Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai

Wang, Wei; Cavailler, Philippe; Ren, Pengpeng; Zhang, Jing; Dong, Wei; Yan, Huajie; Mardy, Sek; Cailhol, Johann; Buchy, Philippe; Sheng, Jun; Fontanet, Arnaud; Denis, Vincent

doi:10.1016/j.jcv.2010.08.005

Cited by 45 publications

(38 citation statements)

References 42 publications

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“…Seasonal cycles in temperature and absolute humidity, rather than relative humidity, may be the critical factors controlling seasonal variations in viruses and bacteria in the atmosphere. Thus, the high incidence of respiratory infections caused by viruses in the winter, such as respiratory syncytial virus, human rhinovirus, human bocavirus, and influenza virus, might be due to a correlation between high viral abundance and meteorological characteristics (39,68,71). Moreover, the lack of any significant difference in viral and bacterial abundances among sites may be attributable to similar meteorological conditions at the three sites (see Table S1 in the supplemental material).…”

Section: Discussionmentioning

confidence: 99%

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

Whon

Kim

Roh

et al. 2012

J Virol

118

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Airborne viruses are expected to be ubiquitous in the atmosphere but they still remain poorly understood. This study investigated the temporal and spatial dynamics of airborne viruses and their genotypic characteristics in air samples collected from three distinct land use types (a residential district [RD], a forest [FR], and an industrial complex [IC]) and from rainwater samples freshly precipitated at the RD site (RD-rain). Viral abundance exhibited a seasonal fluctuation in the range between 1.7 ؋ 10 6 and 4.0 ؋ 10 7 viruses m ؊3 , which increased from autumn to winter and decreased toward spring, but no significant spatial differences were observed. Temporal variations in viral abundance were inversely correlated with seasonal changes in temperature and absolute humidity. Metagenomic analysis of air viromes amplified by rolling-circle phi29 polymerase-based random hexamer priming indicated the dominance of plant-associated single-stranded DNA (ssDNA) geminivirus-related viruses, followed by animal-infecting circovirus-related sequences, with low numbers of nanoviruses and microphages-related genomes. Particularly, the majority of the geminivirus-related viruses were closely related to ssDNA mycoviruses that infect plant-pathogenic fungi. Phylogenetic analysis based on the replication initiator protein sequence indicated that the airborne ssDNA viruses were distantly related to known ssDNA viruses, suggesting that a high diversity of viruses were newly discovered. This research is the first to report the seasonality of airborne viruses and their genetic diversity, which enhances our understanding of viral ecology in temperate regions.

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Section: Discussionmentioning

confidence: 99%

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

Whon

Kim

Roh

et al. 2012

J Virol

118

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“…In China, HBoV-1 was detected in children with positive rates ranging from 4.6 % to 31.0 % [6,[14][15][16][17][18]. However, HBoV-1 was co-detected frequently with other viruses in patients with respiratory or enteric infections; therefore, the impact of HBoV-1 on ARTI occurrence remains unclear.…”

Section: Introductionmentioning

confidence: 99%

Epidemic and molecular evolution of human bocavirus in hospitalized children with acute respiratory tract infection

Wang

et al. 2014

Eur J Clin Microbiol Infect Dis

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Human bocavirus (HBoV) is a novel parvovirus, often associated with respiratory tract diseases in children. This study explored the epidemiological characteristics and molecular evolution of HBoV-1 in southeastern China. Nasopharyngeal aspirates were collected from children admitted to hospital with acute respiratory tract infections. HBoV-1 was detected using real-time reverse transcription polymerase chain reaction and further characterized by complete genome sequences analysis. Among the 3,022 recruited children, 386 (12.77%) were HBoV-1-positive and 300 (77.72%) had co-detection with other respiratory viruses. Seasonal prevalence peaked in summer. HBoV-1 presence was significantly associated with asthma attack [odds ratio = 1.74; 95 % confidence interval: 1.30, 2.31; p < 0.001]. Similar results were obtained when either single detection or co-detection of HBoV-1 was considered, demonstrating the minor impact of co-detection on the clinical characteristics or epidemic pattern. Phylogenetic analysis based on the complete genome sequences showed that all the HBoV-1 sequences clustered together and no branch was formed that was supported by bootstrap value ≥ 750. The overall evolutionary rate of the complete genome of HBoV-1 was estimated at 1.08 × 10(-4) nucleotide substitutions per site per year (s/s/y) [95% highest probability density: (0.40-1.86) × 10(-4) s/s/y]. Selective pressure analysis showed that all the ω-values were less than 1, suggesting that HBoV-1 was under negative selective pressure. Site-by-site analysis identified the codon site 40 of the VP1 gene under positive selection. In conclusion, our study disclosed the epidemiological and genetic dynamics of HBoV-1 epidemics in southeastern China in the most recent 3 years, the information of which might help to further improve our understanding of HBoV-1 infection and guide better surveillance and control strategies in the future.

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“…However, incidences of adenovirus-associated illnesses are higher among children than among adults. As such, in China, the impact of HAdVs on respiratory infection is well characterized in children [10][11][12][13][14][15] but not in adults.…”

Section: Introductionmentioning

confidence: 99%

Detection of three human adenovirus species in adults with acute respiratory infection in China

Guo

Gonzalez

Zhou

et al. 2011

Eur J Clin Microbiol Infect Dis

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Human adenoviruses (HAdVs) are recognized as causal agents in a wide range of human diseases. However, researchers lack sufficient data on the exact HAdV species and serotypes associated with adult acute respiratory tract infections (ARTIs). To detect and characterize HAdV infections in adults in China, clinical specimens were collected from 10,310 adults with ARTIs from May 2005 to July 2010. The partial HAdV hexon gene was amplified by polymerase chain reaction (PCR), sequenced, and phylogenetically analyzed. HAdVs were detected in 86 samples (0.8%), of which 67 (77.9%) were species B (HAdV-3, -7, -11, and -14), 7 (8.1%) were species C (HAdV-1, -2, and -6), and 12 (14%) were species E (HAdV-4). HAdV-3 was the most frequently detected serotype (41/86, 47.7%), followed by HAdV-7 (13/86, 15.1%), HAdV-4 (12/86, 14.0%), and HAdV-11 (11/86, 12.8%). Patients 14-25 years old (60.5%) exhibited a higher rate of adenovirus detection than older patients. Co-infections with other respiratory viruses were observed in samples positive for HAdV species B and E. Human rhinovirus was the most commonly found virus in patients with HAdV infection. These findings provide baseline data for the surveillance and control of HAdV infection in China.

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Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai

Cited by 45 publications

References 42 publications

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

Epidemic and molecular evolution of human bocavirus in hospitalized children with acute respiratory tract infection

Detection of three human adenovirus species in adults with acute respiratory infection in China

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