Detection of an unusual G8P[8] rotavirus in a Rotarix-vaccinated child with acute gastroenteritis using Nanopore MinION sequencing: A case report.

RATIONALE: Rotavirus is routinely diagnosed by the detection of antigens or the viral genome. However, these tests have limitations, in that they do not detect all rotavirus strains. PATIENT CONCERNS: We present a case of a 27-month-old girl who was hospitalized for 4 days with severe gastroenteritis, including high fever, vomiting, diarrhea, mild dehydration, and periumbilical pain. Notably, the patient previously received the Rotarix vaccine. DIAGNOSES: The laboratory tests were negative for rotavirus, astrovirus, adenovirus, and norovirus as well as common diarrhea-causing bacteria. Human-bovine recombinant rotavirus was detected by MinION sequencing. INTERVENTIONS: To investigate the cause agents from the unexplained severe gastroenteritis infant, the stool sample was prepared by random amplification for Nanopore MinION sequencing. OUTCOMES: Treatment through the administration of ORS solution and galtase powder with probiotics was successful after the diagnosis of unusual rotavirus infection. LESSONS: This case report is the first detection of an unusual human-bovine recombinant rotavirus in an idiopathic gastroenteritis using Nanopore MinION sequencing.

Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events.

After the introduction of two global rotavirus vaccines, RotaTeq in 2007 and Rotarix in 2008 in South Korea, G1[P8] rotavirus was the major rotavirus genotype in the country until 2012. However, in this study, an emergence of G2P[4] as the dominant genotype during the 2013 to 2015 season has been reported. Genetic analysis revealed that these viruses had typical DS-1-like genotype constellation and showed evidence of re-assortment in one or more genome segments, including the incorporation of NSP4 genes from strains B-47/2008 from a cow and R4/Haryana/2007 from a buffalo in India, and the VP1 and VP3 genes from strain GO34/1999 from a goat in Bangladesh. Compared to the G2 RotaTeq vaccine strain, 17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

Differentiation of RotaTeq® vaccine strains from wild-type strains using NSP3 gene in reverse transcription polymerase chain reaction assay.

RotaTeq® is a live attenuated human-bovine reassortant vaccine against rotaviruses that is used worldwide. However, shedding of the virus used in RotaTeq® has been detected in the feces of children following vaccination by the oral route, possibly affecting community immunity. Therefore, a simple and efficient method to discriminate between virulent and RotaTeq® vaccine strains is required. In this study, a novel one-step multiplex reverse-transcription polymerase chain reaction (RT-PCR) assay targeting the NSP3 gene was developed to detect RotaTeq® vaccine strains in fecal samples. RotaTeq® vaccine viruses were successfully distinguished from known wild-type rotavirus genotypes. In addition, the developed assay was able to detect rotaviruses in clinical stool samples obtained from South Korea during the 2011-2013 rotavirus seasons. Of the 1106 stool specimens from children with acute gastroenteritis that were screened, 286 rotaviruses were genotyped. RotaTeq® vaccine strains were identified in 39 samples (13.6%). The novel RT-PCR assay that was developed could be used to detect and discriminate between RotaTeq® vaccine strains that are shed in fecal matter, and to estimate the quantification of virus that has been shed after vaccination.

Emergence of Norovirus GII.17 Variants among Children with Acute Gastroenteritis in South Korea.

Of 1,050 fecal specimens collected from January 2013 to August 2015 from children with acute gastroenteritis, 149 (14.2%) were found to be positive for norovirus. Norovirus GII was the most predominant genogroup (98.65%; 147 of 149). The genotypes detected in this study were GI (2; 1.3%), GII.Pe-GII.4 (109; 73.1%), GII.P17-GII.17 (16; 10.7%), GII.P12-GII.3 (8; 5.4%), GII.P12-GII.12 (8; 5.4%), GII.P4-GII.4 (5; 3.4%), and the recombinant GII.Pe-GII.17 (1; 0.7%). Of these, the novel GII.17 strain was the second most predominant, and the number of affected children appeared to continuously increase over time (2013 [2; 4.4%], 2014 [4; 9.3%], and 2015 [10; 16.4%]). Phylogenetic analysis of the full genome and ORF1, ORF2, and ORF3 nucleotide sequences showed that GII.17 was grouped in cluster III with other strains isolated from 2013 to 2015 and had a different evolutionary history from strains collected in 1978 to 2002 and 2005 to 2009 formed clusters I and II. However, the phylogenetic trees also showed that cluster III was divided into subclusters IIIa (CAU-55 and CAU-85) and IIIb (Kawasaki 2014) (CAU-193, CAU-265, CAU-267, CAU-283, and CAU-289). Comparative analysis of the VP1 capsid protein using 15 complete amino acid sequences from noroviruses isolated from 1978 to 2015 showed 99 amino acid changes. These results could be helpful for epidemiological studies to understand circulating norovirus genotypes in population.

Assessment of the association between Apgar scores and seizures in infants less than 1 year old.

PURPOSE: The study aimed to assess the association between Apgar scores at 1 and 5 min after birth and seizures in infants less than 1 year old. METHODS: We conducted a retrospective, observational, hospital-based study by utilising medical records from the Chung-Ang University Hospital admissions from January 2006 to May 2015 in order to identify infants less than 1 year old who had a history of seizures. Using electronic medical records, infants who were diagnosed with infantile seizures at the Chung-Ang University Hospital from January 2006 to May 2015 were included in the seizure group (n=93), and a control group consisting of 296 age-matched cases without a history of seizures was selected from a group of infants born at Chung-Ang University Hospital during the same study period. RESULTS: We found that Apgar scores were significant risk factors for infantile seizures. Apgar scores differed depending on gestational age and birth weight. We found strong associations between Apgar scores and infantile seizures in the full-term and the normal-birth weight groups (bodyweight ≥2.5 kg), regardless of delivery mode. The Apgar scores were inversely correlated with the EEG class, and only the 1-min Apgar scores were correlated with MRI findings. CONCLUSION: Low Apgar scores are significant perinatal risk factors for infantile seizures, especially in full-term and normal-birth weight infants, and have a strong negative linear relationship with EEG and brain MRI results in the seizure group.

Whole-genome analysis of a rare human Korean G3P rotavirus strain suggests a complex evolutionary origin potentially involving reassortment events between feline and bovine rotaviruses.

A rare human rotavirus, G3P[9] strain RVA/Human-tc/KOR/CAU12-2-51/2013/G3P[9], was isolated from the stool of a 9-year-old female hospitalized with acute watery diarrhea in August 2012 in South Korea using a cell culture system, and its genome was analyzed. The complete genomic constellation of the CAU12-2-51 strain revealed a novel genotype constellation for human rotavirus, G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3. Phylogenetic analysis revealed that the CAU12-2-51 strain originated from feline- and bovine-like reassortment strains. The genes encoding VP4, VP7, NSP1, NSP3, NSP4, and NSP5 were related to human/feline-like and feline rotavirus strains, whereas the remaining five genes encoding VP1, VP2, VP3, VP6, and NSP2 were related to the human/bovine-like and bovine rotavirus strains. This novel strain was identified for the first time, providing evidence of feline/bovine-to-human transmission of rotavirus. The data presented herein provide information regarding rotavirus diversity and evolution.

Full genomic characterization of a group C rotavirus isolated from a child in South Korea.

During an epidemiological survey of human rotavirus infection in Seoul, Korea, from 2010 to 2011, one isolate of group C rotavirus (GCRV), named CAU10-312, was detected in a 5-year-old child admitted to the hospital with acute gastroenteritis, and its complete genomic sequence was determined. The 11 gene segments of the strain possessed G4-P[2]-I2-R2-C2-M2-A2-N2-T2-E2-H2 genotypes. The genotype of strain CAU10-312 appears to be closely related to strains from Bangladesh (DhakaC13 and BS347), India (v508), and England (Bristol), but distinct from Far East Asian strains, Chinese (Wu82 and YNR001) and Japanese (OH567 and BK0830). These findings may clarify the relationship of the genetics, evolutionary biology, and epidemiology of GCRVs and suggest that two very distinct genotype strains are in circulation in the world.

Distribution of rotavirus G and P genotypes approximately two years following the introduction of rotavirus vaccines in South Korea.

Genotyping of human rotaviruses was performed on 299 (40.1%) rotavirus-positive samples obtained from 745 children with acute diarrhea in three provinces in South Korea between March 2008 and February 2010, approximately 2 years following the introduction of the RotaTeq (September 2007) and Rotarix (July 2008). The most prevalent G genotypes were G1 (51.5%), followed by G3 (24.0%), G4 (15.4%), G9 (6.4%), and G2 (4.7%). The predominant types of P genotypes were P[8] (72.6%), followed by P[6] (19.1%) and P[4] (6.0%). The phylogenetic analyses of the VP7 genes of G9 strains revealed they were highly identical and belonged in lineage III. This study highlights the consistency of the predominant G1 genotype and slightly higher predominance of the identical G9 strains over the G2 genotype.

The indoor level of house dust mite allergen is associated with severity of atopic dermatitis in children.

We attempted to investigate the correlation between the severity of atopic dermatitis (AD) in children and the indoor level of house dust mite (HDM) allergens. Ninety-five patients (31.1 ± 19.5 months of age) with AD were enrolled in this study, and serum specific IgE against Dermatophagoides pteronyssinus and D. farinae was measured. The severity of AD was assessed using the visual analogue scale on the same day of house dust collection. Living rooms and mattresses where the child usually slept were vacuumed for 2 minutes and concentrations of Der f 1 were measured by enzyme-linked immunosorbent assay. The skin symptoms were more severe in patients with Der f 1 concentrations in living room > 2 µg/g dust than ≤ 2 µg/g dust (P = 0.018). This difference was noted in AD patients without sensitization to HDM (P = 0.004), but not in patients with sensitization. There was no difference in symptom severity according to Der f 1 concentrations in mattresses (P = 0.062). The severity of skin symptoms is associated with indoor concentrations of HDM in children with AD, and it is likely to act as nonspecific irritants as well as allergens in AD skin lesions.

Molecular characterization of serotype G9 rotaviruses circulating in South Korea between 2005 and 2010.

A total of 18 rotavirus G9 strains in South Korea were collected during five rotavirus seasons between 2005 and 2010. The relationship between these strains was examined by analyzing the genetic variation of two major structural genes, VP7 and VP4. All the rotavirus isolates were of the G9P[8] genotype. The VP7 phylogenetic analysis demonstrated that all of the G9 rotaviruses circulating in South Korea belonged to lineage IIId and were within three single clusters. The amino acid comparison of the antigenic regions of the VP7 gene suggests possible common progenitors of these strains. Phylogenetic analysis of P[8] VP4 genotypes indicated three lineages, P[8]-2, P[8]-3, and P[8]-4, with P[8]-3 being the most common. The results of this study provide information on the genetic relatedness of rotavirus G9 strains circulating in South Korea over recent years and can be utilized for the development of effective vaccines and the identification of reference strains for future efficacy studies.

A nationwide study of mass urine screening tests on Korean school children and implications for chronic kidney disease management.

BACKGROUND: Since 1998, urine screening tests have been performed on school children in Korea. We report the findings of the screening program that analyzed patients with proteinuria and/or hematuria. METHODS: Between 1999 and 2008, 5,114 children were referred to pediatric nephrologists at seven nationwide hospitals. Renal biopsies were performed on 1,478 children [28.79 % of total subjects; 26.77 % for isolated hematuria (IH), 9.09 % for isolated proteinuria (IP), and 51.19 % for combined hematuria and proteinuria (CHP)] who showed abnormal renal function, persistent hematuria and/or proteinuria for more than 6 months, nephrotic-range proteinuria, or those with underlying systemic diseases. RESULTS: Chronic glomerulonephritis (GN) was detected in 25 % of all visiting subjects. The most common findings in renal biopsies were immunoglobulin A (IgA) nephropathy in 38.97 %, mesangial proliferative GN in 24.29 %, and thin basement membrane nephropathy in 13.13 %. Compared with the relative frequency of renal diseases associated with urinary abnormalities, CHP (46.90 %) and nephrotic-range proteinuria (69.96 %) groups had more frequent GN than the others. Abnormal findings on renal ultrasound with or without Doppler scan were noted in 462 cases (suspected nutcracker phenomenon, 159; increased parenchymal echogenicity, 92; hydronephrosis, 75; simple cyst, 47). CONCLUSION: Mass urine screening tests could detect asymptomatic GN in its early stages. Initial aggressive diagnosis and treatment for CHP and nephrotic-range groups may prove helpful as interventions that delay chronic kidney disease progression. These findings may assist in the development of diagnostic and management guidelines for relatively mild urinary abnormalities, such as IH or low-grade IP.

Genomic characterization of a cell-culture-adapted Korean human G9P[8] rotavirus, CAU05-202.

The human rotavirus G9 strain is the fifth most common rotavirus worldwide. A human rotavirus G9P[8] strain CAU05-202 was isolated from a young child with diarrhea using a cell culture system, and its major gene sequences were determined. Phylogenetic analysis of the VP7 gene revealed that CAU05-202 clustered into genetic lineage III-d and was most closely related to G9 rotaviruses from Turkey (strain GUH13) and Sri Lanka (strain 05SLC056 and 05SLC057). VP4 and NSP4 gene analysis showed that CAU05-202 belongs to the P[8]-3 lineage and genotype B, respectively. In addition, CAU05-202 has a long RNA electropherotype, supported by VP6 gene analysis, which is clearly associated with subgroup II specificity. Analysis of the G9 rotavirus strain CAU05-202 provides information concerning the genetic relationships among global rotavirus G9 strains, suggesting that closely related G9 strains are persistent and widespread in Asian countries.

Complete genomic characterization of cell culture adapted human G12P[6] rotaviruses isolated from South Korea.

Two unusual human rotavirus G12 strains, CAU195 and CAU214, were isolated from female pediatric diarrhea patients under 12 months of age in 2006 using a cell culture system and their full genome sequences were analyzed. The 11 gene segments of both Korean G12 strains were classified as G12-P[6]-R1-C1-M1-I1-A1-N1-T1-E1-H1 genotypes. Notably, the Korean strains were of the same genotypes as previously reported strains isolated from Bangladesh in 2003 (Dhaka12-03), from the United States in 2005-2006 (US6597), and from Germany in 2008 (GER126-08 and GER172-08), suggesting that closely related G12P[6] strains are persistent and widespread.

Molecular characterization of rotavirus diarrhea among children in South Korea: detection of an unusual G11 strain.

Among 312 rotavirus-positive samples collected from eight hospitals across South Korea during 2008 and 2009, the most prevalent circulating G genotype was G1 (35.9%), followed by G3 (24.7%), G2 (17.0%), G4 (7.7%), and G9 (2.6%). Notably, one unusual G11 lineage III strain-the first hypoendemic infection case in the world-was found. Of the P genotypes, P[8] (43.9%) was the most common, followed by P[6] (29.5%), P[4] (9.3%) and P[9] (0.6%). Determining G- and P-type combinations showed that G1P[8] was the most prevalent (20.5%), followed by G2P[6] (12.8%) and G3P[8] (12.8%). These findings provide new information concerning the current prevalence and spread of the rare G11 rotavirus.

Molecular characterization of rare G12P[6] rotavirus isolates closely related to G12 strains from the United States, CAU 195 and CAU 214.

Two human G12 rotaviruses, CAU 195 and CAU 214, were isolated from South Korea using cell culture and characterized on the basis of sequence divergence in the VP7, VP4, and NSP4 genes. Phylogenetic analysis of the VP7 gene sequences indicated that these strains clustered into lineage III and were most closely related to G12 rotaviruses isolated in the United States. The VP4 and NSP4 gene sequences showed that two strains belonged to the P[6]-Ia lineage and genotype [B]. This finding provides information that can be used to evaluate G12 strains and aid in the development of effective vaccines in the future.

Genetic characterization of norovirus GII.4 2006b variants from Jeju island, South Korea.

Ninety-seven fecal specimens collected from children with acute gastroenteritis between 2007 and 2008 that were found to be negative for group A rotavirus in prescreening by ELISA with VP6-specific antibody were re-screened for viruses by reverse transcription (RT)-PCR. Forty (41.2%) samples were found to be positive for virus by RT-PCR; of these, norovirus (32.5%, n = 13) and rotavirus (32.5%, n = 13) were the most common, followed by astrovirus (5.0%, n = 2) and enterovirus (2.5%, n = 1). Co-infection was found in 11 (27.5%) samples. Phylogenetic analyses of the ORF2 nucleotide sequences of 21 norovirus strains showed that 19 (90.5%) belonged to the genogroup GII genotype 4 and two (9.5%) belonged to genogroup GI genotype 4. The GII.4 strains demonstrated high sequence homology and were closely related to new 2006b variants observed in Europe, China, Hong Kong, and Japan in 2006. This study provides new information concerning the recent global epidemic of 2006b strains.

Genetic variation of prevalent G1P[8] human rotaviruses in South Korea.

The human rotavirus G1P[8] strain is one of the most common rotaviruses worldwide, including Korea. Six Korean G1P[8] human rotaviruses, isolated using cell culture techniques, were characterized on the basis of sequence differences in VP7, VP4, VP6, and NSP4 genes to elucidate the evolutionary relationships in the community. All strains had a long RNA electropherotype, supported by VP6 gene analysis, clearly associated with subgroup II specificity. The phylogenetic analysis of VP7 gene sequences showed that they all clustered into lineage I, as reported for G1 strains in Japan, China, Vietnam, and Thailand. In addition, phylogenetic analysis of the VP4 gene showed that they belong to two distinct lineages, P[8]-II and P[8]-III. With respect to the NSP4 gene, all strains belonged to genotype B. An understanding of the ecology and molecular evolution of rotaviruses circulating in the country is very important for the development of vaccines and vaccination strategies. This study provides new information concerning the genetic variability of the rotavirus strain G1P[8] occurring most commonly as a vaccine candidate.

Genetic variation of G4P[6] rotaviruses: evidence for novel strains circulating between the hospital and community.

One hundred forty-six fecal specimens collected between 2007 and 2008 from infants with acute gastroenteritis were screened for rotavirus by ELISA with VP6-specific antibody. One hundred twenty-three of the samples (84.2%) were confirmed to be positive for group A rotavirus (community-acquired, n = 90 [73.2%] and nosocomial, n = 33 [26.8%]), and were typed subsequently using RT-PCR and sequence analysis methods. Determination of G- and P-type combinations showed that G4P[6] (78.9%) was the most common strain, followed by G3P[8] (7.3%), G1P[8] (6.5%), G2P[4] (0.8%), G2P[6] (0.8%), G1P[6] (0.8%), and G9P[8] (0.8%) strains. Of the 97 G4P[6] strains, 62 (63.8%) were responsible for community-acquired cases and 35 (36.1%) were hospital-acquired cases. Phylogenetic analysis of the VP7 gene from the G4P[6] strains revealed that both the community-acquired and nosocomial strains were segregated to the human rotaviruses circulating world-wide, including the prototype vaccinal strain, ST3, which constituted a novel sublineage in lineage 1. Owing to the recent emergence of G4P[6] rotaviruses within the hospital, as well as in the community, the findings from this study are important since they provide new information concerning the community and nosocomial spread of rotaviruses.

Detection of unusual rotavirus genotypes G8P[8] and G12P[6] in South Korea.

Five hundred four fecal specimens, collected between 2004 and 2006 from young children with acute diarrhea, were screened for rotavirus by ELISA with VP6-specific antibody. Of these samples, 394 (78.2%) were confirmed as group A rotavirus and they underwent G- and P typing using a combination of ELISA, RT-PCR, and sequence analysis methods. The dominant circulating G serotype was G1 (35.6%) followed by G3 (26.4%), G4 (14.7%), and G2 (11.9%). There was a low prevalence of G9 (1.0%) and of unusual G type rotavirus, in particular, G12 (0.5%) and G8 (0.3%). Of the P genotype rotavirus in circulation, P[8] (53.0%) was most common followed by P[6] (15.5%), P[4] (15.2%), and P[9] (2.3%). Determination of G- and P type combinations revealed that G1P[8] strains were most prevalent (25.4%), amid G3P[8] (16.8%), G2P[4] (6.3%), and G4P[6] (6.1%) strains. Unusual or rare combinations such as G2P[6], G2P[8], G3P[4], G2P[9], G1P[9], G3P[9], G12P[6], G1P[4], G3P[6], and G8P[8] were also found. Owing to the recent emergence of G8 and G12 rotavirus, the findings from this study are important since they provide new information concerning the local and global spread of rotavirus genotypes.