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In this study, we report the detection of a G6P[14] rotavirus strain from a human stool sample within the United States. The full genotype constellation of the G6P[14] strain was identified as G6-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3.

Rotavirus (RV) was a common healthcare-associated infection prior to the introduction of the RV vaccine. Following widespread RV vaccination, healthcare-associated rotavirus cases are rare. We describe an investigation of a cluster of rotavirus infections in a pediatric hospital in which an uncommon genotype not typically circulating in the United States was detected.

Background Rotavirus group A (RVA) was the most common cause of infectious gastroenteritis among young children before introduction of rotavirus vaccine in the United States in 2006. Following widespread vaccination, U.S. hospital acquired (HA) rotavirus cases are rare. We describe a cluster of rotavirus infections in a pediatric hospital with a genotype uncommon among U.S. children. Methods Patient cases of HA gastrointestinal (GI) illness were detected through hospital-wide microbiology surveillance, performed by Infection Prevention and Control (IPC) practitioners per state requirements. Cluster procedures were implemented on a unit when 3 cases were identified by symptoms and/or laboratory tests within 48 hours. Due to the current rarity of rotavirus clusters, the hospital partnered with Centers for Disease Control and Prevention (CDC) laboratories to sequence strains in addition to instituting local control measures. RVA strains were genotyped by using the genotype specific qRT-PCR assays for VP7 and VP4 genes. Next Generation Sequencing (NGS) was performed for RVA strain characterization on Illumina MiSeq. Genotypes for all 10 RVA were determined by NCBI’s BLASTN program. Results Epidemiologic surveillance identified a rotavirus cluster of 10 patients aged 10 months to 10 years old, of whom 50% had received rotavirus vaccine. Symptoms included emesis and diarrhea. Cases could not be attributed to vaccine related shedding. All patients had epidemiologic links by contiguous bed spaces or shared care teams. Sequencing was conclusive for 9 of the 10 stool samples to be a G9P[4] genotype, which is rarely detected amongst U.S. children. Local control measures of increased education and cleaning, isolation of positive patients in single rooms, use of soap and water instead of alcohol-based hand sanitizer on room exit, and furlough of symptomatic healthcare workers halted transmission. Conclusion Routine surveillance of HA GI illness identified a cluster; RVA strain genotyping and characterization identified unusual rotavirus genotype G9P[4] as the cause. Partnership between IPC practitioners and laboratorians with CDC demonstrated the need to enhance infection prevention measures to halt transmission and identified a rare rotavirus strain as the likely cause of the cluster. Disclosures Courtney E. Comar, PhD, Pfizer: Stocks/Bonds|Viatris: Stocks/Bonds.

Beachpea (Vigna marina) is a halophytic wild leguminous plant which occurs throughout tropical and subtropical beaches of world. As quantitative trait loci (QTLs) for salt tolerance in V. marina and its crossability with other Vigna species are known, the current study was undertaken to know the presence of these QTLs in the V. marina accessions along with check varieties of pulses. Accordingly, 20 Vigna genotypes (15 accessions of V. marina collected from sea-shore areas of Andaman and Nicobar Islands along with five check varieties of green gram and black gram) were subjected to molecular characterization using seven simple sequence repeat (SSR) markers associated with salt tolerance. Of the markers used, only four SSR markers amplified in the studied germplasm. Number of alleles detected per primer and size of alleles ranged from 1 to 3 and 100 to 325 bp, respectively. Polymorphism information content and heterozygosity values ranged from 0.305 to 0.537 and 0.375 to 0.612, respectively. Three major clusters, cluster I, II and III were obtained at Jaccard's similarity coefficient value of 0.48 through the un-weighted paired group method with arithmetic means method of cluster analysis. It grouped green gram and black gram genotypes in clusters I (04) and II (01), whereas all V. marina genotypes were grouped in cluster III (15). Principal co-ordinate analysis explained 85.9% of genetic variation among genotypes which was further confirmed by cluster analysis. This study indicated the effectiveness of SSR markers in separating cultivated Vigna species from wild V. marina. The findings will be useful for transferring trait of robust salt tolerance of V. marina in cultivated Vigna species using marker-assisted breeding.

Objective Rotavirus A (RVA) remains the main causative agent of gastroenteritis in young children and the young of many mammalian and avian species. In this study we describe a RVA strain detected from a 6-month-old child from Central African Republic (CAR). Results We report the 11 open reading frame sequences of a G29-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 rotavirus strain, RVA/Human-wt/CAR/CAR91/2014/G29P[6]. Nine genes (VP1–VP3, VP6, NSP1–NSP5) shared 90–100% sequence similarities with genogroup 2 rotaviruses. Phylogenetically, backbone genes, except for VP3 and NSP4 genes, were linked with cognate gene sequences of human DS-1-like genogroup 2, hence their genetic origin. The VP3 and NSP4 genes, clustered genetically with both human and animal strains, an indication genetic reassortment human and animal RVA strains has taken place. The VP7 gene shared nucleotide (93–94%) and amino acid (95.5–96.7%) identities with Kenyan and Belgian human G29 strains, as well as to buffalo G29 strain from South Africa, while the VP4 gene most closely resembled P[6]-lineage I strains from Africa and Bangladesh (97%).

Background Following the implementation of rotavirus vaccination in 2006, severe acute gastroenteritis (AGE) due to group A rotavirus (RVA) has substantially declined in US children. We report the RVA genotype prevalence as well as coinfection data from 7 US New Vaccine Surveillance Network sites during 3 consecutive RVA seasons, 2014–2016 Methods A total of 1041 stool samples that tested positive for RVA by Rotaclone enzyme immunoassay were submitted to the Centers for Disease Control and Prevention (CDC) for RVA genotyping and multipathogen testing. Results A total of 795 (76%) samples contained detectable RVA when tested at the CDC. Rotavirus disease was highest in children < 3 years of age. Four G types (G1, G2, G9, and G12) accounted for 94.6% of strains while 2 P types (P[4] and P[8]) accounted for 94.7% of the strains. Overall, G12P[8] was the most common genotype detected in all 3 seasons. Stepwise conditional logistic analysis found year and study site were significant predictors of genotype. Twenty-four percent of RVA-positive specimens contained other AGE pathogens. Conclusions G12P[8] predominated over 3 seasons, but strain predominance varied by year and study site. Ongoing surveillance provides continuous tracking and monitoring of US genotypes during the postvaccine era.

The etiologic agent of an outbreak of pneumonia in Wuhan, China, was identified as severe acute respiratory syndrome coronavirus 2 in January 2020. A patient in the United States was given a diagnosis of infection with this virus by the state of Washington and the US Centers for Disease Control and Prevention on January 20, 2020. We isolated virus from nasopharyngeal and oropharyngeal specimens from this patient and characterized the viral sequence, replication properties, and cell culture tropism. We found that the virus replicates to high titer in Vero-CCL81 cells and Vero E6 cells in the absence of trypsin. We also deposited the virus into 2 virus repositories, making it broadly available to the public health and research communities. We hope that open access to this reagent will expedite development of medical countermeasures.

Species A rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 are represented by the genotypes Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx, respectively. In Benin, ROTAVAC® vaccine was introduced into the Expanded Programme on Immunization in December 2019. To monitor circulating RVA strains for changes that may affect vaccine performance, in-depth analysis of strains prior to vaccine introduction are needed. Here we report, the whole-gene characterization (11 ORFs) for 72 randomly selected RVA strains of common and unusual genotypes collected in Benin from the 2016 to 2018 seasons. The sequenced strains were 15 G1P[8], 20 G2P[4], 5 G9P[8], 14 G12P[8], 9 G3P[6], 2 G1P[6], 3 G2P[6], 2 G9P[4], 1 G12P[6], and 1 G1G9P[8]/P[4]. The study strains exhibited two genetic constellations designed as Wa-like G1/G9/G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and DS-1-like G2/G3/G12-P[4]/P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Genotype G9P[4] strains possessed a DS-1-like genetic constellation with an E6 NSP4 gene, G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2. The mixed genotype showed both Wa-like and DS-1-like profiles with a T6 NSP3 gene G1/G9P[8]/[4]-I1/I2-R1/R2-C1/C2-M1/M2-A1/A2-N1/N2-T1/T6-E1/E6-H1/H2. At the allelic level, the analysis of the Benin strains, reference strains (with known alleles), vaccine strains (with known alleles) identified 2-13 and 1-17 alleles for DS-1-like and Wa-like strains, respectively. Most of the study strains clustered into previously defined alleles, but we defined 3 new alleles for the VP7 (G3 = 1 new allele and G12 = 2 new alleles) and VP4 (P[4] = 1 new allele and P[6] = 2 new alleles) genes which formed the basis of the VP7 and VP4 gene clusters, respectively. For the remaining 9 genes, 0-6 new alleles were identified for both Wa-like and DS-1-like strains. This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. Further detailed studies on these new alleles are needed and these data can also provide a baseline for studies on RVA in the post-vaccination period.

Background Acute gastroenteritis (AGE) burden, etiology, and severity in adults is not well characterized. We implemented a multisite AGE surveillance platform in 4 Veterans Affairs Medical Centers (Atlanta, Georgia; Bronx, New York; Houston, Texas; and Los Angeles, California), collectively serving >320 000 patients annually. Methods From 1 July 2016 to 30 June 2018, we actively identified inpatient AGE case patients and non-AGE inpatient controls through prospective screening of admitted patients and passively identified outpatients with AGE through stool samples submitted for clinical diagnostics. We abstracted medical charts and tested stool samples for 22 pathogens by means of multiplex gastrointestinal polymerase chain reaction panel followed by genotyping of norovirus- and rotavirus-positive samples. We determined pathogen-specific prevalence, incidence, and modified Vesikari severity scores. Results We enrolled 724 inpatients with AGE, 394 non-AGE inpatient controls, and 506 outpatients with AGE. Clostridioides difficile and norovirus were most frequently detected among inpatients (for AGE case patients vs controls: C. difficile, 18.8% vs 8.4%; norovirus, 5.1% vs 1.5%; P < .01 for both) and outpatients (norovirus, 10.7%; C. difficile, 10.5%). The incidence per 100 000 population was highest among outpatients (AGE, 2715; C. difficile, 285; norovirus, 291) and inpatients ≥65 years old (AGE, 459; C. difficile, 91; norovirus, 26). Clinical severity scores were highest for inpatient norovirus, rotavirus, and Shigella/enteroinvasive Escherichia coli cases. Overall, 12% of inpatients with AGE had intensive care unit stays, and 2% died; 3 deaths were associated with C. difficile and 1 with norovirus. C. difficile and norovirus were detected year-round with a fall/winter predominance. Conclusions C. difficile and norovirus were leading AGE pathogens in outpatient and hospitalized US veterans, resulting in severe disease. Clinicians should remain vigilant for bacterial and viral causes of AGE year-round.

Since 2013, group A rotavirus strains characterized as novel DS-1-like intergenogroup reassortant “equine-like G3” strains have emerged and spread across 5 continents among human populations in at least 14 countries. Here, we report a novel one-step TaqMan quantitative real-time reverse transcription-PCR assay developed to genotype and quantify the viral load for samples containing rotavirus equine-like G3 strains. Using a universal G forward primer and a newly designed reverse primer and TaqMan probe, we developed and validated an assay with a linear dynamic range of 227 to 2.3 × 10(9) copies per reaction and a limit of detection of 227 copies. The percent positive agreement, percent negative agreement, and precision of our assay were 100.00%, 99.63%, and 100.00%, respectively. This assay can simultaneously detect and quantify the viral load for samples containing DS-1-like intergenogroup reassortant equine-like G3 strains with high sensitivity and specificity, faster turnaround time, and decreased cost. It will be valuable for high-throughput screening of stool samples collected to monitor equine-like G3 strain prevalence and circulation among human populations throughout the world.

Background The introduction of rotavirus vaccine in the United States has reduced rotavirus disease burden, but outbreaks still occur. Complete-series rotavirus vaccination coverage is Methods Clinical history, signs and symptoms, and vaccination history were abstracted for the 26 patients residing in the facility during the time of the outbreak. A case-patient was defined as one who experienced 3 or more loose stools in a period of 24 hours with onset between April 17 and May 17, 2017. Stool samples from 14 resident patients were tested for rotavirus with reverse-transcription polymerase chain reaction. Results The median patient age at the facility was 2.9 years. Of the 26 resident patients, 22 (85%) met the case definition. One child died. Stool samples from 11 case-patients were positive according to reverse-transcription polymerase chain reaction for rotavirus. Fifteen case-patients were unvaccinated against rotavirus; 3 were partially vaccinated, and 2 were fully vaccinated. Vaccination status could not be completely determined in 2 cases. Conclusions An outbreak of rotavirus affected nearly all resident patients of a subacute care facility and caused 1 death. Because of recommendations against giving rotavirus vaccine in an intensive care setting, infants who require a prolonged intensive care stay might age out of rotavirus vaccine eligibility (the first dose must be given before 15 weeks of age according to Advisory Committee on Immunization Practices recommendations). The result is a vulnerable population of unvaccinated infants who might later congregate in another care setting.

For over a decade, the New Vaccine Surveillance Network (NVSN) has conducted active rotavirus (RVA) strain surveillance in the USA. The evolution of RVA in the post-vaccine introduction era and the possible effects of vaccine pressure on contemporary circulating strains in the USA are still under investigation. Here, we report the whole-gene characterization (eleven ORFs) for 157 RVA strains collected at seven NVSN sites during the 2014 through 2016 seasons. The sequenced strains included 52 G1P[8], 47 G12P[8], 18 G9P[8], 24 G2P[4], 5 G3P[6], as well as 7 vaccine strains, a single mixed strain (G9G12P[8]), and 3 less common strains. The majority of the single and mixed strains possessed a Wa-like backbone with consensus genotype constellation of G1/G3/G9/G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while the G2P[4], G3P[6], and G2P[8] strains displayed a DS-1-like genetic backbone with consensus constellation of G2/G3-P[4]/P[6]/P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Two intergenogroup reassortant G1P[8] strains were detected that appear to be progenies of reassortment events between Wa-like G1P[8] and DS-1-like G2P[4] strains. Two Rotarix® vaccine (RV1) and two RV5 derived (vd) reassortant strains were detected. Phylogenetic and similarity matrices analysis revealed 2–11 sub-genotypic allelic clusters among the genes of Wa- and DS-1-like strains. Most study strains clustered into previously defined alleles. Amino acid (AA) substitutions occurring in the neutralization epitopes of the VP7 and VP4 proteins characterized in this study were mostly neutral in nature, suggesting that these RVA proteins were possibly under strong negative or purifying selection in order to maintain competent and actual functionality, but fourteen radical (AA changes that occur between groups) AA substitutions were noted that may allow RVA strains to gain a selective advantage through immune escape. The tracking of RVA strains at the sub-genotypic allele constellation level will enhance our understanding of RVA evolution under vaccine pressure, help identify possible mechanisms of immune escape, and provide valuable information for formulation of future RVA vaccines.

The aim of this study was to identify stable rice genotypes tolerant to a salt stress environment and to identify ideal mega-environments using AMMI (additive main effects and multiplicative interaction) stability model analysis. A total of 13 rice genotypes and three salt tolerance checks were evaluated across 13 salt stress locations (alkaline and saline) for the two kharif seasons of 2014 and 2015. Genotype CSR 36 (CHK3) was found to be the most ideal of those tested. Genotypes CHK2 (CST 27) and IR 87952-1-1-1-2-3-B (G05) were found to be the most stable, with above average yields. The check CSR 36 (CHK3) genotype was the best performer in the majority of the environments studied, followed by CSR 27 (CHK2) and IR 87952-1-1-1-2-3-B (G05) which were the best genotypes in the mega-environment consisting of 21 environments evaluated across stress locations and year combinations. Overall, the most promising genotype (IR 87952-1-1-1-2-3-B) had high mean yield and stability and could be used for commercial cultivation or used as donor for breeding programs across salt-affected soils. The genotypes GN13 (IR 87938-1-1-2-1-3-B) and GN11 (IR 87938-1-2-2-1-3-B) showed 60–80% yield advantage at specific salt stress locations, showing that these genotypes could be used for specific environments of salt-affected soils in India.

Background Despite the global roll-out of rotavirus vaccines (RotaTeq/Rotarix / ROTAVAC/Rotasiil), mortality and morbidity due to group A rotavirus (RVA) remains high in sub-Saharan Africa, causing 104,000 deaths and 600,000 hospitalizations yearly. In Cameroon, Rotarix™ was introduced in March 2014, but, routine laboratory diagnosis of rotavirus infection is not yet a common practice, and vaccine effectiveness studies to determine the impact of vaccine introduction have not been done. Thus, studies examining RVA prevalence post vaccine introduction are needed. The study aim was to determine RVA prevalence in severe diarrhoea cases in Littoral region, Cameroon and investigate the role of other diarrheagenic pathogens in RVA-positive cases. Methods We carried out a study among hospitalized children Results The ELISA assay detected RVA antigen in 54.6% (71/130) of specimens, with 45, positive by VP6 RT-PCR and 54, positive using Luminex xTAG GPP. Luminex GPP was able to detect all 45 VP6 RT-PCR positive samples. Co-infections were found in 63.0% (34/54) of Luminex positive RVA infections, with Shigella (35.3%; 12/34) and ETEC (29.4%; 10/34) detected frequently. Of the 71 ELISA positive RVA cases, 57.8% (41/71) were fully vaccinated, receiving two doses of Rotarix. Conclusion This study provides insight on RVA prevalence in Cameroon, which could be useful for post-vaccine epidemiological studies, highlights higher than expected RVA prevalence in vaccinated children hospitalized for diarrhoea and provides the trend of RVA co-infection with other enteric pathogens. RVA genotyping is needed to determine circulating rotavirus genotypes in Cameroon, including those causing disease in vaccinated children.

The etiologic agent of the outbreak of pneumonia in Wuhan China was identified as severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) in January, 2020. The first US patient was diagnosed by the State of Washington and the US Centers for Disease Control and Prevention on January 20, 2020. We isolated virus from nasopharyngeal and oropharyngeal specimens, and characterized the viral sequence, replication properties, and cell culture tropism. We found that the virus replicates to high titer in Vero-CCL81 cells and Vero E6 cells in the absence of trypsin. We also deposited the virus into two virus repositories, making it broadly available to the public health and research communities. We hope that open access to this important reagent will expedite development of medical countermeasures.Article SummaryScientists have isolated virus from the first US COVID-19 patient. The isolation and reagents described here will serve as the US reference strain used in research, drug discovery and vaccine testing.

Additional file 1: Table S1. Distribution of the study population by age and gender. Figure S1a. Sample collection sites. (1) Abomey Calavi in the Atlantic Region (a = Central Clinic of Abomey Calavi) and (2) Cotonou in the Central Region (b = Anastasis Hospital, c = Polyclinic St Vincent de Paul and d = Mênontin Hospital). Figure S1b. Distribution of genotypes by age in Cotonou. Figure S1c. Distribution of genotypes from 90 stool samples in Abomey-Calavi. Figure S1d. Distribution of genotypes according to age in Abomey-Calavi.

Group A rotavirus (RVA) associated diarrhoea in piglets represents one of the major causes of morbidity and mortality in pig farms worldwide. A diarrhoea outbreak occurred among nomadic piglets in north-western district of Bangladesh in February 2014. Outbreak investigation was performed to identify the cause, epidemiologic and clinical features of the outbreak. Rectal swabs and clinical information were collected from diarrhoeic piglets (n = 36). Rectal swabs were tested for RVA RNA by real-time reverse transcription polymerase chain reaction (rRT-PCR) using NSP3-specific primers. The G (VP7) and P (VP4) genes were typed by conventional RT-PCR and sanger sequencing and full genome sequences were determined using next-generation sequencing. We found the attack rate was 61% (50/82) among piglets in the nomadic pig herd, and the case fatality rate was 20% (10/50) among piglets with diarrhoea. All study piglets cases had watery diarrhoea, lack of appetite or reluctance to move. A novel RVA strain with a new P[49] genotype combined with G4 was identified among all piglets with diarrhoea. The genome constellation of the novel RVA strains was determined to be G4-P[49]-I1-R1-C1-M1-A8-N1-T7-E1-H1. Genetic analysis shows that the novel G4P[49] strain is similar to Indian and Chinese porcine or porcine-like G4 human strains and is genetically distant from Bangladeshi human G4 strains. Identification of this novel RVA strain warrants further exploration for disease severity and zoonotic potential.

Group A Rotaviruses (RVAs) are the most important etiological agents of acute gastroenteritis (AGE) in children less than 5 years of age. Mortality resulting from RVA gastroenteritis is higher in developing countries than in developed ones, causing a huge public health burden in global regions like Africa and South-East Asia. This study reports RVA genotypes detected in Ashaiman, Greater Accra Region, Ghana, in the postvaccine introduction era for the period 2014-2016. Stool samples were collected from children less than 5 years of age who visited Ashaiman Polyclinic with AGE from November 2014 to May 2015 and from December 2015 to June 2016. The samples were tested by enzyme immunoassay (EIA), and one-step multiplex reverse transcription polymerase chain reaction was performed on the EIA positive samples for gel-based binomial genotyping. Of the 369 stool samples collected from children with AGE, 145 (39%) tested positive by EIA. Five VP7 (G1, G3, G9, G10, and G12) and three VP4 (P[4], P[6] and P[8]) genotypes were detected. Eight G/P combinations were identified of which, G3P[6], G12P[8], G1P[8], and G9P[4] were the most prevalent and responsible for 93 (68%) of the AGE cases, and seven mixed-types were detected which represented 8% of the RVA cases. High prevalence, diversity, and mixed-types of RVAs were detected from Ashaiman with the emergence of unusual genotypes.

Background Acute gastroenteritis (AGE) in hematopoietic cell transplant (HCT) patients causes significant morbidity and mortality. Data regarding the longitudinal assessment of infectious pathogens during symptomatic AGE and asymptomatic periods, particularly in children, are limited. We investigated the prevalence of AGE-associated infectious pathogens in children undergoing allogeneic HCT. Methods From March 2015 through May 2016, 31 pediatric patients at 4 US children’s hospitals were enrolled and had stool collected weekly from pre-HCT through 100 days post-HCT for infectious AGE pathogens by molecular testing. Demographics, clinical symptoms, antimicrobials, vaccination history, and outcomes were manually abstracted from the medical record into a standardized case report form. Results We identified a pathogen in 18% (38/206) of samples, with many detections occurring during asymptomatic periods. Clostridioides difficile was the most commonly detected pathogen in 39% (15/38) of positive specimens, although only 20% (3/15) of C. difficile–positive specimens were obtained from children with diarrhea. Detection of sapovirus, in 21% (8/38) of pathogen-positive specimens, was commonly associated with AGE, with 87.5% of specimens obtained during symptomatic periods. Norovirus was not detected, and rotavirus was detected infrequently. Prolonged shedding of infectious pathogens was rare. Conclusions This multicenter, prospective, longitudinal study suggests that the epidemiology of AGE pathogens identified from allogeneic HCT patients may be changing. Previously reported viruses, such as rotavirus and norovirus, may be less common due to widespread vaccination and institution of infection control precautions, and emerging viruses such as sapoviruses may be increasingly recognized due to the use of molecular diagnostics.

Genotype × environment (G × E) interaction effects are of special interest for identifying the most suitable genotypes with respect to target environments, representative locations and other specific stresses. Twenty-two advanced breeding lines contributed by the national partners of the Salinity Tolerance Breeding Network (STBN) along with four checks were evaluated across 12 different salt affected sites comprising five coastal saline and seven alkaline environments in India. The study was conducted to assess the G × E interaction and stability of advanced breeding lines for yield and yield components using additive main effects and multiplicative interaction (AMMI) model. In the AMMI1 biplot, there were two mega-environments (ME) includes ME-A as CARI, KARAIKAL, TRICHY and NDUAT with winning genotype CSR 2K 262; and ME-B as KARSO, LUCKN, KARSA, GOA, CRRI, DRR, BIHAR and PANVE with winning genotypes CSR 36. Genotypes CSR 2K 262, CSR 27, NDRK 11-4, NDRK 11-3, NDRK 11-2, CSR 2K 255 and PNL 1-1-1-6-7-1 wer...

Fourteen Ralstonia solanacearum strains from solanaceous vegetables on the Andaman Islands, India, were characterized using a polyphasic approach. The strains wilted their respective hosts within 1 to 3 weeks postinoculation. Virulence assays on tomato (Solanum lycopersicum), brinjal (eggplant; S. melongena), and chili pepper (Capsicum annuum) revealed that all strains were infective on all three hosts. However, tomato was more susceptible than eggplant and chili pepper. Strains were identified as R. solanacearum based on carbon substrate utilization profiling with Biolog similarity coefficients >0.82. Species identity was further confirmed by 16S ribosomal RNA and recN gene sequence analysis. Intraspecific identification of strains revealed the presence of race 1 biovar 3 and race 1 biovar 4. Both biovars wilted plants with similar aggressiveness. All strains were identified as phylotype I, and multilocus sequence typing revealed that the strains belong to a small number of clonal complexes that also comprise strains from mainland India, especially West Bengal state and Kerala.

Before the introduction of rotavirus vaccine in 2006, rotavirus was the most common cause of severe diarrhea among U.S. children (1). Currently, two rotavirus vaccines are licensed for use in the United States, both of which have demonstrated good field effectiveness (78%-89%) against moderate to severe rotavirus illness (2), and the use of these vaccines has substantially reduced the prevalence of rotavirus in the United States (3). However, the most recent national vaccine coverage estimates indicate lower full rotavirus vaccine-series completion (73%) compared with receipt of at least 3 doses of vaccines containing diphtheria, tetanus, and pertussis antigens (95%), given on a similar schedule to rotavirus vaccines (4). In the postvaccine era in the United States, rotavirus activity persists in a biennial pattern (3). This report describes three rotavirus outbreaks that occurred in California in 2017. One death was reported; however, the majority of cases were associated with mild to moderate illness, and illness occurred across the age spectrum as well as among vaccinated children. Rotavirus vaccines are designed to mimic the protective effects of natural infection and are most effective against severe rotavirus illness (2). Even in populations with high vaccination coverage, some rotavirus infections and mild to moderate illnesses will occur. Rotavirus vaccination should continue to be emphasized as the best means of reducing disease prevalence in the United States.

Group A rotaviruses are the major cause of severe gastroenteritis in the young of mammals and birds. This report describes characterization of an unusual G20P[28] rotavirus strain detected in a 24 month old child from Suriname. Genomic sequence analyses revealed that the genotype constellation of the Suriname strain RVA/Human-wt/SUR/2014735512/2013/G20P[28] was G20-P[28]-I13-R13-C13-M12-A23-N13-T15-E20-H15. Genes VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5 were recently assigned novel genotypes by the Rotavirus Classification Working Group (RCWG). Three of the 11 gene segments (VP7, VP4, VP6) were similar to cognate gene sequences of bat-like human rotavirus strain Ecu534 from Ecuador and the VP7, NSP3 and NSP5 gene segments of strain RVA/Human-wt/SUR/2014735512/2013/G20P[28] were found to be closely related to gene sequences of bat rotavirus strain 3081/BRA detected in Brazil. Although distantly related, the VP1 gene of the study strain and bat strain BatLi09 detected in Cameroon in 2014 are monophyletic. The NSP1 gene was found to be most closely related to human strain QUI-35-F5 from Brazil. These findings suggest that strain RVA/Human-wt/SUR/2014735512/2013/G20P[28] represents a zoonotic infection from a bat host.

Background Histo-blood group antigens (HBGAs), whose expression is controlled in part by fucosyltransferase 2 (FUT2) and 3 (FUT3) genes, serve as receptors for norovirus and rotavirus. Individuals without functional FUT2 (nonsecretors) or FUT3 (Lewis-negative) genes may have decreased susceptibility to norovirus and rotavirus infections. As the prevalence of secretor and Lewis status can vary by race and ethnicity, we assessed this association in a US Veteran population. Methods Stool and saliva specimens were collected from acute gastroenteritis (AGE) cases and age- and time-matched controls through a multisite, active surveillance platform at four Veterans Affairs hospitals (Atlanta, Bronx, Houston, Los Angeles). Stool specimens were tested with the FilmArray Gastrointestinal Panel; norovirus and rotavirus positive specimens were genotyped. Saliva specimens were analyzed for HBGA expression by EIA using glycan-specific monoclonal antibodies and lectins. Chi-squared and Fisher’s exact tests were conducted to evaluate associations between secretor and Lewis status and infection with norovirus or rotavirus. Results From November 4, 2015–December 30, 2017, 670 AGE cases and 319 controls provided both stool and saliva specimens. Norovirus (21 GII.4 Sydney, 13 GII non-4, 7 GI, 10 untyped) and rotavirus (13 G12P[8], 1 G2P[4], 1 untyped) positive cases were more likely to be secretor positive (90% and 100%, respectively) compared with controls (76%) (P = 0.03 for both). Infections with GII.4 Sydney norovirus (P < 0.01) and G12P[8] rotavirus (P < 0.05) were significantly associated with secretor status. This association was not observed with other norovirus or rotavirus genotypes. No association was observed between Lewis status, race, or ethnicity and infection with norovirus or rotavirus. Conclusion Norovirus and rotavirus infections among a US Veteran population were associated with secretor status in a genotype-dependent manner, and with GII.4 Sydney norovirus and G12P[8] rotavirus, the most common strains. These associations are consistent with previously reported results, and suggest that the efficacy of interventions, such as vaccines, should include consideration of secretor status and predominantly circulating virus strains. Disclosures R. L. Atmar, Takeda Vaccines, Inc.: Investigator, Research grant. V. C. Marconi, ViiV: Investigator, Research support and Salary. Gilead: Investigator, Research support. Bayer: Investigator, Research support.

The current two-step VP7 and VP4 genotyping RT-PCR assays for rotaviruses have been linked consistently to genotyping failure in an estimated 30% of RVA positive samples worldwide. We have developed a VP7 and VP4 multiplexed one-step genotyping assays using updated primers generated from contemporary VP7 and VP4 sequences. To determine assay specificity and sensitivity, 17 reference virus strains, 6 non-target gastroenteritis viruses and 725 clinical samples carrying the most common VP7 (G1, G2, G3, G4, G9, and G12) and VP4 (P[4], P[6], P[8], P[9] and P[10]) genotypes were tested in this study. All reference RVA strain targets yielded amplicons of the expected sizes and non-target genotypes and gastroenteritis viruses were not detected by either assay. Out of the 725 clinical samples tested, the VP7 and VP4 assays were able to assigned specific genotypes to 711 (98.1%) and 714 (98.5%), respectively. The remaining unassigned samples were re-tested for RVA antigen using EIA and qRT-PCR assays and all were found to be negative. The overall specificity, sensitivity and limit of detection of the VP7 assay were in the ranges of 99.0–100%, 94.0–100% and 8.6 × 101 to 8.6 × 102 copies of RNA/reaction, respectively. For the VP4 assay, the overall specificity, sensitivity and limit of detection assay were in the ranges of 100%, 94.0–100% and ≤1 to 8.6 × 102 copies of RNA/reaction, respectively. Here we report two highly robust, accurate, efficient, affordable and documentable gel-based genotyping systems which are capable of genotyping 97.8% of the six common VP7 and 98.3% of the five common VP4 genotypes of RVA strains which are responsible for approximately 88.2% of all RVA infections worldwide.

Rotavirus genotyping is useful for surveillance purposes especially in areas where rotavirus vaccination has been or will be implemented. RT-PCR based molecular methods have been applied widely, but quantitative assays targeting a broad spectrum of genotypes have not been developed. Three real time RT-PCR panels were designed to identify G1, G2, G9, G12 (panel GI), G3, G4, G8, G10 (panel GII), and P[4], P[6], P[8], P[10], P[11] (panel P), respectively. An assay targeting NSP3 was included in both G panels as an internal control. The cognate assays were also formulated as one RT-PCR-Luminex panel for simultaneous detection of all the genotypes listed above plus P[9]. The assays were evaluated with various rotavirus isolates and 89 clinical samples from Virginia, Bangladesh and Tanzania, and exhibited 95% (81/85) sensitivity compared with the conventional RT-PCR-Gel-electrophoresis method, and 100% concordance with sequencing. Real time assays identified a significantly higher rate of mixed genotypes in Bangladeshi samples than the conventional gel-electrophoresis-based RT-PCR assay (32.5% versus 12.5%, P0.05). In these mixed infections, the relative abundance of the rotavirus types could be estimated by Cq values. These typing assays detect and discriminate a broad range of G/P types circulating in different geographic regions with high sensitivity and specificity and can be used for rotavirus surveillance.

Effects of salinity on correlation, path and stress indices, yield and its components were studied in a set of 34 promising rice genotypes collected from various national and international organizations. These genotypes were evaluated in a randomized complete block design with three replications during the wet seasons (kharif) of 2009 and 2010 in normal (ECiw ∼ 1.2 dS/m) and salinity stress (ECiw ∼ 10 dS/m) environments in micro plots at Central Soil Salinity Research Institute (CSSRI), Karnal, India. Grain yield per plant showed positive significant association with plant height, total tillers, productive tillers, panicle length, and biological yield per plant and harvest index under normal environment, whereas grain yield showed positive significant association with biological yield and harvest index under salinity stress. These results clearly indicate that selection of high yielding genotypes would be entirely different under normal and saline environments. The stress susceptibility index (SSI) values...

We report a 64 year old female who presented with epigastric pain and intractable vomiting not respond to treatment and we were not able to pass nasogastric tube. Chest x -ray shows eventration of left sided hemi diaphragm, upper gastro intestinal contrast study conform the diagnosis of gastric volvulus. Plication of left hemidiaphragm with anterior gastropexy was performed through an abdominal approach. Postoperatively the patient's symptoms improved. Acute gastric volvulus carries a mortality rate of 42-56%, secondary to gastric ischemia, perforation or necrosis. 1 Emergency physicians should have suspicion about gastric volvulus when treating patients with abdominal pain and persistent vomiting. The patient should go for surgical consultation as early INTRODUCTION: In diaphragmatic eventration, permanent elevation of an immobile hemidiaphragm occurs in which peripheral muscular attachment is normal with no interruption in peritoneal or pleural layers. It usually remains asymptomatic in early life and presents later with respiratory and occasionally gastrointestinal complications. This may lead to displacement of abdominal organs, especially the stomach. Gastric volvulus is an uncommon complication of eventration of diphragm.2 There are two types of gastric volvulus: organoaxial and mesenteroaxial. The most common type is organoaxial, in which the stomach rotates along the longitudinal axis and is associated with paraesophageal hernias. The mesenteroaxial type, in which the stomach rotates between the lesser and greater curvatures, is believed to be idiopathic, causing chronic symptoms. 3 The presence of persistent vomiting and epigastric pain despite initial antiemetic treatment should trigger one to think of gastric volvulus, despite the patient appearing very stable and healthy. Diagnosis of gastric volvulus, which can have significant morbidity and mortality can be easily missed. Early radiological imaging with x-ray or computed tomography (CT) can facilitate the management of the patient. Eventration of diaphragm is defined as an abnormal elevation of an intact diaphragm and most often is characterized by a developmental abnormality of the diaphragm musculature. 4 It usually remains asymptomatic in early life and presents later with respiratory and occasionally gastrointestinal complications. The abnormally wide diaphragmatic space provides the potential for abnormal rotation of stomach around itself. This abnormal rotation is known as gastric volvulus. It is of two varieties. One is organoaxial (more common) and other is mesentero-axial. We present a case of 60 year old female with eventration of left hemidiaphragm with chronic intermittent organo-axial gastric volvulus.

Background The severity of acute gastroenteritis (AGE) in adult populations and the relative contribution of specific pathogens is not well characterized. In 2016, we implemented a multisite AGE surveillance platform in 4 VA hospitals (Atlanta, Bronx, Houston and Los Angeles), collectively serving > 320,000 patients annually. Methods Inpatient AGE cases and age- and time-matched non-AGE controls were identified through prospective screening of admissions using standardized case definitions. Stool samples were tested for 22 pathogens using the FilmArray® Gastrointestinal Panel. Medical conditions were analyzed as risk factors for AGE by multivariate logistic regression. Results From July 2016 to June 2018, 731 cases and 399 controls were enrolled. Risk factors for AGE cases included HIV-positive status (adjusted odds ratio [aOR] 4.6; 95% confidence interval [CI] 1.6–12.9; P < 0.01), severe kidney disease (aOR 4.5; 95% CI 2.0–9.8; P < 0.01), and immunosuppressive therapy (aOR 4.0; 95% CI 1.2–13.3]; P = 0.02). Clostridioides difficile and norovirus were the most commonly detected pathogens in cases (18% and 5%, respectively); detection of these pathogens in cases was significantly higher than detection in controls (8% and 2%, respectively; P < 0.01 for both). The median duration of hospital stay was longer for C. difficile compared with norovirus cases (5 vs. 3 days; P < 0.01), and cases with both pathogens had intensive care unit (ICU) stays (C. difficile: 18%; norovirus: 8%; P = 0.2). Fourteen deaths occurred among AGE cases; 2 were associated with C. difficile and 1 with norovirus; the remainder did not have a clear etiology or pathogen detected. C. difficile and norovirus were detected year-round with a fall and winter predominance; C. difficile prevalence was highest in October, while norovirus prevalence was six times higher in December than in summer months. Conclusion This surveillance platform captured cases of severe AGE, including ICU stays and deaths, among hospitalized US Veterans. C. difficile and norovirus were leading pathogens in AGE cases. These findings can help guide appropriate clinical management of AGE patients and inform public health efforts to quantify and address the associated burden of disease through targeted interventions. Disclosures All authors: No reported disclosures.

Background Viruses are frequently implicated in acute gastroenteritis (AGE) outbreaks, yet the endemic burden of norovirus and rotavirus disease in adult populations is not well characterized. In 2016, we implemented a multisite AGE surveillance platform capturing cases and controls in 4 VA hospitals (Atlanta, Bronx, Houston, and Los Angeles), collectively serving >320,000 patients annually. Methods Inpatient AGE cases and age- and time-matched controls were identified through prospective screening of admissions via standardized case definitions. Outpatient cases were passively identified using stool samples submitted for routine clinical microbiological diagnostics. Samples were tested with the FilmArray Gastrointestinal Panel, followed by genotyping of virus positives. Incidence was estimated using population denominators of unique patients served annually by site. Results From December 1, 2016 to February 28, 2018, 875 cases (496 inpatients, 379 outpatients), and 374 controls were enrolled. Norovirus and rotavirus prevalence was highest among outpatient AGE cases (11.6% and 2.9%, respectively) followed by inpatient cases (3.4% and 1.6%, respectively); few controls were positive (norovirus, 1.3%; rotavirus, 0%). Norovirus-associated inpatient incidence was 15.2 per 100,000 population (range by site: 10.7–19.9/100,000) and rotavirus-associated inpatient incidence was 7.5 per 100,000 population (range by site: 0–12.8/100,000). The predominant norovirus genotype was GII.P16-GII.4 Sydney (50%), and rotavirus genotype was G12P[8] (83%). Norovirus was detected every calendar month and peaked in December–January, while rotavirus peaked in April. Nine deaths were documented among AGE inpatient cases, including one norovirus-associated death. Conclusion Implementation of a multisite AGE surveillance platform captured a wide spectrum of illness for norovirus and rotavirus in US Veterans including outpatient visits, inpatient hospitalizations, and one norovirus-associated death. Norovirus was the leading viral pathogen and was detected year-round. Ongoing surveillance using this platform will allow for further characterization of the pathogen distribution and associated AGE disease burden in adults. Disclosures V. Marconi, ViiV: Investigator, Research support and Salary. Bayer: Investigator, Research support. Gilead: Investigator, Research support.

Group A rotaviruses (RV-A) are the leading cause of viral gastroenteritis in children worldwide and genotype G9P[8] is one of the five most common genotypes detected in humans. In order to gain insight into the degree of genetic variability of G9P[8] strains circulating in Cameroon, stool samples were collected during the 1999–2000 rotavirus season in two different geographic regions in Cameroon (Southwest and Western Regions). By RT-PCR, 15 G9P[8] strains (15/89 = 16.8%) were identified whose genomic configurations was subsequently determined by complete or partial gene sequencing. In general, all Cameroonian G9 strains clustered into current globally-spread sublineages of the VP7 gene and displayed 86.6–100% nucleotide identity amongst themselves and 81.2–99.5% nucleotide identity with global G9 strains. The full genome classification of all Cameroonian strains was G9-P[8]-I1–R1–C1–M1–A1–N1–T1–E1–H1 but phylogenetic analysis of each gene revealed that the strains were spread across 4 or more distinct lineages. An unusual strain, RVA/Human-wt/CMR/6788/1999/G9P[8], which shared the genomic constellation of other Cameroonian G9P[8] strains, contained a novel G9 subtype which diverged significantly (18.8% nucleotide and 19% amino acid distance) from previously described G9 strains. Nucleotide and amino acid alignments revealed that the 3′ end of this gene is highly divergent from other G9 VP7 genes suggesting that it arose through extensive accumulation of point mutations. The results of this study demonstrate that diverse G9 strains circulated in Cameroon during 1999–2000.

Background Group A rotaviruses (RVA) are a significant cause of pediatric gastroenteritis worldwide. The New Vaccine Surveillance Network (NVSN) has conducted active surveillance for RVA at pediatric hospitals and emergency departments at 3-7 geographically diverse sites in the United States since 2006. Methods Over 6 consecutive years, from 2008 to 2013, 1523 samples from NVSN sites that were tested positive by a Rotaclone enzyme immunoassay were submitted to the Centers for Disease Control and Prevention for genotyping. Results In the 2009, 2010, and 2011 seasons, genotype G3P[8] was the predominant genotype throughout the network, with a 46%-84% prevalence. In the 2012 season, G12P[8] replaced G3P[8] as the most common genotype, with a 70% prevalence, and this trend persisted in 2013 (68.0% prevalence). Vaccine (RotaTeq; Rotarix) strains were detected in 0.6%-3.4% of genotyped samples each season. Uncommon and unusual strains (eg, G8P[4], G3P[24], G2P[8], G3P[4], G3P[6], G24P[14], G4P[6], and G9P[4]) were detected sporadically over the study period. Year, study site, and race were found to be significant predictors of genotype. Conclusions Continued active surveillance is needed to monitor RVA genotypes in the United States and to detect potential changes since vaccine licensure.

Summary Objectives To assess the burden of rotavirus disease in Guatemala, in view of the recent introduction of a national rotavirus vaccination programme. Methods We examined data from an active, facility-based surveillance system in Santa Rosa, Guatemala, from October 2007 through September 2009 among children

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Group A rotavirus (RVA) is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live, attenuated rotavirus vaccines, Rotarix® and RotaTeq®, has dramatically reduced RVA-associated AGE and mortality. High-throughput, sensitive and specific techniques are required to rapidly diagnose and characterize rotavirus strains in stool samples for proper patient treatment and to monitor circulating vaccine and wild-type rotavirus strains. New molecular assays are rapidly developed that are more sensitive and specific than the conventional assays for detection, genotyping and full genome characterization of circulating rotavirus wild-type and vaccine (Rotarix® and RotaTeq®) strains causing AGE.

We report the genomic characterization of a rare human G8P[14] rotavirus strain, identified in a stool sample from Guatemala (GTM) during routine rotavirus surveillance. This strain was designated as RV A/Human-wt/GTM/2009726790/2009/G8P[14], with a genomic constellation of G8-P[14]-I2-R2-C2-M2-A13-N2-T6-E2-H3. The VP4 gene occupied lineage VII within the P[14] genotype. Phylogenetic analysis of each genome segment revealed close relatedness to several zoonotic simian, guanaco and bovine strains. Our findings suggest that strain RVA/Human-wt/GTM/2009726790/2009/G8P[14] is an example of a direct zoonotic transmission event. The results of this study reinforce the potential role of interspecies transmission and reassortment in generating novel and rare rotavirus strains which infect humans.