Identification of a rotavirus G12 strain, Indonesia

Complete genome analyses of G12P[8] rotavirus strains from hospitalized children in Surabaya, Indonesia, 2017-2018

Rotavirus A (RVA) is a major viral cause of acute gastroenteritis (AGE) worldwide. G12 RVA strains have emerged globally since 2007. There has been no report of the whole genome sequences of G12 RVAs in Indonesia. We performed the complete genome analysis by the next-generation sequencing of five G12 strains from hospitalized children with AGE in Surabaya from 2017 to 2018. All five G12 strains were Wa-like strains (G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1) and were clustered into lineage-III of VP7 gene phylogenetic tree. STM430 sample was observed as a mixed-infection between G12 and G1 strains: G12/G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. A phylogenetic tree analysis revealed that all five Indonesian G12 strains (SOEP379, STM371, STM413, STM430, and STM433) were genetically close to each other in all 11 genome segments with 98.0%-100% nucleotide identities, except VP3 and NSP4 of STM430, suggesting that these strains have originated from a similar ancestral G12 RVA. The VP3 and NSP4 genome segments of STM430-G12P[8] were separated phylogenetically from those of the other four G12 strains, probably due to intra-genotype reassortment between the G12 and G1 Wa-like strains. The change from G12P[6] lineage-II in 2007 to G12P[8] lineage-III 2017-2018 suggests the evolution and diversity of G12 RVAs in Indonesia over the past approximately 10 years.

Significance of continuous rotavirus and norovirus surveillance in Indonesia

BACKGROUND

Diarrhea significantly contributes to the global burden of diseases, particularly in developing countries. Rotavirus and norovirus are the most dominant viral agents responsible for diarrheal disease globally. The aim of this review was to conduct a comprehensive assessment of rotavirus and norovirus study in Indonesia.

DATA SOURCES

Articles about rotavirus and norovirus surveillance in Indonesia were collected from databases, including PubMed and Google Scholar. Manual searching was performed to identify additional studies. Furthermore, relevant articles about norovirus diseases were included.

RESULTS

A national surveillance of rotavirus-associated gastroenteritis has been conducted for years, resulting in substantial evidence about the high burden of the diseases in Indonesia. In contrast, norovirus infection received relatively lower attention and very limited data are available about the incidence and circulating genotypes. Norovirus causes sporadic and epidemic gastroenteritis globally. It is also emerging as a health problem in immunocompromised individuals. During post-rotavirus vaccination era, norovirus potentially emerges as the most frequent cause of diarrheal diseases.

CONCLUSIONS

Our review identifies knowledge gaps in Indonesia about the burden of norovirus diseases and the circulating genotypes. Therefore, there is a pressing need to conduct national surveillance to raise awareness of the community and national health authority about the actual burden of norovirus disease in Indonesia. Continuing rotavirus surveillance is also important to assess vaccine effectiveness and to continue tracking any substantial changes of circulating rotavirus genotypes.

Rotavirus infections in Detroit, USA, a region of low vaccine prevalence

After a sharp drop of rotavirus (RV) infections at Children's Hospital of Michigan, Detroit, USA in 2010 season, we noted an increase in the number of cases during the 2011 season including some RV vaccine (RVV) recipients. This study was conducted to determine the circulating genotypes during 2011 season and whether the increase in RV diarrhea was caused by replacement genotypes. G and P genotypes were determined by RT PCR and nucleotide sequencing of selected strains was performed. The vaccination rate among study patients was 24 %. RV strains from 68 stool samples were genotyped including 18 from vaccinated children and 50 from unvaccinated children. The predominant G genotype was G1 (58.8 %) followed by G9 (17.7 %) and G4 (15.5 %). P[8] was the predominant P genotype (68 %) followed by P[6] (17.6 %) and P[4] (3 %). All G9 strains were associated with P[6]. The most prevalent G-P combination was G1P[8] (56 %), followed by G9P[6] (17.6 %). Similar proportions of RV genotypes were found among vaccinated and unvaccinated children. Our local data suggest that 5 years after the introduction of RVV there has been no genotype replacement. Although a small increase in G9P[6] frequency was noted, G1P[8] remained the predominant strain of RV in our inner city community in the Midwestern USA.

Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season

BACKGROUND

We observed an increase in the number of rotavirus cases in the St. Louis area during the 2012-2013 rotavirus season compared with recent seasons. We aimed to determine whether the rotavirus cases during the 2012-2013 rotavirus season were of types not included in licensed vaccines.

METHODS

Microbiology laboratories of 3 children's hospitals in St. Louis provided samples that were positive using rapid antigen tests from 2010 to 2013. The majority of samples were from St. Louis Children's Hospital. We determined rotavirus genotypes by polymerase chain reaction tests and further characterized a subset of viruses by genome sequencing and comparative sequence analysis.

RESULTS

Eighty-six percent (24 of 28) of typed viruses analyzed from the 2012-2013 rotavirus season were G12. We performed whole genome sequencing on 8 G12 viruses, all of which were VP4 type P[8]. The sequenced viruses showed differences from vaccine strains in major antigenic epitopes on the VP7 protein, but most epitopes on VP4 were conserved. Rotavirus vaccine histories were available for 11 G12 cases, of whom 10 had not been vaccinated.

CONCLUSIONS

G12 was a dominant community-wide genotype in 2013. Most of the G12 cases for whom vaccine histories were available had not received rotavirus vaccine. The experience demonstrates the potential for rapid shifts in rotavirus genotype distribution and underscores the need for vigilant surveillance to detect unusual genotypes that might escape from vaccine protection.

Whole Genomic Analysis of Human G12P[6] and G12P[8] Rotavirus Strains that Have Emerged in Myanmar

G12 rotaviruses are emerging rotavirus strains causing severe diarrhea in infants and young children worldwide. However, the whole genomes of only a few G12 strains have been fully sequenced and analyzed. In this study, we sequenced and characterized the complete genomes of six G12 strains (RVA/Human-tc/MMR/A14/2011/G12P[8], RVA/Human-tc/MMR/A23/2011/G12P[6], RVA/Human-tc/MMR/A25/2011/G12P[8], RVA/Human-tc/MMR/P02/2011/G12P[8], RVA/Human-tc/MMR/P39/2011/G12P[8], and RVA/Human-tc/MMR/P43/2011/G12P[8]) detected in six stool samples from children with acute gastroenteritis in Myanmar. On whole genomic analysis, all six Myanmarese G12 strains were found to have a Wa-like genetic backbone: G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 for strains A14, A25, P02, P39, and P43, and G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 for strain A23. Phylogenetic analysis showed that most genes of the six strains examined in this study were genetically related to globally circulating human G1, G3, G9, and G12 strains. Of note is that the NSP4 gene of strain A23 exhibited the closest relationship with the cognate genes of human-like bovine strains as well as human strains, suggesting the occurrence of reassortment between human and bovine strains. Furthermore, strains A14, A25, P02, P39, and P43 were very closely related to one another in all the 11 gene segments, indicating derivation of the five strains from a common origin. On the other hand, strain A23 consistently formed distinct clusters as to all the 11 gene segments, indicating a distinct origin of strain A23 from that of strains A14, A25, P02, P39, and P43. To our knowledge, this is the first report on whole genome-based characterization of G12 strains that have emerged in Myanmar. Our observations will provide important insights into the evolutionary dynamics of spreading G12 rotaviruses in Asia.

Surveillance and molecular characterization of group A rotaviruses in Goroka, Papua New Guinea

In this study, we investigated the molecular epidemiology of group A rotaviruses in cases of acute gastroenteritis in Goroka, Papua New Guinea. From April 2008 through November 2010, 813 diarrheal stool samples were collected from children < 5 years of age hospitalized with acute gastroenteritis. Rotavirus antigen was detected in 31.2% of samples using a commercial enzyme-linked immunosorbent assay. Genotyping revealed the presence of the globally circulating strains G1P[8] (50.0%), G3P[8] (23.0%), and G2P[4] (8.2%). The globally emerging strains G9 and G12 were detected in 1.2% and 6.1% of samples, respectively. Mixed infections were detected in a high proportion of samples (11.9%), with 9.0% and 3.7% of samples displaying multiple G and P genotypes, respectively.

Burden and typing of rotavirus group A in Latin America and the Caribbean: systematic review and meta-analysis

The efficacy of licensed rotavirus vaccines has only been shown against certain rotavirus group A (RV-A) types. It is critical to understand the burden of rotavirus gastroenteritis (RVGE) and its prevalent types to assess the potential impact of these vaccines in Latin America and the Caribbean (LA&C). We performed a systematic review and meta-analyses of all the available evidence reported from 1990 to 2009 on the burden of rotavirus disease and strains circulating in LA&C. Eligible studies--185 country-level reports, 174 951 faecal samples--were selected from MEDLINE, Cochrane Library, EMBASE, LILACS, regional Ministries of Health, PAHO, regional proceedings, doctoral theses, reference lists of included studies and consulting experts. Arc-sine transformations and DerSimonian-Laird random-effects model were used for meta-analyses. The proportion of gastroenteritis cases due to rotavirus was 24.3% (95%CI 22.3-26.4) and the incidence of RVGE was 170 per 1000 children-years (95%CI 130-210). We estimated a global annual mortality for 22 countries of 88.2 (95%CI 79.3-97.1) deaths per 100 000 under 5 years (47 000 deaths).The most common G type detected was G1 (34.2%), followed by G9 (14.6%), and G2 (14.4%). The most common P types detected were P[8] (56.2%), P[4] (22.1%) and P[1] 5.4%, and the most prevalent P-G type associations were P[8]G1 17.9%, P[4]G2 9.1% and P[8]G9 8.8%. In the last 10 years, G9 circulation increased remarkably and G5 almost disappeared. More recently, G12 appeared and P[4]G2 re-emerged. To our knowledge, this is the first meta-analysis of rotavirus infection and burden of disease in LA&C.

Enteric disease surveillance under the AFHSC-GEIS: current efforts, landscape analysis and vision forward

The mission of the Armed Forces Health Surveillance Center, Division of Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) is to support global public health and to counter infectious disease threats to the United States Armed Forces, including newly identified agents or those increasing in incidence. Enteric diseases are a growing threat to U.S. forces, which must be ready to deploy to austere environments where the risk of exposure to enteropathogens may be significant and where routine prevention efforts may be impractical. In this report, the authors review the recent activities of AFHSC-GEIS partner laboratories in regards to enteric disease surveillance, prevention and response. Each partner identified recent accomplishments, including support for regional networks. AFHSC/GEIS partners also completed a Strengths, Weaknesses, Opportunities and Threats (SWOT) survey as part of a landscape analysis of global enteric surveillance efforts. The current strengths of this network include excellent laboratory infrastructure, equipment and personnel that provide the opportunity for high-quality epidemiological studies and test platforms for point-of-care diagnostics. Weaknesses include inconsistent guidance and a splintered reporting system that hampers the comparison of data across regions or longitudinally. The newly chartered Enterics Surveillance Steering Committee (ESSC) is intended to provide clear mission guidance, a structured project review process, and central data management and analysis in support of rationally directed enteric disease surveillance efforts.

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.