key: cord-0797491-ni4hpmp7 authors: Cordey, Samuel; Zanella, Marie‐Celine; Wagner, Noemie; Turin, Lara; Kaiser, Laurent title: Novel human astroviruses in pediatric respiratory samples: A one‐year survey in a Swiss tertiary care hospital date: 2018-07-16 journal: J Med Virol DOI: 10.1002/jmv.25246 sha: 3e5c6597221d05a2dc63f182583bee57fe0b8018 doc_id: 797491 cord_uid: ni4hpmp7 Although classical human astroviruses (HAstV) are known to be a leading cause of viral gastroenteritis, the pathogenesis and clinical manifestations of novel HAstV remain largely unknown. There is mounting evidence that, in contrast to classical astroviruses, novel HAstV exhibit tropism for the upper respiratory tract. This one‐year period prevalence screened all available clinical nasopharyngeal swab samples collected from pediatric patients aged ≤5 years for novel and classical HAstV using real‐time reverse transcription polymerase chain reaction. A total of 205 samples were tested; two novel HAstV cases were detected for a prevalence of 1.3%, with viral loads suggesting active upper respiratory tract replication. No classical HAstV was detected. Classical and novel human astroviruses (HAstV) are nonenveloped, single-stranded RNA viruses belonging to the Astroviridae family. Classical HAstV (serotypes 1-8) are phylogenetically distant from novel HAstV (namely MLB and VA) with amino acid identities being as low as 23% to a maximum of 54.5% depending on the open reading frames. 1 Although classical HAstV are a leading cause of viral gastroenteritis, especially in children, elderly, and immunocompromised patients, 2-4 the clinical manifestations of novel HAstV have not been fully characterized. [5] [6] [7] [8] The spectrum of human diseases for classical and novel HAstV is not restricted to the gastrointestinal tract: both have been reported as causal agents of central nervous system infections. 1 A seroepidemiological study of the novel HAstV MLB1 in the United States suggests that primary infection occurs in childhood, with seropositivity reaching 70%, 90%, and 100% by ages 3, 4-6, and 7-17 years, respectively. 9 A recent survey of classical and novel HAstV in clinical stool samples collected in a tertiary care hospital indicates that, for both viral groups, susceptible populations are young children (≤4 years) and the immunocompromised patients. 10 Yet, for patients with novel HAstV, stool viral loads are lower and upper respiratory tract (URT) symptoms (cough, rhinorrhea, and odynophagia) are more frequent (70%), suggesting a potentially different pathogenic pathway between novel and classical HAstV. Indeed, additional reports of novel HAstV (MLB1, MLB2, and VA1) in pediatric nasopharyngeal specimens continue to emerge. [11] [12] [13] Here, we report the results of a one-year period-prevalence survey of novel and classical HAstV in URT samples collected in pediatric patients in a tertiary care hospital in Switzerland and describe the case presentations of two novel HAstV-positive patients. In this retrospective single-center cohort study, all clinical nasopharyngeal swab (NPS) samples collected at the University Hospitals of Geneva from ambulatory or hospitalized patients aged ≤5 years between 1 October 2016 and 30 September 2017 and with a sufficient leftover volume were analyzed by real-time reverse transcription polymerase chain reaction (rRT-PCR). All NPS samples were collected as a part of routine clinical care to screen both influenza A/B viruses and respiratory syncytial viruses (RSV) A/B or a larger panel of respiratory viruses using the FTD FLU/HRSV and Respiratory pathogens 21 commercial assays (Fast Track Diagnostics, Sliema, Malta), respectively. Samples were collected in universal transport medium (UTM™) Viral Transport (Copan, Brescia, Italy) and stored at −80°C before analysis. Of note, the prevalence of novel and classical HAstV in URT samples was deliberately restricted to NPS samples to ensure that a sufficient leftover volume was available on the vast majority of cases after routine investigations. Each individual NPS specimen (380 μL) was spiked with 20 μL of a standardized canine distemper virus as previously described. 14 Nucleic acids were extracted using the NucliSENS easyMAG (bioMérieux, Geneva, Switzerland) in 100 μL elution volume. Novel and classical HAstV were screened using a set of specific rRT-PCR for MLB1-3 and VA1-4 as previously described. 10 Subjects #1 and #2 both presented with upper respiratory manifestations followed by acute diarrhea, in line with the observations of a previous surveillance study. 10 In particular, the underdiagnosed deletion 22q11, which may cause cardiac malformation and congenital immunodeficiency, was not investigated in this patient. 16 The pathogenic pathways and clinical manifestations of novel HAstV require further characterization. The results obtained in this pilot study underline the need for further investigation using respiratory cell culture systems and prospective studies. Epidemiology of classic and novel human astrovirus: gastroenteritis and beyond Astrovirus biology and pathogenesis Astrovirus infection and diarrhea in 8 countries Astrovirus infection in hospitalized children: molecular, clinical and epidemiological features Astrovirus MLB1 is not associated with diarrhea in a cohort of Indian children Multiple astrovirus MLB1, MLB2, VA2 clades, and classic human astrovirus in children with acute gastroenteritis in Japan Prevalence of classic, MLB-clade and VA-clade astroviruses in Kenya and The Gambia Surveillance of human astrovirus infection in Brazil: the first report of MLB1 astrovirus Seroepidemiology of astrovirus MLB1 Novel and classical human astroviruses in stool and cerebrospinal fluid: comprehensive screening in a tertiary care hospital Astrovirus VA1 identified by nextgeneration sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology Acute encephalopathy in an immunocompromised boy with astrovirus-MLB1 infection detected by next generation sequencing Sequence analysis of the human virome in febrile and afebrile children Critical analysis of rhinovirus RNA load quantification by real-time reverse transcription-PCR The association between immunodeficiency and congenital heart disease Chromosome 22q11.2 deletion syndrome The authors would like to thank Gael Vieille (University Hospitals of Geneva) and Angela Huttner for technical and editorial assistance, respectively. This study was supported by the Swiss National Science Foundation (grant no. 310030_165873 to L Kaiser). The authors declare no conflict of interests. SC and LK, Designed the study. LT, Performed the analysis. SC and MCZ, Analyzed the data. MCZ and NW, Reviewed the medical records. SC and MCZ, wrote the manuscript. http://orcid.org/0000-0002-2684-5680 Additional supporting information may be found online in the Supporting Information section at the end of the article.