Surveillance and genome analysis of human bocavirus in patients with respiratory infection in Guangzhou, China

Abstract

Human bocavirus (HBoV) is a novel parvovirus associated with respiratory tract diseases and gastrointestinal illness in adult and pediatric patients throughout the world. To investigate the epidemiological and genetic variation of HBoV in Guangzhou, South China, we screened 3460 throat swab samples from 1686 children and 1774 adults with acute respiratory infection symptoms for HBoV between March 2010 and February 2011, and analyzed the complete genome sequence of 2 HBoV strains. Specimens were screened for HBoV by real-time PCR and other 6 common respiratory viruses by RT-PCR or PCR. HBoV was detected in 58 (1.68%) out of 3460 samples, mostly from pediatric patients (52/58) and inpatient children (47/58). Six adult patients were detected as HBoV positive and 5 were emergency cases. Of these HBoV positive cases, 19 (32.76%) had co-pathogens including influenza virus (n = 5), RSV (n = 5), parainfluenza (n = 4), adenovirus (n = 1), coronavirus (n = 7). The complete genome sequences of 2 HBoVs strains (Genbank no. JN794565 and JN794566) were analyzed. Phylogenetic analysis showed that the 2 HBoV strains were HBoV1, and were most genetically close to ST2 (GenBank accession number DQ0000496). Recombination analysis confirmed that HBoV strain GZ9081 was an intra-genotype recombinant strain among HBoV1 variants.

Figure 1. Monthly distribution of HBoV from 3460 patients with acute respiratory infection symptoms during 2010–2011.

Human bocavirus (HBoV)-positive case number of each month from March 2010 to February 2011 and the monthly detection rate (% of monthly detected cases) were shown.

Figure 2. Age distribution of HBoV-positive patients from 3460 patients with acute respiratory infection symptoms during 2010–2011.

The number of HBoV-positive patients in different age groups and the corresponding detection rate (% of detected cases in corresponding age group) were shown.

Figure 3. Phylogenetic analysis of human bocavirus based on complete genome.

Phylogenetic tree with 1,000 bootstrap replicates was generated using the neighbor-joining method with Mega 4 software. Parvovirus B19, bovine parvovirus, canine minute virus, and representative strains of HBoV1-4 were used as reference strains for genotype analysis of GZ4785 (labeled with red triangle) and GZ9081 (labeled with blue diamond). The HBoV strains obtained in this study GZ4785 and GZ9081 were identified as HBoV1.

Figure 4. Phylogenetic analysis of GZ4785, GZ9081, and other reference strains based on full length (A), complete NS1 (B), NP1 (C), and VP1/VP2 (D) gene sequences.

Phylogenetic trees (1,000 bootstrap replicates, Kimura two-parameter model) based on GZ4785 (labeled with red triangle), GZ9081 (labeled with blue diamond), and other HBoV1 reference strains. Swedish prototype strains ST1 and ST2, American strain CRD2, Japanese strain JPOC07–511, Thai strains CU6 and CU74, Taiwanese strains TW925_07, TW2715_06 and TW2717_06, Chinese strains HK1, HK19, WLL–1, WLL–2, CZ643, FZ1, FZ40, BJ3064, BJ3722, GD-HBoV-571, GD-HBoV-594, GD-HBoV-621 were used (GenBank accession no. DQ000495, DQ000496, DQ340570, AB481080, EF203920, EF203922, EU984245, EU984232, EU984233, EF450717, EF450735, DQ778300, EF441262, DQ457413, GQ455988, GQ455987, DQ988933, DQ988934, GQ926981, GQ926982, GQ926982).

Figure 5. Identification of recombination event between CU74 and ST1, which led to the recombinant strains GZ9081.

BOOTSCAN evidence for the recombination origin on the basis of pair-wise distance, modeled with a window size 1000, step size 10, and 100 Bootstrap replicates; The right part of the panel were phylogenetic trees constructed based on recombination regions (1–1272+4385-end) and non-recombination regions (1272–4385) using Mega 4 software.