Ljungan virus is endemic in rodents in the UK.

Ljungan virus is a recently identified member of the family Picornaviridae that was isolated from bank voles in Sweden. LjV has been associated with [corrected] type 1 diabetes-like symptoms and myocarditis in bank voles (Myodes glareolus), and it has been suggested that it has zoonotic potential. Here, we show for the first time that Ljungan virus is prevalent (20-27 % positive by PCR) in four species of UK rodent (Myodes glareolus [bank vole], Apodemus sylvaticus [wood mouse], Microtus agrestis [field vole] and Mus musculus [house mouse]). Sequence analysis showed that Ljungan virus of genotypes 1 and 2 were present, although genotype 1 was more prevalent and more frequently associated with brain tissue. This study highlights the prevalence of Ljungan virus in the UK and the need for assessment [corrected] of its zoonotic potential.

G8 rotaviruses with conserved genotype constellations detected in Malawi over 10 years (1997-2007) display frequent gene reassortment among strains co-circulating in humans.

Rotavirus A, the most common cause of severe diarrhoea in children worldwide, occurs in five major VP7 (G) and VP4 (P) genotype combinations, comprising G1P[8], G2P[4], G3P[8], G4P[8] and G9P[8]. However, G8, a common bovine rotavirus genotype, has been reported frequently among children in African countries. Surveillance of rotavirus gastroenteritis conducted in a sentinel hospital in Blantyre, Malawi between 1997 and 2007 provided a rare opportunity to examine the whole genotype constellation of G8 strains and their evolution over time. A sample of 27 (9.0 %) of 299 G8 strains was selected to represent each surveillance year and a range of P genotypes, which shifted in predominance from P[6] to P[4] and P[8] during the study period. Following cell culture adaptation, whole genome sequencing demonstrated that the genetic background of 26 strains possessed the DS-1 genotype constellation. A single G8P[6] strain was a reassortant in which both NSP2 and NSP5 genes from strains with the Wa genotype constellation had been inserted into a strain with the DS-1 genotype background. Phylogenetic analysis suggested frequent reassortment among co-circulating strains with the DS-1 genotype constellation. Little evidence was identified to suggest the introduction of contemporary bovine rotavirus genes into any of the 27 G8 strains examined. In conclusion, Malawian G8 strains are closely related to other human strains with the DS-1 genotype constellation. They have evolved over the last decade through genetic reassortment with other human rotaviruses, changing their VP4 genotypes while maintaining a conserved genotype constellation for the remaining structural and non-structural proteins.

Detection and molecular characterisation of noroviruses in hospitalised children in Malawi, 1997-2007.

Despite the increasing recognition of noroviruses as major pathogens associated with community-acquired diarrhoea in children, there are few studies from Africa. Long-term surveillance studies of rotavirus gastroenteritis in Malawian children have provided an opportunity to undertake a study of the importance and epidemiological features of norovirus infection in this population. Faecal specimens were collected from children <5 years of age admitted to hospital with acute diarrhoea, as well as from a comparison group of diarrhoea-free children, in Blantyre, Malawi between 1997 and 2007. Norovirus was detected using real-time PCR and strains genotyped by nucleotide sequence analysis. Norovirus was detected in 220/1,941 (11.3%) faecal specimens, comprising genogroup GI (1.8%), GII (9.4%) and mixed GI/GII (0.1%). The median age of children with norovirus was 6 months (range, 0-48 months). Norovirus was detected throughout the year, with peaks at the end of the rainy season (March) and towards the end of the dry season (August-November). Norovirus GII.4 was the most commonly detected genotype accounting for 70% of strains characterised, followed by GII.2 (6%), GII.6 (4%) and GII.12 (4%). Sub typing of GII.4 noroviruses demonstrated local circulation of strains prior to their subsequent detection in association with global epidemics of gastroenteritis. The prevalence of norovirus in children without diarrhoea was similar to the level in cases. This largest study to date of norovirus infection in African children indicates the potential role of paediatric surveillance in predicting the emergence of norovirus strains with global epidemic potential.

Clinical features and molecular epidemiology of rotavirus and norovirus infections in Libyan children.

Rotaviruses and noroviruses are leading viral causes of diarrhoea in children. A cross-sectional study was undertaken among children aged <5 years with acute gastroenteritis at Al-Jala Children's Hospital, Tripoli, Libya, from October 2007 to September 2008. Of 1,090 fecal samples collected, 260 from inpatients and 830 from outpatients, all inpatients and approximately a third of outpatients, selected systematically, were investigated for rotavirus and norovirus infection by ELISA and real-time RT-PCR, respectively. Of 520 fecal samples examined (inpatients = 260, outpatients = 260), 164 (31.5%) had rotavirus and 91 (17.5%) had norovirus detected. Rotavirus was identified more often among inpatients than outpatients (35.8% vs. 27.3% respectively, P = 0.038). Norovirus was detected more commonly among outpatients than inpatients (21.2% vs. 13.8% respectively, P = 0.028). The peak incidence of infection with both viruses was among children aged between 6 and 11 months. The number of rotavirus cases was highest between November and June with a peak detection rate of 50% in January. Norovirus occurred most commonly from May through August with a peak detection rate of 47% in August. The most prevalent rotavirus genotypes were P[8], G9 (n = 116, 65.9%), followed by P[8],G1 (n = 49, 27.8%); a single P[9], G3 strain was detected. There were seven distinct electropherotypes among the G9 strains and all belonged to VP7 Lineage III. Among 91 noroviruses identified, 90 were genogroup II. Of 26 genogroup II noroviruses examined, all were genotype GII.4. Rotaviruses and noroviruses are both important causes of gastrointestinal infection among young children in Libya.

Rotavirus and norovirus infections in children in Sana'a, Yemen.

OBJECTIVES: To describe the epidemiology of rotavirus and norovirus infection among children with acute gastroenteritis in Sana'a, Yemen. METHODS: A cross-sectional study from November 2007 to March 2009 of children aged 1 month to 5 years attending the emergency and outpatient departments of two hospitals in Sana'a with acute gastroenteritis. Rotavirus was detected by ELISA and genotyped by RT-PCR. Norovirus was detected by End Point RT-PCR and nucleotide sequencing. RESULTS: A total of 290 children (48% in the emergency department and 52% in the outpatient department of the children respectively) were enrolled. Rotavirus infections were detected in 78 (27%) and norovirus infections in 30 (10%). Rotavirus genotypes included G1P[8] (55%), G9P[8] (21%) and G2P[4] (12%) with G12 comprising 3% of strain types. The main norovirus genotype was GII.4 (27%) with >10 other genotypes detected. CONCLUSIONS: Rotavirus and norovirus infections are common causes of gastroenteritis in Yemen. Rotavirus vaccines could play a significant role in the control of acute childhood diarrhoea in this setting.

Detection and molecular characterisation of rotavirus and norovirus infections in Jordanian children with acute gastroenteritis.

Rotavirus and norovirus are globally important causes of paediatric gastroenteritis, but no studies of viral genotypes have been reported from Jordan. We undertook a molecular epidemiological study in children hospitalised with acute gastroenteritis in Jordan between January 2006 and December 2007. Among 368 children, rotavirus and norovirus infections were detected in 49.5% and 11.4% of children, respectively. Rotavirus genotypes P[8],G1 (56%), P[4],G2 (14%) and P[8],G9 (13%) were most commonly identified, consistent with results of global rotavirus surveillance studies. Norovirus GII.3 was the most commonly detected genotype, followed by GII.4, contrasting with most studies in which GII.4 has predominated.

Acute diarrhoea in a community cohort of children who received an oral rotavirus vaccine in Northeast Brazil.

Rotavirus is an important cause of childhood diarrhoea. A monovalent rotavirus vaccine (Rotarix®) was introduced into the Immunization Program of Brazil in 2006. In this study, we describe the incidence and burden of disease of rotavirus diarrhoea in two cohorts of children (vaccinated and unvaccinated). We followed two groups of 250 children under one year old, who were enrolled in December 2006 from a low-income residential area in Northeast Brazil. The children were monitored every two weeks for two years. Stool samples from children with diarrhoea were examined for the presence of rotavirus. Rotaviruses were genotyped using real time-polymerase chain reaction. The mean numbers of all-cause diarrhoea episodes/child (adjusted for age) in the first year were 0.87 and 0.84, in vaccinated and unvaccinated children, respectively. During the second year, the number of episodes/child decreased to 0.52 and 0.42. Only 16 (4.9%) of 330 stool samples were rotavirus-positive (10 vaccinated and 6 unvaccinated children) and only P[4]G2 rotaviruses were identified. All-cause diarrhoea episodes were more severe in unvaccinated children in the first year of age (p < 0.05), while vaccinated children had more severe episodes 18 months after vaccination. Rotavirus diarrhoea incidence was very low in both groups.

Epidemiology of rotavirus infection in children in Blantyre, Malawi, 1997-2007.

Acute gastroenteritis caused by rotavirus infection is an important cause of morbidity and mortality among infants and young children in Africa. From 1997 through 2007, we enrolled 3740 children <5 years of age with acute gastroenteritis who received hospital care at the Queen Elizabeth Central Hospital in Blantyre, Malawi. Group A rotavirus was detected in fecal specimens by enzyme immunoassay. Rotavirus strains were characterized for VP7 (G) and VP4 (P) types with use of reverse-transcription polymerase chain reaction. Overall, rotavirus was detected in one-third of children. The median age of children with rotavirus gastroenteritis was 7.8 months, compared with 10.9 months for those without rotavirus in stool specimens (P > .001). Rotavirus circulated throughout the year, with the detection proportion greatest during the dry season (from May through October). A total of 15 single rotavirus strain types were detected during the study period, with genotypes P[8]G1, P[6]G8, P[4]G8, P[6]G1, P[8]G3, and P[6]G9 comprising 83% of all strains characterized. Serotype G12 was detected for the first time in Blantyre during the final 2 years of study. Zoonotic transmission and viral reassortment contributed to the rich diversity of strains identified. Current rotavirus vaccines have the potential to greatly reduce the rotavirus disease burden in Malawi, but they will be required to protect against a broad range of rotavirus serotypes in a young population with year-round rotavirus exposure.

Incidence of rotavirus and all-cause diarrhea in northeast Brazil following the introduction of a national vaccination program.

BACKGROUND & AIMS: Rotavirus vaccines were introduced in Brazil in 2006; we evaluated their effects in the state of Sergipe, Brazil. METHODS: We performed a cross-sectional survey of children with diarrhea attending emergency services in Aracaju, Brazil, between October 2006 and April 2008 and a cluster sampling survey to assess vaccination coverage. Vaccine efficacy was assessed using the screening method. Diarrhea consultation and hospitalization data (2003-2007) were obtained from state and national surveillance systems. RESULTS: Rotavirus was detected in 59 of 534 stool samples (11%) from children attending emergency services. The number of rotavirus-positive samples decreased from 18 of 74 (24%) in 2006 to 31 of 321 (9.5%) in 2007 and 10 of 136 (7.4%) in 2008 (P < .01). Diarrhea severity was greater in children with rotavirus (P < .01) but decreased over time (P < .001). Of the rotaviruses detected, 56 of 59 (95%) were P[4]G2 genotype, 1 was P[4]G-non-typeable (NT), 1 was P[NT]G2, and 1 was P[NT]GNT. Diarrhea consultations decreased from 3020 in 2004 to 604 in 2007; reductions were greatest among children under 5 years old. Diarrhea hospitalizations decreased from 2121 in 2003 to 1176 in 2007. Vaccine coverage was 90.3%. Vaccines were highly effective against the strain P[8]G1; efficacy against P[4]G2 genotype was 89% (95% confidence interval: 0.87-0.92) in Aracaju and 95% in Sergipe. CONCLUSIONS: Since vaccines were introduced in 2006, there has been an overall reduction in diarrhea consultations and hospitalizations in northeast Brazil, with the greatest reductions in young children. This might have resulted from vaccination and improved sanitation. Although a single rotavirus genotype (P[4]G2) was recovered, vaccine efficacy was high against this genotype.

Molecular epidemiology of rotavirus diarrhea among children aged <5 years in nepal: predominance of emergent G12 strains during 2 years.

A 2-year surveillance was performed in Kathmandu, Nepal, by collection of stool specimens from 1139 children aged <5 years who were hospitalized for acute diarrhea from November 2005 through October 2007. Of the 1139 samples, 379 (33%) had rotavirus strains identified by enzyme-linked immunosorbent assay; the most prevalent G type was G12, accounting for 50% of typed strains in 2005-2006 and 29% in 2006-2007, followed by G1 (26%) in 2005-2006 and by G9 (28%) and G2 (20%) in 2006-2007. The most prevalent P type was P[8], accounting for 47% of strains in 2005-2006 and 35% in 2006-2007, followed by P[6] (37% in 2005-2006 and 33% in 2006-2007) and P[4] (10% in 2005-2006 and 24% in 2006-2007). Of combined genotypes, G12P[6] was the most prevalent, accounting for 34% of strains in 2005-2006 and 24% in 2006-2007, followed by G1P[8] (23%) in 2005-2006 and G2P[4] (20%) in 2006-2007. An unusually high detection of G12 strains underscores the importance of continued surveillance of rotavirus strains.

Serotype g12 rotaviruses, Lilongwe, Malawi.

To assess diversity of rotavirus strains in Lilongwe, Malawi, we conducted a cross-sectional study of children with acute gastroenteritis, July 2005-June 2007. Serotype G12 was identified in 30 (5%) of 546 rotavirus-positive fecal specimens. The G12 strain possessed multiple electropherotypes and P-types, but their viral protein 7 sequences were closely related, indicating that reassortment has occurred.

Human astrovirus gastroenteritis in children, Madagascar, 2004-2005.

We report data regarding the molecular epidemiology of human astrovirus (HAstV) infections among children in Madagascar. In a 13-month study, 5 HAstV isolates were detected in fecal samples from 237 children (2.1%) by reverse transcription-PCR. Phylogenetic analysis showed the cocirculation of usual and unusual HAstVs.

Molecular epidemiology of rotavirus diarrhea among children in Saudi Arabia: first detection of G9 and G12 strains.

In anticipation of rotavirus vaccine introduction in Saudi Arabia, this study was undertaken to determine the distribution of the G and P genotypes of rotaviruses in order to examine whether there was any emerging serotype or unusual strain circulating in children in Saudi Arabia. Of 984 stool specimens collected between 17 April 2004 and 16 April 2005, rotavirus was detected by an enzyme-linked immunosorbent assay in 187 (19%) diarrheal children less than 5 years of age. Of these, 160 (86%) were classified into G and P genotypes as follows: G1P[8] (44%), G2P[4] (20%), G9P[8] (11%), G12P[8] (4%), and G3P[8] (4%). RNA polyacrylamide gel electrophoresis identified 94 (50%) specimens as long RNA patterns, 30 (16%) specimens as short RNA patterns, and 1 mixed infection. Only a single long RNA electropherotype was identified for seven specimens containing G12P[8] rotavirus. RNA-RNA hybridization demonstrated that the G12P[8] strains were similar in their genomic constellation to locally cocirculating strains and to a Nepalese G12P[8] strain. The Saudi Arabian G12 VP7 gene had a 99% nucleotide sequence identity with Nepalese and Indian G12 VP7 genes and belonged to the third lineage. This study is the first to describe the distribution of rotavirus G and P types and also the first to identify G9P[8] and G12P[8] strains in the country.

Characterization of rotavirus strains detected among children and adults with acute gastroenteritis in Gizan, Saudi Arabia.

OBJECTIVE: To assess the circulating rotavirus strains among hospitalized children and adults in Gizan City. METHODS: This cross-sectional study was based in 5 hospitals in the Gizan area. Stool samples were collected between November 2004 and March 2005, from sequential patients with acute, dehydrating diarrhea. Rotavirus antigen was detected in stool by enzyme-linked immunosorbent assay. The diversity of rotavirus strains was investigated using electropherotying and reverse transcription-polymerase chain reaction amplification of the VP7 and VP4 genes (G and P genotyping). RESULTS: Rotavirus was detected in 54 of 454 (12%) subjects. The ages of those infected with rotavirus ranged from 15 days to 20 years, with a median age of 36 months. The highest rotavirus detection rate (24%) occurred in children aged 48-59 months. Overall, 50 (93%) of strains could be assigned both a G- and P-type; G1P[8] was the most frequently detected strain type (n=48, 89%) with one rotavirus each of G2P[4] and G9P[8]. CONCLUSION: Rotavirus strains circulating in Gizan would be well covered by current rotavirus vaccines. Rotavirus serotype G9 has been detected in Saudi Arabia for the first time. Continued surveillance of rotavirus strains is required.

Predominance of rotavirus P[4]G2 in a vaccinated population, Brazil.

We identified 21 rotaviruses in 129 patients with diarrhea in a Brazilian city with high rotavirus vaccine coverage. All rotaviruses were genotype P[4]G2 with 1 mixed infection with P[NT]G9. Although virus predominance could have occurred randomly, the vaccine may be less protective against P[4]G2. Prospective surveillance is urgently needed.

Respiratory syncytial virus and human metapneumovirus in children with acute respiratory infections in Yemen.

A survey of 604 Yemeni children younger than 2 years with acute respiratory infections identified respiratory syncytial virus (RSV) in 244 (40%), human metapneumovirus (HMPV) in 41 (7%) and RSV/HMPV coinfection in 25 (4%) children. RSV infections occurred in younger children and were associated with more severe hypoxia than observed with HMPV. Both viruses are important causes of severe acute respiratory infection in Yemen.

Surveillance of rotavirus gastro-enteritis in children in Blantyre, Malawi.

BACKGROUND: Rotavirus is a leading cause of acute gastro-enteritis in infants and young children worldwide. Previous studies of rotavirus gastro-enteritis in Malawi have documented a high disease burden with an extensive diversity of circulating rotavirus strains. METHODS: In anticipation of the introduction of national rotavirus vaccination, a 2-year surveillance study was undertaken in 2008 and 2009 of children in Blantyre seeking hospital care for acute gastro-enteritis. Rotavirus was detected in faecal specimens by ELISA. Rotavirus G and P types were determined by RT-PCR. RESULTS: Rotavirus, which circulated throughout the year, was detected in 220/720 (31%) children. Over 85% of patients with rotavirus gastro-enteritis were <1 year of age. A total of 13 rotavirus G/P types were identified, the most common strains being G1P[8] (39·5%), G12P[6] (23·2%), G2P[4] (9·5%), G9P[8] (6·8%) and G8P[4] (6·4%). CONCLUSIONS: The data confirm the importance of rotavirus infection in young Malawian children and highlight the continuing diversity of circulating rotavirus strains in Blantyre. Together with previous observations, the findings contribute to a baseline of data against which the impact of future rotavirus vaccination in Malawi can be assessed.

Campylobacter infection in children in Malawi is common and is frequently associated with enteric virus co-infections.

BACKGROUND: Campylobacter species are the most common cause of bacterial gastroenteritis in the developed world. However, comparatively few studies have determined the epidemiological features of campylobacteriosis in resource-poor settings. METHODS: A total of 1,941 faecal specimens collected from symptomatic (diarrhoeic) children and 507 specimens from asymptomatic (non-diarrhoeic) children hospitalised in Blantyre, Malawi, between 1997 and 2007, and previously tested for the presence of rotavirus and norovirus, was analysed for C. jejuni and C. coli using a real time PCR assay. RESULTS: Campylobacter species were detected in 415/1,941 (21%) of diarrhoeic children, with C. jejuni accounting for 85% of all cases. The median age of children with Campylobacter infection was 11 months (range 0.1-55 months), and was significantly higher than that for children with rotavirus and norovirus (6 months and 7 months respectively; P<0.001). Co-infection with either rotavirus or norovirus was noted in 41% of all cases in the diarrhoeic group. In contrast, the detection rate of Campylobacter in the non-diarrhoeic group was 14%, with viral co-infection identified in 16% of children with Campylobacter. There was no association between Campylobacter detection rate and season over the 10 year period. DISCUSSION: Using molecular detection methodology in hospitalised Malawian children, we have demonstrated a high prevalence of Campylobacter infection, with frequent viral co-infection. The burden of Campylobacter infection in young African children may be greater than previously recognised.

Unusual norovirus and rotavirus genotypes in Ethiopia.

BACKGROUND: Gastro-enteritis is associated with significant mortality in low- and middle-income countries, and rotavirus and norovirus are the principal viral agents implicated. AIMS: To investigate the molecular epidemiology and burden of disease associated with rotavirus and norovirus in children attending a health centre in Ethiopia. METHODS: A cross-sectional study was conducted in children attending a health centre in Awassa, southern Ethiopia. Children with diarrhoea (cases) and without diarrhoea (controls) were recruited over a 6-month period from December 2008 to May 2009. Rotavirus was detected by ELISA and genotyped by RT-PCR, and norovirus was amplified by RT-PCR with genotyping by sequence analysis of RT-PCR products. RESULTS: Rotavirus was detected in 44/200 (22%) cases and in none of the controls, with genotypes G3P[6] (48%), G1P[8] (27%) and G2P[4] (7%) being the strains most commonly identified. Norovirus was detected in 16 (8%) of 200 cases and in 4 (7%) of 57 controls. Norovirus GII.3 was the strain most commonly detected (40%: 8/20) and ten other genotypes were also detected. CONCLUSION: Rotavirus is a common cause of severe gastro-enteritis in children in Ethiopia; however, norovirus occurred with a similar frequency in cases and controls. A globally uncommon strain type, G3P[6], predominated within the rotavirus strains detected.

PCR based bronchoscopic detection of common respiratory pathogens in chronic cough: a case control study.

BACKGROUND: Viral respiratory tract infection is the most frequent cause of acute cough and is reported at onset in about one third of patients with chronic cough. Persistent infection is therefore one possible explanation for the cough reflex hypersensitivity and pulmonary inflammation reported in chronic cough patients. METHODS: Bronchoscopic endobronchial biopsies and bronchoalveolar lavage cell counts were obtained from ten healthy volunteers and twenty treatment resistant chronic cough patients (10 selected for lavage lymphocytosis). A screen for known respiratory pathogens was performed on biopsy tissue. Chronic cough patients also underwent cough reflex sensitivity testing using citric acid. RESULTS: There was no significant difference in incidence of infection between healthy volunteers and chronic cough patients (p = 0.115) or non-lymphocytic and lymphocytic groups (p = 0.404). BAL cell percentages were not significantly different between healthy volunteers and chronic cough patients without lymphocytosis. Lymphocytic patients however had a significantly raised percentage of lymphocytes (p < 0.01), neutrophils (p < 0.05), eosinophils (p < 0.05) and decreased macrophages (p < 0.001) verses healthy volunteers. There was no significant difference in the cough reflex sensitivity between non-lymphocytic and lymphocytic patients (p = 0.536). CONCLUSIONS: This study indicates latent infection in the lung is unlikely to play an important role in chronic cough, but a role for undetected or undetectable pathogens in either the lung or a distal site could not be ruled out. TRIALS REGISTRATION: Current Controlled Trials ISRCTN62337037 & ISRCTN40147207.