BackgroundNext-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing.ResultsIn this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i) k-mer-based error correction (KEC) and (ii) empirical frequency threshold (ET). Both were compared to a previously published clustering algorithm (SHORAH), in order to evaluate their relative performance on 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. All three algorithms show similar accuracy in finding true haplotypes. However, KEC and ET were significantly more efficient than SHORAH in removing false haplotypes and estimating the frequency of true ones.ConclusionsBoth algorithms, KEC and ET, are highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses.The implementations of the algorithms and data sets used for their testing are available at: http://alan.cs.gsu.edu/NGS/?q=content/pyrosequencing-error-correction-algorithm

WHAT'S KNOWN ON THIS SUBJECT: Human rhinovirus has been known as the common cold agent. Recently, studies have reported that this virus is responsible for severe infections of the lower respiratory tract in children. Reports of factors that increase disease severity have been contradictory. WHAT THIS STUDY ADDS:This study identifies some of the factors involved in disease severity in HRV infections in children. We expect that children at risk for developing severe disease could be identified sooner and appropriate measures could be taken. abstract OBJECTIVE: To evaluate retrospectively human rhinovirus (HRV) infections in children up to 5 years old and factors involved in disease severity.METHODS: Nasopharyngeal aspirates from 434 children presenting a broad range of respiratory infection symptoms and severity degrees were tested for presence of HRV and 8 other respiratory viruses. Presence of host risk factors was also assessed.RESULTS: HRV was detected in 181 (41.7%) samples, in 107 of them as the only agent and in 74 as coinfections, mostly with respiratory syncytial virus (RSV; 43.2%). Moderate to severe symptoms were observed in 28.9% (31/107) single infections and in 51.3% (38/74) coinfections (P = .004). Multivariate analyses showed association of coinfections with lower respiratory tract symptoms and some parameters of disease severity, such as hospitalization. In coinfections, RSV was the most important virus associated with severe disease. Prematurity, cardiomyopathies, and noninfectious respiratory diseases were comorbidities that also were associated with disease severity (P = .007).CONCLUSIONS: Our study showed that HRV was a common pathogen of respiratory disease in children and was also involved in severe cases, causing symptoms of the lower respiratory tract. Severe disease in HRV infections were caused mainly by presence of RSV in coinfections, prematurity, congenital heart disease, and noninfectious respiratory disease. Pediatrics 2014;133:e312-e321 AUTHORS:

Respiratory syncytial virus (RSV) is well recognized as the most important pathogen causing acute respiratory disease in infants and

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The main viruses involved in acute respiratory diseases among children are: respiratory syncytial virus (RSV), influenzavirus (FLU), parainfluenzavirus (PIV), adenovirus (AdV), human rhinovirus (HRV), and the human metapneumovirus (hMPV). The purpose of the present study was to identify respiratory viruses that affected children younger than five years old in Uberlândia, Midwestern Brazil. Nasopharyngeal aspirates from 379 children attended at Hospital de Clínicas (HC/UFU), from 2001 to 2004, with acute respiratory disease, were collected and tested by immunofluorescence assay (IFA) to detect RSV, FLU A and B, PIV 1, 2, and 3 and AdV, FLU A and B in 9.5% (36/379), PIV 1, 2 and 3 in 6.3% (24/ 379) and AdV in 3.7% (14/379). HRV were detected in 29. 6% (112/379) Viruses are the most frequent agents that cause acute respiratory infections (ARIs) and are responsible for a considerable percentage of childhood mortality (Williams et al. 2002). In Brazil, some reports from different geographical areas has revealed the viruses as the main cause of respiratory infections, as related in the cities of Fortaleza (Arruda et al. 1991), Rio de Janeiro (Nascimento et al. 1991), São Paulo (Miyao et al. 1999, Vieira et al. 2001), and Curitiba (Tsuchiya et al. 2005.The most important viruses involved in ARI are: respiratory syncytial virus (RSV), influenzaviruses types A and B (FLU A/B), parainfluenzavirus (PIV), adenovirus (AdV), human rhinovirus (HRV), and the human metapneumovirus (hMPV) (Miyao et al. 1999, Kuiken et al. 2003, Tsuchiya et al. 2005). The last one was recently identified by Hoogen et al. (2001).RSV is the main cause of viral lower respiratory tract illness in children (Miyao et al. 1999), particularly in those younger than six months old (mo.) (Queiróz et al. 2002. In addition, RSV infections are responsible for most cases of severe symptoms such as bronchiolitis with recurrent wheezing and pneumonia (Calegari et FLU is a serious public health problem worldwide, were children constitute the age group most affected (Neuzil et al. 2002). Although many infections caused by FLU could be prevented by effective vaccination program, it has been predicted that a pandemic is likely to emerge in a near future (Cox et al. 2003), caused by a virus variant not covered by the current vaccine, requiring, thus, a constant epidemiological surveillance.PIV seems to have pattern of seasonal occurrence and is considered an important cause of respiratory illnesses, particularly among young children (Monto 2002).AdV infections are common in all age groups, causing both hospital-and community-acquired epidemics. Moreover, AdV has been associated with hospitalizations of near-fatal asthma patients (Tan et al. 2003) and with cases of acute otitis media in children younger than two years old (Monobe et al. 2003).HRV is responsible for the majority of common colds during winter, causing upper respiratory infections (Arruda et al. 1991, Savolainen et al. 2003 and is considered a risk factor for acute otitis media (Monobe at al. 2003). ...