Occurrence and reassortment of avian influenza A (H7N9) viruses derived from coinfected birds in China.

UNLABELLED: Over the course of two waves of infection, H7N9 avian influenza A virus has caused 436 human infections and claimed 170 lives in China as of July 2014. To investigate the prevalence and genetic diversity of H7N9, we surveyed avian influenza viruses in poultry in Jiangsu province within the outbreak epicenter. We found frequent occurrence of H7N9/H9N2 coinfection in chickens. Molecular clock phylogenetic analysis confirms coinfection by H7N9/H9N2 viruses and also reveals that the identity of the H7N9 outbreak lineage is confounded by ongoing reassortment between outbreak viruses and diverse H9N2 viruses in domestic birds. Experimental inoculation of a coinfected sample in cell culture yielded two reassortant H7N9 strains with polymerase segments from the original H9N2 strain. Ongoing reassortment between the H7N9 outbreak lineage and diverse H9N2 viruses may generate new strains with the potential to infect humans, highlighting the need for continued viral surveillance in poultry and humans. IMPORTANCE: We found frequent occurrence of H7N9/H9N2 coinfection in chickens. The H7N9 outbreak lineage is confounded by ongoing reassortment between H7N9 and H9N2 viruses. The importance of H9N2 viruses as the source of novel avian influenza virus infections in humans requires continuous attention.

Epidemical features of HAdV-3 and HAdV-7 in pediatric pneumonia in Chongqing, China.

Human adenoviruses (HAdV) of species B, C, and E (HAdV-B, -C, -E) are frequent causative agents of acute respiratory infections worldwide. No specific analysis has been done on the epidemiological and clinical features of HAdV in pediatric pneumonia in China. Nasopharyngeal aspirates were collected from hospitalized children with pneumonia from June 2009 to May 2014. All samples that tested positive for HAdV were typed by sequencing the hexon and fiber genes. From a total of 3089 samples, 208 (6.7 %) were positive for HAdV, identified as belonging to HAdV-B (186, 89.4 %), HAdV-C (9, 4.3 %) and HAdV-E (1, 0.5 %). HAdV-7 (104, 50.0 %) and HAdV-3 (78, 37.5 %) were the two major types, followed by HAdV-1, HAdV-55 and HAdV-14. There were 87 (41.8 %) single HAdV infections, of which 80 % were HAdV-7 infections. Multivariate analysis showed that single infections with HAdV-7 were associated with a higher prevalence of severe pneumonia. Temporal patterns showed that, except for a simultaneous outbreak of HAdV-3 and HAdV-7 during the years 2010-2011, HAdV-7 and HAdV-3 were alternately predominant, and the dominance shifted to HAdV-3 after 2014. Identification of the predominant HAdV genotypes and their epidemical features is useful for determining preventive strategies. HAdV-7 associated severe pneumonia needs to be considered with high priority in clinical practice.

Detection and complete genome characterization of human enterovirus 118 from children with acute respiratory disease in China.

Enterovirus 118 (EV-118) within species HEV-C was detected in two 5-month-old boys with pneumonia in China. The EV-118 from both cases was genetically closer to ISR10 strain from Israel than to PER161 strain from Peru based on VP1 gene sequences. The complete genome of the detected EV-118 consists of 7,360 nucleotides, excluding the poly (A) tail. The 5'UTR contains 669 nucleotides, and 3'UTR consists of 73 nucleotides. A single open reading frame from base 670 to 7,287 that encodes a 2,206-amino-acid polyprotein was featured. The base composition of the full genome is 27.9 % A, 24.2 % C, 24.4 % G, and 23.6 % U. Phylogenetic analysis of the full genome sequences illustrated EV-118 was genetically closer to EV-109 and EV-105, and the Chinese strain differed from Peru strain. In summary, the presence of EV-118 was confirmed in pediatric pneumonia cases and complete genome sequences were identified for the first time in China.

Severe fever with thrombocytopenia syndrome in children: a case report.

BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by a novel bunyavirus (SFTSV) in China. Humans of all ages living in endemic areas have high risk of acquiring SFTS. Most clinical data so far have been from adults and no clinical study was available from children yet. The present study identified four SFTSV infected children through hospital based surveillance. A prospective observational study was performed to obtain their clinical and laboratory characteristics. CASE PRESENTATION: The patients' age ranged from 4-15 years old and two were male. On hospitalization, fever, malaise and gastrointestinal syndromes were the most commonly presenting symptoms. Hemorrhagic symptoms or neurological manifestation was not recorded in any of the four pediatric patients. Hematological abnormalities at admission into hospital included leucopenia (4 cases), thrombocytopenia (1 case) and bicytopenia (1 case). The abnormal parameters included elevated aminotransferase (1 case), alanine transaminase (2 case), and lactate dehydrogenase (3 case). Laboratory parameters indicative of renal damage was not observed during the hospitalization. All the patients recovered well without sequelae being observed. CONCLUSION: Compared with adults, pediatric patients with SFTSV infection seem to have less vague subjective complaints and less aggressive clinical course. Thrombocytopenia is suggested to be used less rigorously in recognizing SFTSV infection in pediatric patients, especially at early phase of disease.

Prevalence of enteroviruses in children with and without hand, foot, and mouth disease in China.

BACKGROUND: To determine the prevalence of human enteroviruses (HEVs) among healthy children, their parents, and children with hand, foot, and mouth disease (HFMD). METHODS: We conducted a case-control study that included throat samples from 579 children with HFMD and from 254 healthy controls. Throat samples from 49 households (98 parents and 53 healthy children) were also analyzed. Phylogenetic analysis was carried out to study genetic relationships of EV71 strains. RESULTS: The HEV positive rate in HFMD patients was significantly higher than that in healthy controls (76.0% vs. 23.2%, P < 0.001). The EV71 (43.7% vs. 15.0%, P < 0.001), CVA16 (18.0% vs. 2.8%, P < 0.001), and CVA10 (5.7% vs. 0.8%, P = 0.001) serotypes were significantly overrepresented in HFMD patients in comparison to healthy children. Other HEV serotypes were detected with comparable frequency in cases and controls. The HEV positive rate in severe HFMD patients was significantly higher than that in mild group (82.1% vs. 73.8%, P = 0.04). The EV71 (55.0% vs. 39.7%, P = 0.001) and CVA16 (11. 9% vs. 20.0%, P = 0.024) positive rate differed significantly between severe and mild HFMD patients. Other HEV serotypes were detected with comparable frequency between severe and mild HFMD patients. Among 49 households, 22 households (44.9%) had at least 1 family member positive for HEV. Children had significantly higher HEV positive rate than adult (28.3% vs. 14.3%, P = 0.037). The HEV positive rate was similar between mothers and fathers (12.24% vs. 16.32%, P = 0.56). The VP1 sequences of EV71 from HFMD patients and healthy children were nearly identical and all were clustered in the same clade, C4a. CONCLUSIONS: Our study demonstrated the co-circulation of multiple HEV serotypes in children with and without HFMD during epidemic. Our study deserves the attention on HFMD control.

Molecular epidemiology of WU polyomavirus in hospitalized children with acute respiratory tract infection in China.

AIM: To explore the molecular epidemiology and clinical characteristics of Washington University polyomavirus (WUPyV) infection in pediatric patients with acute respiratory tract infections in China. MATERIALS & METHODS: A laboratory surveillance was performed to recruit pediatric patients with acute respiratory tract infections. WUPyV was detected using real-time PCR and complete genome was sequenced for randomly selected positive nasopharyngeal aspirate. RESULTS: Altogether 122 (7.5%) of 1617 children found to be infected with WUPyV and 88 (72.1%) were coinfected with other viruses during 2012-2015. The phylogenetic analysis showed that 14 strains from our study formed two new clusters (Id and IIIc) within the Branch I and Branch III, respectively. CONCLUSION: WUPyV is persistently circulating in China. Surveillance on WUPyV infection in wider areas and long persistence is warranted.

Fatal pneumonia cases caused by human adenovirus 55 in immunocompetent adults.

BACKGROUND: Adenovirus is a frequent cause of mild self-limiting upper respiratory tract infection, gastroenteritis, and conjunctivitis. Severe or fatal infection mostly occurs in newborn, elderly or immunocompromised persons. METHODS: Fatal adenovirus pneumonia in three immunocompetent adults was identified. The clinical data and virological findings were reported from patients. Additional review of recently recorded fatal patients with adenovirus infection was carried out. RESULTS: The patients presented with sudden onset respiratory distress that progressed rapidly to respiratory failure and death. Human adenovirus (HAdV)-55 was detected in both nasopharyngeal aspirates and serum samples in all three cases, and moreover detected in lung, liver, and kidney in one case. In another case, remarkably elevated aspartate aminotransferase, alanine transaminase, and lactate dehydrogenase were identified. Three HAdV-55 strains were isolated and genome sequencing revealed a high similarity with other strains from mild infection. CONCLUSIONS: Fatal infection with HAdv-55 might occur in otherwise healthy adults. Diagnosis of adenovirus infection should be considered in patients with severe pneumonia yielding negative bacterial culture and presenting no response to antibiotic therapy.

Prevalence and genetic characteristics of Saffold cardiovirus in China from 2009 to 2012.

The epidemiology and clinical features of the Saffold cardiovirus (SAFV) remain ambiguous. The present study was designed to systematically and intensively investigate the epidemiological features of SAFV in pediatric patients in China. Three cohorts of pediatric patients were recruited from 2009 to 2012. Cohort 1 comprised patients with acute respiratory tract infections. Cohort 2 comprised patients with diarrhea. Cohort 3 comprised hand, foot, and mouth disease (HFMD) patients. A total of 115 patients (1.6%) among 6052 (17/1647, 12/2013, and 86/2392 in cohorts 1, 2, and 3, respectively) were SAFV-positive. The samples from 82 SAFV-positive patients were successfully sequenced, and four genotypes were identified: 8 SAFV-1, 41 SAFV-2, 29 SAFV-3, and 4 SAFV-6. A significantly higher detection rate was found in the HFMD patients than in other two cohorts (both P <0.001). A higher frequency of severe clinical outcome and nervous system manifestation were also observed in the SAFV-positive HFMD patients. Additionally, 6 (3.5%) cerebrospinal fluid and 7 (2.2%) serum samples from the HFMD-associated encephalitis patients were SAFV-positive. Based on the VP1 sequences, all four genotypes displayed distinct geographical clustering. SAFV infection might be associated with a wide clinical spectrum and contribute to HFMD.

Molecular epidemiology of human rhinovirus in children with acute respiratory diseases in Chongqing, China.

Human rhinovirus-C (HRV-C) has been increasingly detected in patients with acute respiratory diseases (ARDs). Prolonged surveillance was performed on children with ARD to investigate the molecular epidemiology and clinical characteristics of HRV in Chongqing, China. Nasopharyngeal aspirates (NPA) were collected from hospitalized children with ARD during 2009-2012. HRV-C was genotyped by sequencing the VP4/VP2 coding region. Among the 1,567 NPAs obtained, 223 (14.2%) were HRV positive, and 75.3% of these 223 NPAs were co-infected with other viruses. HRV-A (54.7%) and HRV-C (39.9%) accounted for the majority of HRV infections. Logistic regression models demonstrated significant associations between HRV-A, HRV-C, and asthma attacks, as well as between HRV-C and wheezing. A phylogenetic tree showed that HRV-C2 was the predominant type of HRV-C, followed by HRV-C43, HRV-C1, and HRV-C17. Three novel genotypes were proposed on the basis of a low identity with the known HRVs. Our results showed that HRV-A and HRV-C were the predominant types of HRV infection, and HRV-C showed a high genetic variation in Chongqing, China. HRV infection was associated with asthma attacks and wheezing; furthermore, HRV infections played a minor role in causing severe pneumonia. This knowledge provides information for the prevention and control of HRV associated with ARDs.

Epidemiology of human adenovirus and molecular characterization of human adenovirus 55 in China, 2009-2012.

BACKGROUND: Human adenovirus 55 (HAdV-55) has caused recent outbreaks of acute respiratory disease (ARD) among adults and military trainees. The active surveillance for HAdV infections was sparse in China, and current knowledge on the HAdV-type distributions and its molecular evolution is lacking. OBJECTIVES: To acquire better understanding on the prevalence and molecular evolution of HAdV-55 strains in China, for an informed strategy for disease control and prevention. POPULATION/METHODS: Nasopharyngeal aspirates were collected from hospitalized children with ARTI in Chongqing during 2009-2012. The genotype of HAdV isolates were determined by sequencing the partial hexon and fiber genes. Whole genome sequences of HAdV-55 were obtained for molecular evolution analysis. RESULTS: About 191 (8·55%) HAdV were detected in 2234 children, including 92 (48·2%) with HAdV-7, 72 (37·7%) with HAdV-3, 6 (3·1%) with HAdV-55, 5 (2·6%) with HAdV-5, 4 (2·1%) with HAdV-1, 1 (0·5%) with HAdV-2, and 11(5·8%) with untyped HAdV. Four of these children developed pneumonia, two of whom were diagnosed with severe pneumonia and/or encephalopathy. HAdV-55 isolates clustered with HAdV-11 sequences based on the hexon gene and clustered with HAdV-14 sequences based on the fiber gene and the whole genome. The overall evolutionary rates of hexon gene, fiber gene, and whole genome of HAdV-55 were estimated at 6·2 × 10(-5) s/s/y, 8·0 × 10(-5 ) s/s/y, and 1·7 × 10(-5) s/s/y, respectively. CONCLUSIONS: This study suggested HAdV-55 as an emerging infectious disease pathogen has conserved genetic structure and is closely related to each other. Further molecular investigation based on HAdV-55 of wider origin might facilitate understanding its diversity, dissemination, and transmission in China.

Detection of enterovirus 68 as one of the commonest types of enterovirus found in patients with acute respiratory tract infection in China.

Human enterovirus 68 (HEV-68) is an enterovirus associated with respiratory illness. In China, no information about HEV-68 is available for children yet. This study aimed to investigate the presence of HEV-68 in mainland China between 2009 and 2012 and to explore the migration events of HEV-68 across the world. Among 1565 samples tested from children, 41 (2.6%) were positive for HEV and 223 (14.3%) for human rhinovirus (HRV). Seven (17.1%) of 41 HEVs were HEV-68. Two HEV-68- and five HRV-positive samples were detected in 585 adult samples. HEV-68 is the predominant type of enterovirus in children with acute respiratory tract infection (ARTI), followed by HEV-71 and coxsackievirus A6. Three HEV-68-infected children presented with severe pneumonia and one presented with a severe asthma attack. The viruses were attributed to two novel distinct sublineages of HEV-68 based on phylogenetic analysis of partial VP1 gene sequences. Migration events analysis showed that the USA and the Netherlands were possible geographical sources of HEV-68, from where three strains migrated to China. In conclusion, HEV-68 may play a predominant role among the enteroviruses associated with ARTI in children. Additional surveillance is needed to clarify the reason why HEV-68 causes such a wide spectrum of disease, from asymptomatic to severe respiratory disease and even death.

Circulation of Coxsackievirus A10 and A6 in hand-foot-mouth disease in China, 2009-2011.

Coxsackieviruses A10 (CV-A10) and A6 (CV-A6) have been associated with increasingly occurred sporadic hand-foot-mouth disease (HFMD) cases and outbreak events globally. However, our understanding of epidemiological and genetic characteristics of these new agents remains far from complete. This study was to explore the circulation of CV-A10 and CV-A6 in HFMD and their genetic characteristics in China. A hospital based surveillance was performed in three heavily inflicted regions with HFMD from March 2009 to August 2011. Feces samples were collected from children with clinical diagnosis of HFMD. The detection and genotyping of enteroviruses was performed by real-time PCR and sequencing of 5'UTR/VP1 regions. Phylogenetic analysis and selection pressure were performed based on the VP1 sequences. Logistic regression model was used to identify the effect of predominant enterovirus serotypes in causing severe HFMD. The results showed 92.0% of 1748 feces samples were detected positive for enterovirus, with the most frequently presented serotypes as EV-71 (944, 54.0%) and CV-A16 (451, 25.8%). CV-A10 and CV-A6 were detected as a sole pathogen in 82 (4.7%) and 44 (2.5%) cases, respectively. Infection with CV-A10 and EV-71 were independently associated with high risk of severe HFMD (OR = 2.66, 95% CI: 1.40-5.06; OR = 4.81, 95% CI: 3.07-7.53), when adjusted for age and sex. Phylogenetic analysis revealed that distinct geographic and temporal origins correlated with the gene clusters based on VP1 sequences. An overall ω value of the VP1 was 0.046 for CV-A10 and 0.047 for CV-A6, and no positively selected site was detected in VP1 of both CV-A10 and CV-A6, indicating that purifying selection shaped the evolution of CV-A10 and CV-A6. Our study demonstrates variety of enterovirus genotypes as viral pathogens in causing HFMD in China. CV-A10 and CV-A6 were co-circulating together with EV-71 and CV-A16 in recent years. CV-A10 infection might also be independently associated with severe HFMD.