Genetic variability of human metapneumo- and bocaviruses in children with respiratory tract infections

Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022

The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next-generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in-house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co-infection. Subsequent HAdV typing for HBoV1-positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1-associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.

Outcomes of viral coinfections in infants hospitalized for acute bronchiolitis

BACKGROUND AND OBJECTIVE

The clinical relevance of the detection of multiple respiratory viruses in acute bronchiolitis (AB) has not been established. Our goal was to evaluate the effect of viral coinfections on the progression and severity of AB.

METHODS

A retrospective observational study was conducted in a tertiary hospital in Spain from September 2012 to March 2020. Infants admitted for AB with at least one respiratory virus identified by molecular diagnostic techniques were included. A comparison was made between single-virus infections and viral coinfections. The evolution and severity of AB were determined based on the days of hospitalization and admission to the pediatric intensive care unit (PICU).

RESULTS

Four hundred forty-five patients were included (58.4% male). The median weight was 5.2 kg (IQR 4.2-6.5), and the median age was 2.5 months (IQR 1.4-4.6). A total of 105 patients (23.6%) were admitted to the PICU. Respiratory syncytial virus (RSV) was the most frequent etiological agent (77.1%). A single virus was detected in 270 patients (60.7%), and viral coinfections were detected in 175 (39.3%), of which 126 (28.3%) had two viruses and 49 (11%) had three or more viruses. Hospital length of stay (LOS) increased in proportion to the number of viruses detected, with a median of 6 days (IQR 4-8) for single infections, 7 days (IQR 4-9) for coinfections with two viruses and 8 days (IQR 5-11) for coinfections with ≥ 3 viruses (p = 0.003). The adjusted Cox regression model showed that the detection of ≥ 3 viruses was an independent risk factor for a longer hospital LOS (HR 0.568, 95% CI 0.410-0.785). No significant association was observed between viral coinfections and the need for PICU admission (OR 1.151; 95% CI 0.737-1.797).

CONCLUSIONS

Viral coinfections modified the natural history of AB, prolonging the hospital LOS in proportion to the number of viruses detected without increasing the need for admission to the PICU.

Human Bocavirus infection among children with respiratory tract infection in Ibadan, Nigeria

Background. Human Bocavirus (HBoV), which is an ssDNA virus of the family Parvoviridae, is responsible for 21.5 % of childhood respiratory tract infections (RTIs) annually. Among the four genotypes currently known, HBoV-1 has been associated with acute RTI. Although there have been studies on HBoV in some countries, there is limited information on this virus in sub-Saharan Africa where there is the highest burden of RTI. This study aimed to characterize the circulating strains of HBoV in Ibadan, Nigeria.

Methods. Nasopharyngeal and oropharyngeal swab samples were collected from 333 children ≤5 years old presenting with RTI attending hospitals in Ibadan, whose parents assented, from 2014 to 2015. Twenty-three HBoV isolates were sequenced after a nested PCR and phylogenetic analysis was carried out using mega 6 software.

Prevalence and Genetic Characteristics of Human Bocaviruses Detected in Patients with Acute Respiratory Infections in Bulgaria

Нuman bocaviruses (hBoVs) are often associated with acute respiratory infections (ARIs). Information on the distribution and molecular epidemiology of hBoVs in Bulgaria is currently limited. The objectives of this study were to investigate the prevalence and genetic characteristics of hBoVs detected in patients with ARIs in Bulgaria. From October 2016 to September 2019, nasopharyngeal/oropharyngeal swabs were prospectively collected from 1842 patients of all ages and tested for 12 common respiratory viruses using a real-time RT-PCR. Phylogenetic and amino acid analyses of the hBoV VP1/VP2 gene/protein were performed. HBoV was identified in 98 (5.3%) patients and was the 6^th most prevalent virus after respiratory-syncytial virus (20.4%), influenza A(H1N1)pdm09 (11.1%), A(H3N2) (10.5%), rhinoviruses (9.9%), and adenoviruses (6.8%). Coinfections with other respiratory viruses were detected in 51% of the hBoV-positive patients. Significant differences in the prevalence of hBoVs were found during the different study periods and in patients of different age groups. The detection rate of hBoV was the highest in patients aged 0-4 years (6.9%). In this age group, hBoV was the only identified virus in 9.7%, 5.8%, and 1.1% of the children diagnosed with laryngotracheitis, bronchiolitis, and pneumonia, respectively. Among patients aged ≥5 years, hBoV was detected as a single agent in 2.2% of cases of pneumonia. Phylogenetic analysis showed that all Bulgarian hBoV strains belonged to the hBoV1 genotype. A few amino acid substitutions were identified compared to the St1 prototype strain. This first study amongst an all-age population in Bulgaria showed a significant rate of hBoV detection in some serious respiratory illnesses in early childhood, year-to-year changes in the hBoV prevalence, and low genetic variability in the circulating strains.

A review on epidemiology and impact of human metapneumovirus infections in children using TIAB search strategy on PubMed and PubMed Central articles

Acute respiratory tract infections (ARTI) contribute to morbidity and mortality in children globally. Viruses including human metapneumovirus (hMPV) account for most ARTIs. The virus causes upper and lower respiratory tract infections mostly in young children and contributes to hospitalization of individuals with asthma,chronic obstructive pulmonary diseases and cancer. Moreover, hMPV pauses a considerable socio-economic impact creating a substantial disease burden wherever it has been studied, although hMPV testing is relatively new in many countries. We aimed to comprehensively analyze the epidemiological aspects including prevalence, disease burden and seasonality of hMPV infections in children in the world. We acquired published data extracted from PubMed and PubMed Central articles using the title and abstract (TIAB)search strategy for the major key words on hMPV infections from 9/54 African, 11/35 American, 20/50 Asian, 2/14 Australian/Oceanian and 20/51 European countries. According to the findings of this review, the prevalence of hMPV infection ranges from 1.1 to 86% in children of less than 5 years of age globally. Presence of many hMPV genotypes (A1, A2, B1, B2) and sub-genotypes (A2a, A2b, A2c, B2a, B2b) suggests a rapid evolution of the virus with limited influence by time and geography. hMPV infection mostly affects children between 2 to 5 years of age. The virus is active throughout the year in the tropics and epidemics occur during the winter and spring in temperate climates, contributing to a substantial disease burden globally.

Phylogenic analysis of human bocavirus detected in children with acute respiratory infection in Yaounde, Cameroon

Objective

Human Bocavirus (HBoV) was first identified in 2005 and has been shown to be a common cause of respiratory infections and gastroenteritis in children. In a recent study, we found that 10.7% of children with acute respiratory infections (ARI) were infected by HBoV. Genetic characterization of this virus remains unknown in Central Africa, particularly in Cameroon Leeding us to evaluate the molecular characteristics of HBoV strains in Cameroonian children with ARI.

Results

Phylogenetic analysis of partial HBoV VP1/2 sequences showed a low level of nucleotide variation and the circulation of HBoV genotype 1 (HBoV-1) only. Three clades were obtained, two clustering with each of the reference strains ST1 and ST2, and a third group consisting of only Cameroon strains. By comparing with the Swedish reference sequences, ST1 and ST2, Cameroon sequences showed nucleotide and amino acid similarities of respectively 97.36–100% and 98.35–100%. These results could help improve strategies for monitoring and control of respiratory infections in Cameroon.

Evolutionary and genetic analysis of human bocavirus genotype-1 strains reveals an evidence of intragenomic recombination

PURPOSE

Human bocavirus (HBoV) exsits in four genotypes: 1 to 4, with HBoV-1 being the most prevalent genotype. The aim of the current study was to genetically analyze the full-length genome of the HBoV-1 of recently detected Egyptian strains.

METHODOLOGY

Seven overlapping sets of primers were developed to amplify an almost complete HBoV-1 genome from the clinical samples. The primer sets were tested on three recently identified Egyptian HBoV-1 strains with viral loads ≥105 ml-1. Sequencing was conducted using the same sets of primers. HBoV-1 virus strains were genetically analyzed based on the sequences of their complete genomes and the individual ORFs.

RESULTS

The new sets of primers successfully amplified the three tested strains. Sequence analysis of the full-length genome of the HBoV-1 revealed a considerable level of genetic heterogenicity between different strains. Based on the full genome and VP1 ORF, HBoV-1 viruses were clustered into three main lineages, A to C, and lineage A was further subdivided into three sublineages, A1-A3. The Egyptian strains were clustered within two sublineages, A1 and A2. New amino acid substitutions were detected in NS1 and VP1/VP2 proteins. Both inter- and intragenomic recombination events were detected among the Egyptian strains.

CONCLUSION

The existence of both intragenomic recombination event and multiple amino acid substitutions in the examined Egyptian HBoV-1 strains elucidates considerable level of genetic alterations among bocaviruses. Their possible effects on the virus virulence and multiplication efficiency need to be investigated.

Molecular Epidemiology of Human Metapneumovirus in Riyadh Province, Saudi Arabia

Human metapneumovirus (HMPV) is an important cause of respiratory tract illness in children. Two HMPV subgroups, A and B, and four genotypes, A1, A2, B1 and B2, have been identified. Concurrent circulation of the different genotypes in yearly epidemics has been recorded globally, but not in Saudi Arabia. The current report was designed to study HMPV epidemiology in Saudi children and to analyze the genetic diversity and circulation patterns. Nasopharyngeal aspirates (n = 174) were collected from hospitalized children in Riyadh (2008-2009). The screening of samples using real-time RT-PCR identified 19 HMPV strains. The majority of the strains belonged to subgroup B, while all strains of subgroup A were members of genotype A2. In 2008, only subgroup B was recognized, whereas in 2009 both subgroups were identified to be cocirculating at similar rates. The full-length attachment (G) gene and a partial sequence of the fusion (F) gene of positive samples were sequenced. The G gene showed a high degree of genetic diversity and exhibited a variable number of positively selected sites in different lineages. In contrast, the F gene demonstrated an extensive genetic stability with a higher tendency toward purifying selection. This is the first report on HMPV genotype circulation in Saudi Arabia; however, the exact circulation kinetics requires further retrospective and prospective study.

Genetic characterization of human bocavirus among children with severe acute respiratory infection in China

OBJECTIVES

To investigate the genetic character of Human bocavirus (HBoV) among children with severe acute respiratory infection (SARI) in China.

METHODS

We screened 993 respiratory samples for HBoV by PCR among hospitalized children with SARI between September 2007 and March 2014. Four of HBoV1 samples were selected for complete genomes analysis by next-generation sequencing.

RESULTS

The results show that 200 (20.1%) out of 993 samples were HBoV-positive, most of these HBoV belong to HBoV1 subtype (n = 197), HBoV2 (n = 1) and HBoV3 (n = 2) were also detected. Fifty (5.04%) of 993 SARI patient were detected as HBoV-positive only. Four HBoV1 genomes in this study were conserved and showed no significant difference among the nucleotide diversity from different regions. Analyses of evolutionary rates showed that NS1 exhibited the highest degree of conservation while the VP1 gene exhibited the fastest rate of evolution at 4.20 × 10(-4) substitutions/site/year. The nucleotide deletions and substitutions occurred in NP1 and VP1 represented novel molecular signatures enabling subtype differentiation between HBoVs.

CONCLUSIONS

We described some new characteristics in the epidemiology of HBoV among children with SARI, these data will significantly expand the current knowledge of HBoV epidemic and genomic characterization among children with SARI.