Daryl Lamson

MassTag Polymerase-Chain-Reaction Detection of Respiratory Pathogens, Including a New Rhinovirus Genotype, That Caused Influenza-Like Illness in New York State during 2004–2005

Abstract In New York State during winter 2004, there was a high incidence of influenza-like illness that tested negative both for influenza virus, by molecular methods, and for other respiratory viruses, by virus culture. Concern that a novel pathogen might be implicated led us to implement a new multiplex diagnostic tool. MassTag polymerase chain reaction resolved 26 of 79 previously negative samples, revealing the presence of rhinoviruses in a large proportion of samples, half of which belonged to a previously uncharacterized genetic clade. In some instances, knowledge of the detected viral and/or bacterial (co)infection could have altered clinical management

Evaluation of the RIDAQuick norovirus immunochromatographic test kit

BACKGROUND Norovirus infections occur frequently and are widespread throughout the US population causing greater than half of all foodborne gastroenteritis cases. A rapid norovirus assay would be a useful clinical tool for identification of this common virus in gastroenteritis patient samples, thereby identifying outbreaks and facilitating rapid implementation of control measures. OBJECTIVES To determine the suitability of the RIDAQuick norovirus kit as a clinical tool by determining the specificity and sensitivity of the assay, and its cross-reactivity with other enteric viruses. STUDY DESIGN Archived stool specimens containing norovirus genogroup I or II or other viruses were tested using the RIDAQuick norovirus assay and results compared to those obtained with real-time RT-PCR. RESULTS We tested 62 samples: 19 norovirus genogroup I, 25 genogroup II samples, and 18 norovirus negative samples. Compared to PCR results, RIDAQuick assay sensitivity was 61.4%, and specificity was 100%. The low sensitivity was mainly due to poor results with genogroup I specimens; only 11 of 19 were detected. Additionally, samples of four other common enteric viruses all tested negative with the RIDAQuick assay. CONCLUSIONS The RIDAQuick kit effectively detects norovirus genogroup II strains, but not genogroup I strains. We found no cross-reactivity with several common enteric viruses. As most norovirus cases are currently genogroup II strains, positive results with RIDAQuick can be used for rapid detection of norovirus in a large percentage of cases, thus also aiding in identification of outbreaks. However, final confirmation and negative results require further testing with more sensitive methods.

Phylogenetic analysis of human metapneumovirus from New York State patients during February through April 2010

BACKGROUND Human metapneumovirus (hMPV) is the second leading cause of lower respiratory infection (LRI) in children around the world and has been linked to LRI in multiple studies. Currently, hMPV is classified into 2 major subtypes (A and B), each with 2 subgroups (1 and 2). OBJECTIVE To determine which hMPV genotypes were present in NYS patients with influenza-like illness (ILI) from February through April 2010, during a period of unusually heightened activity. STUDY DESIGN Specimens were collected from February through April of 2010 from patients presenting with ILI who were previously confirmed as positive for hMPV by real-time RT-PCR. A 700 base pair region of the hMPV fusion (F) gene was amplified, sequenced and resulting sequences aligned. A phylogenic tree was constructed based on prototype strains, and the partial F gene sequences obtained in this study. RESULTS Bi-directional sequence was obtained from 30 patient samples and included in the phylogenic analysis. Specimen sequences grouped into hMPV genotype A2a (16), A2b (9), B2 (4) and B1 (1). No A1 genotypes were found. CONCLUSION Previously, reports have demonstrated that genotypes A1, A2, B1 and B2 circulate every season, usually with one dominant strain. In contrast, late in the 2009-2010 respiratory season, 4 of the 5 recognized genotypes of hMPV were isolated from NYS ILI patients, and by sequencing a larger portion of the fusion gene, we were able to identify the A2a and A2b genotypes.

Clinical and molecular epidemiology of human rhinovirus infections in patients with hematologic malignancy

Abstract Background Human rhinoviruses (HRVs) are common causes of upper respiratory tract infection (URTI) in hematologic malignancy (HM) patients. Predictors of lower respiratory tract infection (LRTI) including the impact of HRV species and types are poorly understood. Objectives This study aims to describe the clinical and molecular epidemiology of HRV infections among HM patients. Study design From April 2012–March 2013, HRV-positive respiratory specimens from symptomatic HM patients were molecularly characterized by analysis of partial viral protein 1 (VP1) or VP4 gene sequence. HRV LRTI risk-factors and outcomes were analyzed using multivariable logistic regression. Results One hundred and ten HM patients presented with HRV URTI (n =78) and HRV LRTI (n =32). Hypoalbuminemia (OR 3.0; 95% CI, 1.0–9.2; p =0.05) was independently associated with LRTI, but other clinical and laboratory markers of host immunity did not differ between patients with URTI versus LRTI. Detection of bacterial co-pathogens was common in LRTI cases (25%). Among 92 typeable respiratory specimens, there were 58 (64%) HRV-As, 12 (13%) HRV-Bs, and 21 (23%) HRV-Cs, and one Enterovirus 68. LRTI rates among HRV-A (29%), HRV-B (17%), and HRV-C (29%) were similar. HRV-A infections occurred year-round while HRV-B and HRV-C infections clustered in the late fall and winter. Conclusions HRVs are associated with LRTI in HM patients. Illness severity is not attributable to specific HRV species or types. The frequent detection of bacterial co-pathogens in HRV LRTIs further substantiates the hypothesis that HRVs predispose to bacterial superinfection of the lower airways, similar to that of other community-acquired respiratory viruses.

Detection of coxsackievirus A10 in multiple tissues of a fatal infant sepsis case

Non-polio enteroviruses are a common cause of childhood infections varying in symptomatology and severity. While infections with many of the enterovirus serotypes can be severe and even fatal, coxsackievirus A10 (CVA10) has most commonly been associated with more mild disease. Here we present the detection of CVA10 in multiple organ tissues in the investigation of an infant death.

Pediatric Adenovirus Infection: Relationship of Clinical Spectrum, Seasonal Distribution, and Serotype

Adenovirus is a common virus found worldwide. A total of 53 serotypes have been identified. It is primarily associated with respiratory, gastrointestinal, and conjunctival illness, which distinguishes it from other exclusively respiratory or gastrointestinal viruses. It may also be recovered from humans without any apparent clinical disease and was, in fact, first isolated from the tonsils and adenoids in children undergoing tonsillectomy and adenoidectomy. Although it does not display a definite seasonal pattern, peaks of adenoviral disease may occur throughout the year, another feature that distinguishes it from respiratory viruses such as respiratory syncytial virus (RSV) and influenza virus, which occur during winter, or a gastrointestinal virus such as rotavirus, which occurs in winter. The lack of a seasonal distribution hinders the diagnosis of adenoviral infection. Similarly, prolonged excretion of adenovirus in the respiratory or gastrointestinal tracts may diminish the diagnostic relevance of the presence of the virus in clinical specimens. The present study examines the relationship between symptom complexes, month of presentation, and serotype of adenoviruses in children.

Detection and Genetic Characterization of Adenovirus Type 14 Strain in Students with Influenza-Like Illness, New York, USA, 2014–2015

During the 2014–15 influenza season, 13/168 respiratory samples from students with influenza-like illness (ILI) at a college in New York, USA, were positive for human adenovirus (HAdV); 4/13 samples were positive for HAdV-B14p1. During influenza season, HAdV should be included in the differential diagnostic panel used to determine the etiology of ILI.

Pseudo-Outbreak of Adenovirus Infection in a Neonatal Intensive Care Unit Due to a False-Positive Antigen Detection Test

ABSTRACT Twenty-eight of 56 infants in a neonatal intensive care unit had stools positive for adenovirus by the Sure-Vue adenovirus test. Virus cultures of conventionally processed and chloroform-extracted stool samples, as well as conventional and real-time PCR tests, were negative for adenovirus. The cause for the 50% false-positive rate with the antigen test was not determined.

Identification of a novel intertypic recombinant species D human adenovirus in a pediatric stem cell transplant recipient

BACKGROUND Human adenoviruses (HAdV) are known opportunistic pathogens in hematopoietic stem cell transplant (SCT) recipients. The detection of HAdV infection in children after SCT has been implicated as a determinant of poor outcome but specific associations between HAdV species or individual HAdV types and disease are poorly understood. OBJECTIVES Characterization of a HAdV-D strain isolated from multiple clinical specimens of an 11-year-old female recipient of a matched unrelated donor peripheral SCT for T-cell lymphoma and case report. STUDY DESIGN Archived HAdV PCR-positive plasma, urine, and stool specimens were processed for virus isolation and detailed molecular typing. Complete genomic sequencing was carried out on 2 isolates. RESULTS The patient tested positive for HAdV DNA by real-time PCR of a stool specimen at 44 days after initiation of a SCT conditioning regimen. In the subsequent 3 months, HAdV was detected in plasma, urine and stool specimens in association with symptoms of gastroenteritis and hemorrhagic cystitis. A novel HAdV-D with a HAdV20-like hexon gene was isolated from both urine and stool specimens. All isolates yielded identical restriction profiles with endonucleases BamHI, BglII, BstEII, HindIII, PstI and SmaI. Analysis of 2 complete genomic sequences further identified the virus as a novel intertypic recombinant HAdV-D (P20/H20/F42) closely related to HAdV42. CONCLUSIONS This case highlights the identification of a previously unknown HAdV-D from an immunocompromised host. In this patient, the course of adenovirus infection is compatible with reactivation of a latent virus or a primary opportunistic infection. Adenoviremia in this patient resolved without definitive adenovirus-directed antiviral therapy.

Incidence of respiratory viral infection in infants with respiratory symptoms evaluated for late-onset sepsis

Objective:To determine the frequency, etiology and impact of respiratory viral infection (RVI) on infants evaluated for late-onset sepsis (LOS), defined as sepsis occurring >72 h of life, in the neonatal intensive care unit.Study design:Prospective observational study conducted from 6 March 2014 to 3 May 2016 on infants evaluated for LOS. PCR viral panel performed on nasopharyngeal specimens among infants with clinical suspicion for RVI. Sequence analysis was performed to determine viral subtypes. Fisher’s exact or χ2 tests were done to determine the impact of RVI.Results:During the 26-month study, there were 357 blood cultures obtained for LOS evaluations, 29 (8%) had a respiratory virus detected. Only 88 (25%) of infants evaluated for LOS also had clinical suspicion for a respiratory viral infection. RSV (14 of 29; 48%) was the predominant virus detected. Almost all infants (13 of 14; 93%) with RSV required increased respiratory support. Antimicrobial therapy was withheld or discontinued on most infants with a virus detected (18 of 29; 62%) and in the majority where there was no confirmed bacterial co-infection (18 of 20; 90%).Conclusion:The incidence of RVI in infants being evaluated for LOS is about 8%. RVI should be considered in LOS evaluation to prevent unnecessary antibiotic therapy.