key: cord-0898191-gylmwmpq authors: Ferguson, Patricia E.; Gilroy, Nicole M.; Faux, Cassandra E.; Mackay, Ian M.; Sloots, Theo P.; Nissen, Michael D.; Dwyer, Dominic E.; Sorrell, Tania C. title: Human rhinovirus C in adult haematopoietic stem cell transplant recipients with respiratory illness date: 2013-03-31 journal: Journal of Clinical Virology DOI: 10.1016/j.jcv.2012.11.010 sha: 8bb97f186e7855381df305f55156b88182fcc465 doc_id: 898191 cord_uid: gylmwmpq Abstract Background A previously unidentified species of human rhinovirus, HRV-C, was described in 2006 in association with lower respiratory tract infection (LRTI). Features of infection in immunosuppressed adults are poorly characterised. Objectives This study aims to determine the epidemiology of HRV-C in haematopoietic stem cell transplant (HSCT) recipients in a single centre. Study design A prospective cohort study of all HSCT recipients admitted to Westmead Hospital, Westmead, Australia from 1 July 2005 to 30 September 2007 was undertaken. Nose/throat samples were collected from all patients at the time of admission and patients developing pre-defined symptoms and/or signs of respiratory infection during the admission. Samples were processed and tested for rhinoviruses and 14 other respiratory viruses using nucleic acid-based methods, immunofluorescence and culture. HRV genotyping was performed by sequencing a region of the rhinovirus 5′ untranslated region (UTR). Clinical data on each episode were collected prospectively. Results HRVs were identified in 24 episodes: 8% of 299 episodes of clinically- defined respiratory infections and 39% of 61 episodes in which respiratory viruses were detected. HRV-C was most frequent (HRV-C: nine, HRV-A: eight and HRV-B: two). Seven episodes of HRV-C, five with pneumonia, occurred within 100 days of HSCT. Co-pathogens were frequent. Conclusions The newly described HRV-C was the most common rhinovirus group detected in HSCT recipients with respiratory infection, with co-pathogens being frequent. Further research is required to understand the activity and pathogenicity of this virus in HSCT recipients. A previously unidentified human rhinovirus (HRV) species, HRV-C, was described in 2006 1,2 in association with lower respiratory tract infection and wheezing in children. 3, 4 Features of infection in adults are poorly described. While HRVs are the most frequent respiratory viruses detected by polymerase chain reaction (PCR) in adult haematopoietic stem cell transplant (HSCT) allogeneic and 15-25 autologous adult HSCTs annually. Institutional ethics approval was granted. The nursing staff completed a daily check list comprising six clinical features of possible respiratory virus infection: cough; fever >38 • C in the last 24 h; sneezing or runny nose; dyspnoea; oxygen saturation <95% on air; and clinician-documented crackles on chest examination. 7 Paired nose/throat swabs (NTSs) were collected into a viral transport medium (Copan Diagnostics, Murrieta, CA, USA) when ≥2 clinical features were present, and from all patients on admission to the haematology ward regardless of symptoms. Bronchoalveolar lavage (BAL) was performed at the discretion of treating physicians. Repeated A region of the HRV 5 untranslated region (UTR) was sequenced, with a type assigned when it shared ≥97% nucleotide identity with the same region of a fully sequenced HRV using methods described previously (Table 1 ). 9 Briefly, 2 l of nucleic acid extract was reverse transcribed in a total 20 l reaction volume (OneStep RT-PCR kit, QIAGEN, Australia; 50 • C for 60 min), subjected to a hot-start (95 • C for 15 min) then a ∼380 bp complementary DNA (cDNA) was amplified using 45 cycles of 94 • C for 20 s, 55 • C for 20 s and 72 • C for 50 s with a final incubation at 72 • C for 10 min. The product from positive reactions was subjected to nucleotide sequencing using the PRISM BigDye sequencing kit v3.1 (Applied Biosystems, Foster City, CA, USA). Sequence analysis on products ranging from >200 nucleotides (nt) in length was conducted using Geneious Pro. 10 This assay has been shown to be at least as clinically sensitive as others widely used. 11 If an HRV was repeatedly positive in the screening assay but no useful sequence could be obtained it was called untypeable. Sequences containing two picornavirus templates (a member of an enterovirus (EV) and HRV species) that could not be further interpreted were designated "double" infections. A post hoc analysis of all HRV samples and review of clinical data were undertaken. The presence of two or more of rhinorrhoea, sneezing or cough, with a normal chest examination and radiological imaging (chest X-ray or computed tomography). The presence of fever and hypoxia or pulmonary infiltrates reported on radiological imaging. Symptom onset 4 or more days following hospital admission, in keeping with previous definitions. 12,13 Other respiratory viruses (including those detected by PCR), bacteraemia or candidaemia detected from samples collected during the episode of respiratory infection. Respiratory virus testing was performed in 213 of the 299 episodes of respiratory tract information (RTI) from 193 HSCT recipients. In symptomatic patients, the first sample was collected a median of 2 days (range 0-5) following symptom onset. At least one respiratory virus was detected in 61 episodes, with HRV in 24 (39%; 12 URTIs, 12 LRTIs, including four with upper respiratory symptoms). Asymptomatic infection was detected from four of 205 (2.0%) samples (three episodes). Phylogenetic analysis was performed on the 26 HRVs identified by PCR; the viral species was identified in 19 (73%). One culturepositive, PCR-negative isolate was unavailable for sequencing. Four HRVs were untypeable, one showed double infection, one was not reproducible and another was identified as EV-D68 (Table 2) . HRV-C was most frequent (nine, 47%), followed by HRV-A (eight, 42%) and HRV-B (two, 11%) (Tables 2 and 3 ). Pneumonia was present in five of nine episodes with HRV-C (56%), both with HRV-B, and three of eight with HRV-A. Infection was acquired nosocomially in eight episodes. Co-pathogens were present in seven episodes, with co-viruses in six (Table 2) . Invasive ventilation was required in two HRV-C episodes (patients #10 and #12), both with co-pathogens. Patient #10 died from overwhelming sepsis with Haemophilus influenzae bacteraemia and probable invasive aspergillosis within 24 h of symptom onset. While episodes occurred over 26 months (Fig. 1) , a cluster of four cases of HRV-C occurred in July-August 2007. The phylogenetic tree (Fig. 2) shows the same strain (C11) causing two of these episodes; these were nosocomially acquired and related in time and place (cases #12 and #14). The newly described HRV-C was present in almost half of all episodes of rhinovirus infection in this cohort. This follows a report of HRV-C predominance in a cohort of Thai children hospitalised with LRTI. 14 HRV-A has dominated cohorts of adults and children hospitalised with RTI, with HRV-C in 25-35% of episodes. 4, [15] [16] [17] [18] This includes renal transplant recipients and others with immunocompromise. 15, 16 Although HRV-C and HRV-A caused a similar number of episodes, HRV-C had a higher proportion with pneumonia (56% and 38%, respectively), occurring in the early post-transplant period (78% and 38%) and associated with co-pathogens (44% and 25%). An association with HRV-C, but not HRV-A, and pneumonia in adults with underlying medical conditions or advanced age has been noted, 18 but not in all cohorts, including outpatient renal transplant recipients. 16 Seven of the nine episodes of HRV-C occurred within 100 days of HSCT when patients have severe immunosuppression and high infection risk, particularly post allogeneic transplant. While HRV-B and HRV-C were more commonly associated with pneumonia, in only one episode was HRV-C the sole pathogen. The presence of co-pathogens in earlier HRV-C studies is limited to co-virus detections in 8% in adults 17 and 26% in children, 19 with a similar proportion in this cohort. Polyomavirus KI was the most frequent co-virus; however, its clinical importance remains uncertain. 20 This study is limited by the small number of HRV detected from symptomatic samples compared with 30% detection in a prior HSCT cohort 6 in which routine weekly testing occurred within the first 100 days post HSCT, and BAL sampling was frequent in pneumonia. In our study, 52 BAL samples were collected from 223 episodes of pneumonia. A diagnostic BAL was obtained in only one of 12 HRV-associated pneumonias, with the remaining episodes inferred from positive upper respiratory samples. It is recognised that upper respiratory samples are less sensitive in pneumonia 21 and HRV in this setting may be missed. We acknowledge that without lower respiratory samples for histopathology and further microbiologic testing we cannot state definitively that HRV-C caused pneumonia. In summary, HRV-C was detected in adult HSCT recipients with viral RTIs including pneumonia, with the poorest outcomes in the presence of co-pathogens. Patients appear to be most at risk during the early post-HSCT period when immunosuppression is greatest. Further characterisation of the epidemiology and pathogenicity of HRV-C in other geographically representative adult HSCT populations is warranted. All authors report no conflicts of interest relevant to this article. Ethical approval was given by Western Sydney Area Health Service Ethics Committee, HREC2006/2/4.32(2309). Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children Human rhinovirus C associated with wheezing in hospitalised children in the middle east Frequent detection of respiratory viruses in adult recipients of stem cell transplants with the use of real-time polymerase chain reaction, compared with viral culture Human rhinovirus and coronavirus detection among allogeneic hematopoietic stem cell transplantation recipients Evaluation of a clinical scoring system and directed laboratory testing for respiratory virus infection in hematopoietic stem cell transplant recipients Amplification of rhinovirus specific nucleic acids from clinical samples using the polymerase chain reaction Community-wide, contemporaneous circulation of a broad spectrum of human rhinoviruses in healthy Australian preschool-aged children during a 12-month period Usefulness of published PCR primers in detecting human rhinovirus infection Prospective study of the incidence, clinical features, and outcome of symptomatic upper and lower respiratory tract infections by respiratory viruses in adult recipients of hematopoietic stem cell transplants for hematologic malignancies Molecular epidemiology of two consecutive outbreaks of parainfluenza 3 in a bone marrow transplant unit High prevalence of human rhinovirus C infection in Thai children with acute lower respiratory tract disease Clinical severity and molecular typing of human rhinovirus C strains during a fall outbreak affecting hospitalized patients Rhinovirus species and their clinical presentation among different risk groups of non-hospitalized patients Human rhinovirus C infections mirror those of human rhinovirus A in children with community-acquired pneumonia Clinical and molecular epidemiology of human rhinovirus C in children and adults in Hong Kong reveals a possible distinct human rhinovirus C subgroup Role of rhinovirus C respiratory infections in sick and healthy children in Spain The role of polyomaviruses in human disease Rapid-test sensitivity for novel swine-origin influenza A (H1N1) virus in humans Ken McPhie and Mala Ratnamohan for IF and virus isolation.