were HRSV‐positive. HRSV was isolated from 70 (63%), and 52 (74%) of them were positive for at least one additional virus. HRSV‐positive diseases were more severe than HRSV‐negative ones, but there was no difference in disease severity between patients with viable‐HRSV and those HRSV‐positives by RT‐PCR. Co‐detection of other viruses did not correlate with increased disease severity. HRSV isolation in cell culture does not seem to be superior to RT‐PCR to distinguish infections associated with HRSV replication in studies of clinical impact of HRSV. A high rate of co‐detection of other respiratory viruses was found in samples with viable‐HRSV, but this was not associated with more severe HRSV infection. J Med. Virol. 85:1852–1859, 2013. © 2013 Wiley Periodicals, Inc.

Influenza Vaccination Is Not Associated With Detection of Noninfluenza Respiratory Viruses in Seasonal Studies of Influenza Vaccine Effectiveness

The test-negative control study design is the basis for observational studies of influenza vaccine effectiveness (VE). Recent studies have suggested that influenza vaccination increases the risk of noninfluenza respiratory virus infection. Such an effect could create bias in VE studies using influenza-negative controls. We investigated the association between influenza infection, vaccination, and detection of other respiratory viruses among children <5 years old and adults ≥50 years old with acute respiratory illness who participated in seasonal studies of influenza vaccine effectiveness. Nasal/nasopharyngeal samples collected from 2004–2005 through 2009–2010 were tested for 19 respiratory virus targets using a multiplex reverse-transcription polymerase chain reaction (RT-PCR) platform. Vaccination status was determined using a validated registry. Adjusted odds ratios for influenza and vaccination status were calculated using three different control groups: influenza-negative, other respiratory virus positive, and pan-negative. Influenza was detected in 12% of 2010 children and 20% of 1738 adults. Noninfluenza respiratory viruses were detected in 70% of children and 38% of adults without influenza. The proportion vaccinated did not vary between virus-positive controls and pan-negative controls in children (P = .62) or adults (P = .33). Influenza infection was associated with reduced odds of vaccination, but adjusted odds ratios differed by no more than 0.02 when the analysis used influenza-negative or virus-positive controls. Influenza vaccination was not associated with detection of noninfluenza respiratory viruses. Use of influenza-negative controls did not generate a biased estimate of vaccine effectiveness due to an effect of vaccination on other respiratory virus infections.

Clinical relevance of mixed respiratory viral infections in adults with influenza A H1N1

To the Editors: Throughout the pandemic circulation of the 2009 influenza A H1N1 virus (A/H1N1p), concomitant detection of other respiratory viruses in the same patient was reported [1, 2], but their clinical relevance remains unknown. Mixed respiratory viral infections in adults have scarcely been studied. The aim of this study was to assess both the incidence of multiple viral respiratory infections and their clinical significance in adult patients with confirmed A/H1N1p. From October 1 to November 30, 2009, nasopharyngeal and oropharyngeal swabs were obtained from consecutive adults (>18 yrs of age) presenting with acute respiratory illness to the emergency department of Hospital Clinic (Barcelona, Spain). Specimens were placed in a tube containing viral transport medium (VTM) and were immediately sent to and processed at the microbiology laboratory for virological confirmation. Total nucleic acids were extracted from 200 μL of fresh specimen and eluted in 25 μL of RNase-free elution buffer using NucliSense easyMAG (BioMerieux, Marcy l’Etoile, France) according to the manufacturer’s instructions. The presence of A/H1N1p was confirmed by two specific one-step, multiplex, real-time RT-PCRs for influenza virus typing (A or B) and subtyping (H1, H3 or H5) as previously described [3, 4]. Laboratory results for A/H1N1p were provided to clinicians in <24 h. In those patients diagnosed with pneumonia, regular sampling for microbiological diagnosis was also performed as previously described [5]. For the purpose of the study, samples with confirmed A/H1N1p were retrospectively assessed by multiplex PCR using the xTAG® RVP FAST Assay (Luminex–Abbott Molecular, Wiesbaden, Germany) according …

Calu-3/A-549 mixed cells as a replacement for primary rhesus monkey kidney cells for virus detection

Background Primary kidney cells derived from rhesus macaques (pRhMK) are heavily relied upon for the detection and culture of a wide range of clinically relevant viruses. The use of these cultures is problematic due to the possible presence of endogenous viruses, the need to sacrifice a primate, and the inherent variance found in primary cultures. Objective To develop a continuous cell line or mixed cell co-culture that could replace dependence on pRhMK cells. Study design Cells from the Calu-3 and A-549 cell lines were used to prepare mixed cell monolayers that were compared to pRhMK cells for their ability to detect respiratory viruses, measles, mumps, enteroviruses, and herpes viruses. Clinically derived and laboratory virus strains were used for these comparisons in culture plates or 16 mm tubes. Results Calu-3/A-549 cells are more sensitive than pRhMK for the detection of adenovirus, enteroviruses and herpes simplex virus and are about equally sensitive for the detection of other respiratory viruses, measles, mumps and varicella-zoster virus. Conclusions Calu-3/A-549 cells are an equivalent or better alternative to pRhMK cells for the detection of many clinically relevant viruses.

Adenovirus type 7 associated with severe and fatal acute lower respiratory infections in Argentine children.

BackgroundAdenoviruses are the second most prevalent cause of acute lower respiratory infection of viral origin in children under four years of age in Buenos Aires, Argentina. The purpose of this study was to analyze the clinical features and outcome of acute lower respiratory infection associated with different adenovirus genotypes in children.MethodsTwenty-four cases of acute lower respiratory infection and adenovirus diagnosis reported in a pediatric unit during a two-year period were retrospectively reviewed. Adenovirus was detected by antigen detection and isolation in HEp-2 cells. Adenovirus DNA from 17 isolates was studied by restriction enzyme analysis with Bam HI and Sma I.ResultsSubgenus b was found in 82.3% of the cases, and subgenus c in 17.7%. Within subgenus b, only genotype 7 was detected, with genomic variant 7h in 85.7% (12/14) and genomic variant 7i in 14.3% (2/14).Mean age was 8.8 ±; 6 months, and male to female ratio was 3.8: 1. At admission, pneumonia was observed in 71% of the cases and bronchiolitis in 29%. Malnutrition occurred in 37% of the cases; tachypnea in 79%; chest indrawing in 66%; wheezing in 58%; apneas in 16%; and conjunctivitis in 29%. Blood cultures for bacteria and antigen detection of other respiratory viruses were negative.During hospitalization, fatality rate was 16.7% (4 /24). Of the patients who died, three had Ad 7h and one Ad 7i. Thus, fatality rate for adenovirus type 7 reached 28.6% (4/14).ConclusionsThese results show the predominance of adenovirus 7 and high lethality associated with the genomic variants 7h and 7i in children hospitalized with acute lower respiratory infection.

Mink Lung Cells and Mixed Mink Lung and A549 Cells for Rapid Detection of Influenza Virus and Other Respiratory Viruses

Mink lung cells were more sensitive than the commonly used MDCK or pRhMK cells for rapid detection of influenza virus A from clinical specimens. Mixed Mv1Lu and A549 cells in a single shell vial were synergistic for detection of influenza virus A and were as sensitive as individual cells for detection of other respiratory viruses.

Direct and indirect fluorescent-antibody staining techniques using commercial monoclonal antibodies for detection of respiratory syncytial virus

A comparison was made between direct and indirect fluorescent-antibody staining techniques using commercial monoclonal antibodies for detection of respiratory syncytial virus in respiratory secretions. Overall agreement between the two tests was 94%. Using virus isolation as the reference method, the indirect test had a higher sensitivity but a similar specificity when compared with the direct test. The slight delay in reporting using the indirect technique is not clinically significant and is offset by the possibility of convenient combination of the technique with indirect fluorescent-antibodies for detection of other respiratory viruses in respiratory secretions.

Intranasal interferon (rIFN-αA, Ro 22-8181) for contact prophylaxis against common cold: A randomized, double-blind and placebo-controlled field study

The prophylactic efficacy of low-dose intranasal recombinant leucocyte interferon alpha (rIFN-αA, Ro 22-8181) was investigated under field conditions in 147 families ( n = 587 participants), randomized to receive placebo or rIFN-αA intranasally in daily doses of 1.5 or 0.3 × 10 6 IU. Treatment was started within 2 days after the appearance of an index case in the household and was continued for 5 days. Clinical data of the index case and of all members of the household were recorded for 10 days. In index cases and all ill contact persons nasal washes were collected for rhinovirus isolation and immunochemical detection of other respiratory viruses. The local tolerance of the intranasal rIFN-αA was excellent. Both doses of rIFN-αA failed to exert therapeutic effects on established common cold or to prevent the spread of common cold within families. Prophylactic treatment with 1.5 × 10 6 IU did however shorten the duration of the cold (median of 2 days vs. 4 in the placebo group, P = 0.01) and reduced the severity of any ensuing common cold (median total score of 10.5 vs. 30, P < 0.001). No correlation was found between viral etiology (55% rhinoviruses vs. 13% other respiratory viruses, n = 122 nasal washes) and prophylactic efficacy or clinical severity.