Analysis of rotavirus genotypes in Korea during 2013: an increase in the G2P[4] genotype after the introduction of rotavirus vaccines

Molecular Epidemiology of Adenoviral Keratoconjunctivitis in Korea

Human adenoviruses (HAdVs) are a major cause of epidemic keratoconjunctivitis. We investigated the types of adenoviruses responsible for the recent epidemic of keratoconjunctivitis in Korea. From January to November 2019, 218 conjunctival swab samples were collected from patients clinically suspected as having adenoviral keratoconjunctivitis. Genotyping targeting of adenovirus capsid hexon genes was performed using PCR and sequencing. Of the 218 samples collected, 128 (58.7%) were positive for the adenovirus genes by PCR, and 126 samples were successfully genotyped. Adenovirus type 8 (HAdV-D8) was the most common type (67.5%), followed by HAdV-D64 (11.1%), HAdV-D37 (9.5%), HAdV-B3 (5.6%), HAdV-D53 (4.0%), HAdV-E4 (1.6%), and HAdV-D56 (0.8%). Adenoviral keratoconjunctivitis cases were the most frequent in July and August 2019, which were mainly caused by type 8. Phylogenetic analyses revealed little genetic distance among adenoviruses of the same type detected in our study. Our results provide basic data for further studies of adenoviral keratoconjunctivitis.

Relationship Between Rotavirus P[6] Infection in Korean Neonates and Histo-Blood Group Antigen: a Single-Center Study

Background

Rotaviruses are a major cause of pediatric gastroenteritis. The rotavirus P[6] genotype is the most prevalent genotype isolated from Korean neonates but has rarely been reported in other countries. Histo-blood group antigen (HBGA) is known to play an important role in rotavirus infection. We investigated the relationship between rotavirus genotype and HBGA-Lewis blood type in Korean children and explored the reasons for the predominance of rotavirus P[6] strain in Korean neonates.

Methods

Blood and stool samples were collected from 16 rotavirus-infected patients. Rotavirus G (VP7) and P (VP4) genotyping was performed using reverse transcription-PCR and sequencing. Lewis antigen phenotypes (Le^a/Le^b) were tested, and HBGA-Lewis genotype was determined by sequencing the secretor (FUT2) and Lewis (FUT3) genes. Deduced amino acid sequences and three-dimensional structures of the VP8* portion of the rotavirus VP4 protein were analyzed.

Results

All P[6] rotaviruses were isolated from neonates under one month of age, who were negative or weakly positive for the Le^b antigen. However, 10 of the 11 non-P[6] rotaviruses were isolated from older children who were Le^b antigen-positive. The VP8* amino acid sequences differed among P[6], P[4], and P[8] genotypes. Korean P[6] strains showed a unique VP8* sequence with amino acid substitutions, including Y169 > L169, which differed from the sequences of P[6] strains from other countries.

Conclusions

The predominance of the rotavirus P[6] genotype in Korean neonates may be related to the interaction between HBGA-Lewis antigen and the VP8* portion of the VP4 protein, and this information will be helpful in future neonatal vaccine development.

Increasing detection of rotavirus G2P[4] strains in Nizhny Novgorod, Russia, between 2016 and 2019

Rotavirus infection is one of the leading causes of acute gastroenteritis in children in their first years of life. We studied the genotypic diversity of rotavirus A (RVA) strains in Nizhny Novgorod, Russia, during the period 2016-19. In total, 4714 samples of faeces from children admitted to the Nizhny Novgorod Hospital for Infectious Diseases with acute gastroenteritis were examined. The share of rotavirus-positive samples was 31.5% in 2016-17. It decreased to 21.6% in 2018-19. In Nizhny Novgorod, all six global types of RVA were detected (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]), as well as sporadic samples with genotypes G9P[4], G3P[9], G9P[9], G8P[8], G2P[8], G4P[4], G3P[9]. The fraction of strains with genotype G2P[4] gradually increased from 5.9% in 2016-17 to 39.1% in 2018-19. Simultaneously, the proportion of G9P[8] strains decreased from 63.2% to 27.7% in the same period. Phylogenetic analysis showed that rotaviruses with the G2P[4] genotype carried ubiquitous alleles of the VP7 and VP4 genes during the period of their prevalence: G2-IVa-1 and G2-IVa-3; P[4]-IVa and P[4]-IVb. As rotavirus vaccination is not widely used in the region because it is not included in the national vaccination calendar in Russia so far, the increase in the number of G2P[4] RVA is likely due to natural strain fluctuations.

G2P[4] rotavirus outbreak in Belu, East Nusa Tenggara Province, Indonesia, 2018

Rotavirus is a major cause of acute gastroenteritis (AGE) in children worldwide. However, rotavirus outbreak has rarely been reported in Indonesia. This study aims to identify the causative agent for AGE outbreak among children in Belu, East Nusa Tenggara, Indonesia in 2018. All the samples were negative for bacteria (Salmonella, V. cholera) and Norovirus. Ten out of 11 stool samples were rotavirus-positive by immunochromatography testing. Reverse-transcription polymerase chain reaction (RT-PCR) and phylogenetic analyses revealed that rotavirus G2P[4] was the possible causative agent for the AGE outbreak, although sample size was limited. These findings suggest that the AGE outbreak was caused by rotavirus G2P[4], highlighting the importance of rotavirus surveillance.

Whole-genome analysis of rotavirus G4P[6] strains isolated from Korean neonates: association of Korean neonates and rotavirus P[6] genotypes

Background

Group A rotaviruses are the major causative agents of pediatric gastroenteritis worldwide. Several studies have reported the predominance of G4P[6] rotavirus genotypes in Korean neonates, which is uncommon in other countries. Therefore, the purposes of this study were to determine the genotype constellations of complete genomes of G4P[6] rotavirus strains isolated from Korean neonates using next-generation sequencing, to compare these sequences with other G4P[6] strains in other countries, and to determine the reason for the predominance of G4P[6] genotypes in Korean neonates.

Results

Twenty rotavirus G4P[6] strains, isolated from January 2013 to January 2016, were selected for whole-genome sequencing. Eleven rotavirus genes were amplified using specific primer sets, and sequencing was carried out using an Ion S5 XL next-generation sequencing platform. Genotypes of each gene were determined, and phylogenetic analyses were performed to investigate genetic distances between genes of rotaviruses in this study and those of other rotavirus G4P[6] strains whose whole-genome sequences were previously published. All 20 rotavirus strains in this study had the same genotype: G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, representing the Wa-like genotype constellation. BLAST searches of 20 G4P[6] rotavirus strains revealed that all G4 sequences in this study showed the highest nucleotide identity to G4 sequences of G4P[6] rotavirus strains isolated in Korea in 2008 (GenBank accession number: FJ603447). Additionally, P[6] gene sequences in this study showed the highest nucleotide identity to P[6] sequences of G4P[6] strains detected in Korea in 2002 (AY158093). Phylogenetic and nucleotide sequence analyses showed that G4P[6] strains in this study and previously reported G4P[6] strains in Korea were mostly detected in neonates and had similar G4 and P[6] sequences compared with other G4P[6] strains detected in other countries.

Conclusions

This study showed that the whole-genome constellation of rotavirus G4P[6] strains from Korean neonates resembled a Wa-like genotype constellation. Additionally, rotavirus genotypes detected in Korean neonates had unique P[6] sequences, which may be the cause of Korean neonatal rotavirus infection.

Electronic supplementary material

The online version of this article (10.1186/s13099-019-0318-5) contains supplementary material, which is available to authorized users.

Performance Evaluation of the Automated Fluorescent Immunoassay System Rotavirus Assay in Clinical Samples

Background

The Automated Fluorescent Immunoassay System (AFIAS) rotavirus assay (Boditech Med Inc., Chuncheon, Korea) is a new rapid antigen test for rotavirus detection. We evaluated the performance of this assay for detecting rotaviruses and their specific genotypes in clinical stool samples.

Methods

AFIAS rotavirus assay was performed in 103 rotavirus-positive and 103 rotavirus-negative stool samples (confirmed by both PCR and ELISA), and its results were compared with those of PCR, ELISA, and immunochromatographic assay (ICA). We evaluated diagnostic sensitivity/specificity, the detectability of rotavirus subtypes, lower limit of detection (LLOD), reproducibility, cross-reactivity, and interference of AFIAS rotavirus assay.

Results

Based on PCR and ELISA results, diagnostic sensitivity and specificity of the AFIAS rotavirus assay were both 99.0%. LLOD results showed that the AFIAS assay had sensitivity similar to or greater than ICA and ELISA. High reproducibility was confirmed, and no cross-reactivity or interference was detected. This assay could detect genotypes G1P[8], G2P[4], G3P[8], G4P[6], G4P[8], G8P[4], G8P[8], G9P[4], and G9P[8].

Conclusions

The AFIAS rotavirus assay showed high reproducibility, sensitivity, and specificity as well as excellent agreement with ELISA, PCR, and ICA. It detected the most common as well as unusual genotypes of rotavirus prevalent in Korea. It could be a useful on-site assay for rapid, convenient, and cost-effective detection of rotavirus infection.

Evaluation of a New Multiplex Real-Time PCR Assay for Detecting Gastroenteritis-Causing Viruses in Stool Samples

Background

Diarrhea has been the second leading cause of death among children under the age of five, and the rapid and accurate pathogen diagnosis in patients with diarrhea is crucial for reducing morbidity and mortality. A newly developed one-step multiplex real-time PCR assay, the Allplex GI-Virus Assay, was evaluated for its ability to detect six diarrhea-causing viruses (rotavirus, norovirus genogroup I (GI) and genogroup II (GII), enteric adenovirus, astrovirus, and sapovirus) in stool samples.

Methods

The performance of the Allplex assay was compared with those of another multiplex PCR assay (Seeplex Diarrhea-V Ace Detection) and genotyping by sequencing, using 446 stool samples from patients with acute gastroenteritis.

Results

The overall agreement rates between the results of the Allplex and Seeplex assays were 98.7% for rotavirus, 99.1% for norovirus GI, 93.3% for norovirus GII, 98.0% for adenovirus, and 99.6% for astrovirus. The overall agreement rates between the Allplex assay and genotyping were 99.1% for rotavirus, 99.1% for norovirus GI, 98.7% for norovirus GII, 89.7% for adenovirus, 98.2% for astrovirus, and 99.8% for sapovirus. In addition, eight rotavirus genotypes, three norovirus GI genotypes, four norovirus GII genotypes, eight adenovirus genotypes, two astrovirus genotypes, and two sapovirus genotypes were detected.

Conclusions

The Allplex assay showed high agreement with Seeplex and genotyping results, and was able to additionally detect sapoviruses. The Allplex assay could be useful in identifying viral gastrointestinal infections in patients with acute gastroenteritis symptoms.

Emergence of G8P[6] rotavirus strains in Korean neonates

Background

Rotaviruses are the major causes of pediatric gastroenteritis worldwide. The genotypic distribution of rotavirus strains shows temporal and geographical fluctuations, and knowledge of the molecular epidemiology of rotaviruses is important for the development of vaccines and diagnostic reagents. We investigated VP4 and VP7 capsid genotypes of rotaviruses isolated from 211 stool specimens collected from Korean neonates in a neonatal intensive care unit from September 2017 to March 2018.

Results

Of 211 stool specimens, 15 specimens (7.1%) were rotavirus-positive. Eleven specimens (73.3%) were G8P[6] type and 4 (26.7%) were G4P[6] type. Sequence analysis revealed that all G8 sequences in this study showed the highest nucleotide identity to G8 sequences of G8P[8] rotavirus strains isolated in Vietnam in 2014, and P[6] gene sequences showed the highest nucleotide identity to P[6] sequences of G4P[6] strains detected in Korea in 2012. Only one amino acid difference in VP7 was found in 3 of the 11 G8P[6] strains in this study, but multiple amino acid substitutions in VP7 were detected between these G8P[6] strains and the commonly used vaccine strains.

Conclusions

This study showed that rotavirus G8P[6] strains were firstly detected at high frequency in Korean neonates from September 2017 to March 2018. These new rotavirus G8P[6] strains were estimated to be derived from reassortment events between the G8 of G8P[8] strains in Asian region and the P[6] of G4[6] in Korea. Whether the emergence of this unusual G8P[6] strain reflects continuous prevalence or transient occurrence will require continuous monitoring of rotavirus epidemiology.

Phylogenetic comparison of the VP7, VP4, VP6, and NSP4 genes of rotaviruses isolated from children in Nizhny Novgorod, Russia, 2015-2016, with cogent genes of the Rotarix and RotaTeq vaccine strains

Group A rotaviruses (RVA) are one of the leading causes of gastroenteritis in young children worldwide. The introduction of universal mass vaccination around the world has contributed to a reduction in hospitalizations and outpatient visits associated with rotavirus infection. Continued surveillance of RVA strains is needed to determine long-term effects of vaccine introduction. In the present work, we carried out the analysis of the genotypic diversity of RVA strains isolated in Nizhny Novgorod (Russia) during the 2015-2016 epidemic season. Also we conducted a comparative analysis of the amino acid sequences of T-cell epitopes of wild-type and vaccine (RotaTeq and Rotarix) strains. In total, 1461 samples were examined. RVAs were detected in 30.4% of cases. Rotaviruses with genotype G9P[8] (40.5%) dominated in the 2015-16 epidemic season. Additionally, RVAs with the following genotypes were detected: G4P[8] (25.4%), G1P[8] (13%), G2P[4] (3.2%). Rotaviruses with genotypes G3P[9], G6P[9], and G1P[9] totaled 3%. The number of partially typed and untyped RVA samples was 66 (14.9%). The findings of a RVA of G6P[9] genotype in Russia were an original observation. Our analysis of VP6 and NSP4 T-cell epitopes showed highly conserved amino acid sequences. The found differences seem not to be caused by the immune pressure but were rather related to the genotypic affiliations of the proteins. Vaccination against rotavirus infection is not included in the national vaccination schedule in Russia. Monitoring of the genotypic and antigenic diversity of contemporary RVA will allow providing a comparative analysis of wild-type strains in areas with and without vaccine campaign.

Changes in Rotavirus Genotypes before and after Vaccine Introduction: a Multicenter, Prospective Observational Study in Three Areas of Japan

In Japan, monovalent and pentavalent rotavirus (RV) vaccines were approved in 2011 and 2012, respectively. To monitor changes in the RV genotypes before and after vaccine introduction, we performed a prospective observational study among children (＜ 5 years) with gastroenteritis who tested RV-positive on antigen rapid tests. Stool samples were collected from 3 different sites in Japan: Tsu City, Mie Prefecture; Kurashiki City, Okayama Prefecture; and Isumi City, Chiba Prefecture. RV genotypes were determined using reverse transcription-polymerase chain reaction. In Tsu City, G3P[8] was dominant (61.0-77.1%) before vaccine introduction, but decreased after introduction. Meanwhile, in an inverse proportion to the decrease in G3P[8], G1P[8] increased until the 2013/14 season, when a sudden predominance of G2P[4] (100%) occurred. A similar trend was observed in Kurashiki City in terms of the extent of reduction in G3P[8] and the emergence of G2P[4]. In Isumi City, G1P[8] was dominant (70.3%) before vaccine introduction, and G9P[8] became predominant (83.3%) in the 2013/14 season. To determine whether the genotype changes are attributable to vaccines or natural epidemiological changes, ongoing continuous monitoring of the RV genotypes is required.

Rotavirus vaccine and health-care utilization for rotavirus gastroenteritis in Tsu City, Japan

Background

Rotavirus vaccines were introduced in Japan in November 2011. We evaluated the subsequent reduction of the health-care burden of rotavirus gastroenteritis.

Methods

We conducted active surveillance for rotavirus gastroenteritis among children under 5 years old before and after the vaccine introduction. We surveyed hospitalization rates for rotavirus gastroenteritis in children in Tsu City, Mie Prefecture, Japan, from 2007 to 2015 and surveyed the number of outpatient visits at a Tsu City clinic from 2010 to 2015. Stool samples were obtained for rotavirus testing and genotype investigation. We assessed rotavirus vaccine coverage for infants living in Tsu City.

Results

In the pre-vaccine years (2007–2011), hospitalization rates for rotavirus gastroenteritis in children under 5 years old were 5.5, 4.3, 3.1 and 3.9 cases per 1000 person-years, respectively. In the post-vaccine years (2011–2015), the rates were 3.0, 3.5, 0.8 and 0.6 cases per 1000 person-years, respectively. The hospitalization rate decreased significantly in the 2013–2014 and 2014–2015 seasons compared to the average of the seasons before vaccine introduction (P < 0.0001). In one pre-vaccine year (2010–2011), the number of outpatient visits due to the rotavirus infection was 66. In the post-vaccine years (2011–2015), the numbers for each season was 23, 23, 7 and 5, respectively. The most dominant rotavirus genotype shifted from G3P[8] to G1P[8] and to G2P[4]. The coverage of one dose of rotavirus vaccine in Tsu City was 56.5% in 2014.

Conclusion

After the vaccine introduction, the hospitalization rates and outpatient visits for rotavirus gastroenteritis greatly decreased.

Whole genomic analysis of G2P[4] human Rotaviruses in Mymensingh, north-central Bangladesh

Rotavirus A (RVA) is a dominant causative agent of acute gastroenteritis in children worldwide. G2P[4] is one of the most common genotypes among human rotavirus (HRV) strains, and has been persistently prevalent in South Asia including Bangladesh. In the present study, whole genome sequences of a total of 16 G2P[4] HRV strains (8 strains each in 2010 and 2013) detected in Mymensingh, north-central Bangladesh were determined. These strains had typical DS-1-like genotype constellation. Most of gene segments from DS-1 genogroup exhibited high level sequence identities to each other (>98%), while slight diversity was observed for VP1, VP3, and NSP4 genes. By phylogenetic analysis, individual RNA segments were classified into one (V) or two-three lineages (V–VI or V–VII). In terms of lineages (sublineages) of 11 gene segments, the 16 Bangladeshi strains could be further classified into four clades (A-D) containing 8 lineage constellations, revealing the presence of three clades (A-C) with three lineage constellations in 2010, and a single clade (D) with four constellations in 2013. Therefore, co-existence of multiple G2P[4] HRV strains with different lineage constellations, and change in clades for the study period were demonstrated. Although amino acids in the antigenic regions on VP7 and VP4 were mostly identical to those of global G2P[4] strains after 2000, VP4 of clade D RVAs in 2013 had alanine and proline at positions 88 and 114, respectively, which are novel substitutions compared with recent global G2P[4] strains. Replacement of lineage constellations associated with unique amino acid changes in the antigenic region in VP4 suggested continuous genetic evolutionary state for emerging new G2P[4] rotavirus strains in Bangladesh.

High incidence of group A rotaviruses G4P[6] strains among children in Gyeonggi province of South Korea, from 2009 to 2012

The genotype distribution of group A rotaviruses (RVAs) circulating in Gyeonggi province, South Korea between 2009 and 2012 was investigated. A total of 2619 stool specimens from sporadic acute gastroenteritis cases and 117 acute gastroenteritis outbreaks were analyzed. Among them, RVAs were detected from 263 (10.0%) sporadic cases and 3 (2.6%) outbreaks. The G4P[6] strains predominated (29.7%), followed by G1P[8] (19.4%), G2P[4] (15.6%), G3P[8] (13.3%) and G9P[8] (6.5%) strain. Especially 96.2% of the genotype G4P[6] strains were isolated from children<1year of age. Phylogenetic analysis revealed that genotype G4P[6] strains were members of sub-lineage Ie(G4) and Ia(P[6]). Intensified monitoring of RVAs, especially G4P[6] strains among young children, is essential to control RVA infections.

Changing distribution of age, clinical severity, and genotypes of rotavirus gastroenteritis in hospitalized children after the introduction of vaccination: a single center study in Seoul between 2011 and 2014

Background

This study aimed to explore changes in clinical epidemiology and genotype distribution and their association among hospitalized children with rotavirus gastroenteritis after the introduction of vaccines.

Methods

Between November 2010 and October 2014, hospitalized children with acute gastroenteritis were enrolled. Rotavirus genotypes were confirmed through reverse transcription-polymerase chain reaction (RT-PCR), semi-nested PCR, and sequencing. Clinical information including vaccination status and the modified Vesikari scores were collected.

Results

Among 179 children with rotavirus infection, nineteen (10.6 %) were completely vaccinated. During the study period, the number of children between three and 23 months of age decreased significantly compared to the number of children older than 24 months of age (P = 0.010), who showed lower diarrhea severity (duration, P = 0.042; frequency, P = 0.021) but higher vomiting severity (P = 0.007, 0.036) compared to the former. Vaccination status was also significantly associated with lower vomiting severity after adjustment for age (frequency only, P = 0.018). The predominant genotypes were G2P[4] (18.4 %), G1P[8] (14.5 %), and G1P[4]P[8] (12.8 %), and the prevalence of genotypes with uncommon and mixed combinations was more than 50 %. Children infected with G2P[4] strains tended to be older (P = 0.005) and had more severe vomiting (P = 0.018, 0.006) than those with G1P[8].

Conclusions

Increase in age of infected, hospitalized children was accompanied by change in clinical severity during 2011–2014 after the introduction of vaccines in Seoul. Clinical severity was also associated with vaccination status and genotype. Long-term large scale studies are needed to document the significance of the increase in genotypes of uncommon and mixed combinations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-1623-y) contains supplementary material, which is available to authorized users.

G2 rotavirus within an emergent VP7 evolutionary lineage circulating in children with acute diarrhea in Guangxi Province of China, 2014

Routine surveillance revealed that the prevalence of P[4] rotaviruses circulating in children with acute diarrhea in Guangxi Province, China, increased in 2014. However, VP7 genotyping for these P[4] rotaviruses was unsuccessful. Exhaustive database searching and sequence analysis indicated that the G genotype of these P[4] rotaviruses was G2, and the VP7 genes clustered with recently emerging G2 strains in several countries within an emergent evolutionary lineage that was distinct from the previously designated lineages I-IV as well as lineage V including porcine rotaviruses. Further studies are essential to monitor the potential global spread of this emerging G2 rotavirus.

Detection of Rotavirus Genotypes in Korea 5 Years after the Introduction of Rotavirus Vaccines

Rotavirus (RV) is one of the most important viral etiologic agents of acute gastroenteritis (AGE) in children. Although effective RV vaccines (RVVs) are now used worldwide, novel genotypes and outbreaks resulting from rare genotype combinations have emerged. This study documented RV genotypes in a Korean population of children with AGE 5 yr after the introduction of RVV and assessed potential genotype differences based on vaccination status or vaccine type. Children less than 5-yr-old diagnosed with AGE between October 2012 and September 2013 admitted to 9 medical institutions from 8 provinces in Korea were prospectively enrolled. Stool samples were tested for RV by enzyme immunoassay and genotyped by multiplex reverse-transcription polymerase chain reaction. In 346 patients, 114 (32.9%) were RV-positive. Among them, 87 (76.3%) patients were infected with RV alone. Eighty-six of 114 RV-positive stool samples were successfully genotyped, and their combinations of genotypes were G1P[8] (36, 41.9%), G2P[4] (12, 14.0%), and G3P[8] (6, 7.0%). RV was detected in 27.8% of patients in the vaccinated group and 39.8% in the unvaccinated group (P=0.035). Vaccination history was available for 67 of 86 cases with successfully genotyped RV-positive stool samples; RotaTeq (20, 29.9%), Rotarix (7, 10.4%), unvaccinated (40, 59.7%). The incidence of RV AGE is lower in the RV-vaccinated group compared to the unvaccinated group with no evidence of substitution with unusual genotype combinations.