LAUSR

Human adenoviruses (HAdVs) are associated with respiratory, gastrointestinal, ophthalmological, genitourinary, and neurological infections. To date, more than 100 genotypes of HAdVs have been identified. They are classified into seven species, A to G (HAdV Working Group, http://hadvwg.gmu.edu/). HAdVs associated with lower respiratory tract infection endanger children’s health due to their poor prognosis, high mortality, severe complications, and serious sequelae (Hong et al. 2001). In 2012, an outbreak of adenovirus pneumonia occurred in Shenzhen. During that period, HAdV-B7 and HAdV-B3 were identified as dominant types and the children’s symptoms were generally mild (Wang et al. 2015). In 2017, another outbreak of adenovirus pneumonia with more severe symptoms occurred in Shenzhen. To increase physicians’ awareness of adenovirus pneumonia and improve clinical practice, we reviewed the clinical characteristics of adenovirus pneumonia among children in the 2017 Shenzhen outbreak. Fifty-seven children diagnosed with adenovirus pneumonia between April and July 2017 were included in this study. All patients had fever and coughing. Twenty-eight patients were diagnosed with mild pneumonia, the other 29 patients were diagnosed with severe pneumonia. Severe adenovirus pneumonia was more common in patients with the following characteristics: (1) age B 2 years old; (2) higher level of C-reactive protein (CRP) and procalcitonin (PCT); (3) atelectasis in chest computerized tomography (CT); (4) presence of extrapulmonary complications (Table 1). Nasopharyngeal (NP) secretions of all the patients were collected and tested for antigens of adenovirus, respiratory syncytial virus, parainfluenza virus (type 1, 2, 3), and influenza virus (type A and B) using a D3 UltraTM DFA (direct fluorescent antibody) Respiratory Virus Screening and Identification Kit (Diagnostic Hybrids, Inc. US). The NP specimens of 28 mild pneumonia patients were tested positive for adenovirus. Bronchoscopy and adenovirus typing were not performed in any of the patients. The other 29 patients diagnosed with severe pneumonia were tested negative for adenovirus and underwent bronchoalveolar lavage (BAL). Metagenomics next-generation sequencing (mNGS) and DFA respiratory virus screening were further performed in all the bronchoalveolar lavage fluid (BALF) specimens. In mNGS analysis, nucleic acid (including DNA and RNA) was extracted directly from BALF using the TIANamp DNA/RNA Isolation Kit (DP422, Tiangen Biotech) in accordance with the manufacturer’s standard protocols. Agilent 2100 was used for quality control of the DNA libraries, which were sequenced on BGISEQ-100 platform. All sequencing reagents (PMSEQ) and PMseq software were approved by China Drug Administration (CDA). The sequencing data were deposited in the GenBank database under accession number PRJNA572371. Processed by removing low-quality and short (length\ 35 bp) reads, sequencing data then were aligned with the human reference genome (hg19) to remove human-derived sequences using Burrows–Wheeler Alignment. The remaining data were classified by simultaneously aligning to four Microbial Genome Databases (ftp://ftp.ncbi.nlm.nih.gov/gen omes/), which contains 4152 whole-genome sequence of viral taxa, 3446 bacterial genomes or scaffolds, 206 fungi related to human infection, and 140 parasites associated with human diseases. The number of unique alignment reads was calculated and standardized to get the number of reads stringently mapped to pathogen species (SDSMRN) and the number of reads stringently mapped to pathogen genus (SDSMRNG). In case it was regarded as likely & Yuejie Zheng [email protected]