74 results on '"Rashi Gautam"'
Search Results
2. Whole gene analysis of a genotype G29P[6] human rotavirus strain identified in Central African Republic
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Virginie Banga-Mingo, Mathew D. Esona, Naga S. Betrapally, Rashi Gautam, Jose Jaimes, Eric Katz, Diane Waku-Kouomou, Michael D. Bowen, and Ionela Gouandjika-Vasilache
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RVA ,Whole genome analysis ,Central African Republic ,Medicine ,Biology (General) ,QH301-705.5 ,Science (General) ,Q1-390 - Abstract
Abstract 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%).
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- 2021
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3. Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018
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Jijoho Michel Agbla, Mathew D. Esona, Jose Jaimes, Rashi Gautam, Alidéhou Jerrold Agbankpé, Eric Katz, Tamegnon Victorien Dougnon, Annick Capo-Chichi, Nafissatou Ouedraogo, Osseni Razack, Honoré Sourou Bankolé, and Michael D. Bowen
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Rotavirus ,Whole genome ,Alleles ,Benin ,Pre-vaccine era strains ,Microbiology ,QR1-502 ,Infectious and parasitic diseases ,RC109-216 - Abstract
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.
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- 2022
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4. Molecular characteristics of rotavirus genotypes circulating in the south of Benin, 2016–2018
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Jijoho Michel Agbla, Mathew D. Esona, Alidehou Jerrold Agbankpe, Annick Capo-Chichi, Rashi Gautam, Tamegnon Victorien Dougnon, Osseni Razack, Michael D. Bowen, and Honore Sourou Bankole
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Pediatric ,Rotavirus ,Surveillance ,Genotypes ,Benin ,Medicine ,Biology (General) ,QH301-705.5 ,Science (General) ,Q1-390 - Abstract
Abstract Objective Rotavirus remains the main causative agent of gastroenteritis in young children in countries that have not yet introduced the vaccine. In Benin, rotavirus vaccine was introduced late December 2019 into the EPI. This study aims to provide pre-vaccination era rotavirus genotyping data in Benin. These data can supplement data from the surveillance system of Ministry of Health of Benin which is supported by the World Health Organization (WHO). Results Of the 420 diarrheal stool samples, actively collected in southern Benin from July 2016 through November 2018 from children under 5 years old and suffering from gastroenteritis, 167 (39.8%) samples were rotavirus EIA positive. 186 (44.3%) samples contained amplifiable rotavirus RNA detected by qRT-PCR method and were genotyped using one-step RT-PCR multiplex genotyping method. G1P[8] represents the predominant genotype (32%) followed by the G2P[4] (26%), G3P[6] (16%), G12P[8] (13%) and mixed G and P types (1%). Four samples (2%) could not be assigned both G and P type specificity.
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- 2020
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5. Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with Coronavirus Disease, United States
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Jennifer Harcourt, Azaibi Tamin, Xiaoyan Lu, Shifaq Kamili, Senthil K. Sakthivel, Janna Murray, Krista Queen, Ying Tao, Clinton R. Paden, Jing Zhang, Yan Li, Anna Uehara, Haibin Wang, Cynthia Goldsmith, Hannah A. Bullock, Lijuan Wang, Brett Whitaker, Brian Lynch, Rashi Gautam, Craig Schindewolf, Kumari G. Lokugamage, Dionna Scharton, Jessica A. Plante, Divya Mirchandani, Steven G. Widen, Krishna Narayanan, Shinji Makino, Thomas G. Ksiazek, Kenneth S. Plante, Scott C. Weaver, Stephen Lindstrom, Suxiang Tong, Vineet D. Menachery, and Natalie J. Thornburg
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coronavirus ,viruses ,severe acute respiratory syndrome coronavirus 2 ,SARS-CoV-2 ,novel coronavirus disease 2019 ,COVID-19 ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
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.
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- 2020
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6. Rotavirus Strain Trends in United States, 2009–2016: Results from the National Rotavirus Strain Surveillance System (NRSSS)
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Slavica Mijatovic-Rustempasic, Jose Jaimes, Charity Perkins, M. Leanne Ward, Mathew D. Esona, Rashi Gautam, Jamie Lewis, Michele Sturgeon, Junaid Panjwani, Gail A. Bloom, Steve Miller, Erik Reisdorf, Ann Marie Riley, Morgan A. Pence, James Dunn, Rangaraj Selvarangan, Robert C. Jerris, Dona DeGroat, Umesh D. Parashar, Margaret M. Cortese, and Michael D. Bowen
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rotavirus ,RVA ,genotype ,prevalence ,surveillance ,vaccine ,Microbiology ,QR1-502 - Abstract
Before the introduction of vaccines, group A rotaviruses (RVA) were the leading cause of acute gastroenteritis in children worldwide. The National Rotavirus Strain Surveillance System (NRSSS) was established in 1996 by the Centers for Disease Control and Prevention (CDC) to perform passive RVA surveillance in the USA. We report the distribution of RVA genotypes collected through NRSSS during the 2009–2016 RVA seasons and retrospectively examine the genotypes detected through the NRSSS since 1996. During the 2009–2016 RVA seasons, 2134 RVA-positive fecal specimens were sent to the CDC for analysis of the VP7 and VP4 genes by RT-PCR genotyping assays and sequencing. During 2009–2011, RVA genotype G3P[8] dominated, while G12P[8] was the dominant genotype during 2012–2016. Vaccine strains were detected in 1.7% of specimens and uncommon/unusual strains, including equine-like G3P[8] strains, were found in 1.9%. Phylogenetic analyses showed limited VP7 and VP4 sequence variation within the common genotypes with 1–3 alleles/lineages identified per genotype. A review of 20 years of NRSSS surveillance showed two changes in genotype dominance, from G1P[8] to G3P[8] and then G3P[8] to G12P[8]. A better understanding of the long-term effects of vaccine use on epidemiological and evolutionary dynamics of circulating RVA strains requires continued surveillance.
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- 2022
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7. One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples
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Rashi Gautam, Slavica Mijatovic-Rustempasic, Mathew D. Esona, Ka Ian Tam, Osbourne Quaye, and Michael D. Bowen
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Gastroenteritis ,Rotavirus genotyping ,Multiplex qRT-PCR ,Rotarix® ,RotaTeq® ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8–100% sensitivity, 99.7–100% specificity, 85–95% efficiency and a limit of detection of 4–60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81–92% efficiency and limit of detection of 150–600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8–100% sensitivity, 100% specificity, 86–89% efficiency and a limit of detection of 12–400 copies per singleplex reactions. The VP4 qRT-PCRs exhibited 82–90% efficiency and limit of detection of 120–4000 copies in multiplex reaction. Discussion. The one-step multiplex qRT-PCR assay will facilitate high-throughput rotavirus genotype characterization for monitoring circulating rotavirus wild-type strains causing rotavirus infections, determining the frequency of Rotarix® and RotaTeq® vaccine strains and vaccine-derived reassortants associated with AGE, and help to identify novel rotavirus strains derived by reassortment between vaccine and wild-type strains.
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- 2016
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8. Coding-Complete Genome Sequences of G6P[14] Rotavirus Strain Detected in a Human Stool Specimen within the United States
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Mary C. Casey-Moore, Slavica Mijatovic-Rustempasic, Jose Jaimes, Charity Perkins, Ann Marie Riley, Margaret M. Cortese, Rashi Gautam, and Michael D. Bowen
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Immunology and Microbiology (miscellaneous) ,Genetics ,Molecular Biology - Abstract
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.
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- 2023
9. Genotypic investigation of a rotavirus cluster at a quaternary-care pediatric hospital
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Eimear M. Kitt, Hee-won Yoon, Courtney E. Comar, Kenneth P. Smith, Rebecca M. Harris, Mathew D. Esona, Rashi Gautam, Slavica Mijatovic-Rustempasic, Amy L. Hopkins, Jose Jaimes, and Lori K. Handy
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Microbiology (medical) ,Infectious Diseases ,Epidemiology - Abstract
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.
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- 2023
10. GUI Development of IRNSS Receiver
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Rashi Gautam, Vaisvik Chaudhary, and Sachin Gajjar
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- 2022
11. 1218. Genotypic Investigation of a Rotavirus Cluster at a Pediatric Hospital in 2022
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Hee-won Yoon, Eimear Kitt, Kenneth Smith, Courtney E Comar, Rebecca Harris, Amy Hopkins, Jose Jaimes, Slavica Mijatovic Rustempasic, Rashi Gautam, Mathew D Esona, and Lori Handy
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Infectious Diseases ,Oncology - Abstract
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.
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- 2022
12. Molecular characterization of Vigna marina (Burm.f.) Merr. from the Andaman and Nicobar Islands for salt tolerance using SSR markers
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Shyam Sunder Rao, P. K. Singh, Suman Pandey, Rashi Gautam, K. Sakthivel, M. Prithivi, D. R. Manimaran, S.K. Zamir Ahmed, and K. Venkatesan
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Vigna marina ,biology ,Botany ,Genetics ,Plant Science ,biology.organism_classification ,Agronomy and Crop Science - Abstract
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.
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- 2021
13. Whole gene analysis of a genotype G29P[6] human rotavirus strain identified in Central African Republic
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Diane Waku-Kouomou, Eric M Katz, Rashi Gautam, Virginie Banga-Mingo, Jose Jaimes, Michael D. Bowen, Mathew D. Esona, Naga S. Betrapally, and Ionela Gouandjika-Vasilache
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0106 biological sciences ,0301 basic medicine ,Rotavirus ,Science (General) ,Genotype ,QH301-705.5 ,viruses ,Reassortment ,Genome, Viral ,Biology ,medicine.disease_cause ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Rotavirus Infections ,03 medical and health sciences ,South Africa ,Q1-390 ,Human rotavirus ,medicine ,Animals ,Humans ,Biology (General) ,Gene ,Phylogeny ,Genetics ,Bangladesh ,Strain (biology) ,virus diseases ,General Medicine ,Kenya ,RVA ,Central African Republic ,Open reading frame ,Research Note ,030104 developmental biology ,Whole genome analysis ,Child, Preschool ,Medicine ,Vp7 gene - Abstract
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%).
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- 2021
14. Rotavirus Genotype Trends and Gastrointestinal Pathogen Detection in the United States, 2014–2016: Results From the New Vaccine Surveillance Network
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James D. Chappell, Eileen J. Klein, Michael D. Bowen, Janet A. Englund, Rangaraj Selvarangan, Geoffrey A. Weinberg, Mary E Wikswo, Christopher J. Harrison, Slavica M Rustempasic, Monica M. McNeal, Mathew D. Esona, M Leanne Ward, Umesh D. Parashar, Charity Perkins, Daniel C. Payne, Julie A. Boom, Mary Allen Staat, Natasha B. Halasa, and Rashi Gautam
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Rotavirus ,Veterinary medicine ,Pathogen detection ,Genotype ,Biology ,medicine.disease_cause ,Group A ,Rotavirus Infections ,Feces ,Prevalence ,medicine ,Humans ,Immunology and Allergy ,Child ,Genotyping ,Phylogeny ,Vaccines ,Infant ,medicine.disease ,Disease control ,United States ,Gastroenteritis ,Infectious Diseases ,Population Surveillance ,Logistic analysis ,Coinfection - Abstract
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.
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- 2021
15. Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with Coronavirus Disease, United States
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Shifaq Kamili, Kenneth S. Plante, Yan Li, Rashi Gautam, Craig Schindewolf, Lijuan Wang, Krishna Narayanan, Hannah A. Bullock, Janna Murray, Brett Whitaker, Brian Lynch, Natalie J. Thornburg, Azaibi Tamin, Cynthia S. Goldsmith, Scott C. Weaver, Shinji Makino, Clinton R. Paden, Stephen Lindstrom, Dionna Scharton, Ying Tao, Kumari G. Lokugamage, Anna Uehara, Jing Zhang, Krista Queen, Senthil Kumar K. Sakthivel, Steven G. Widen, Vineet D. Menachery, Haibin Wang, Xiaoyan Lu, Suxiang Tong, Thomas G. Ksiazek, Divya Mirchandani, Jennifer L Harcourt, and Jessica A. Plante
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Epidemiology ,Expedited ,viruses ,coronavirus ,Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with 2019 Novel Coronavirus Disease, United States ,Oropharynx ,lcsh:Medicine ,medicine.disease_cause ,Virus Replication ,0302 clinical medicine ,Nasopharynx ,Pandemic ,Chlorocebus aethiops ,Medicine ,characterization ,030212 general & internal medicine ,Coronavirus ,biology ,Infectious Diseases ,PCR ,Coronavirus Infections ,isolation ,severe acute respiratory syndrome coronavirus 2 ,Microbiology (medical) ,Washington ,030231 tropical medicine ,Pneumonia, Viral ,Genome, Viral ,Virus ,2019 novel coronavirus disease ,Cell Line ,lcsh:Infectious and parasitic diseases ,03 medical and health sciences ,respiratory infections ,Betacoronavirus ,Animals ,Humans ,lcsh:RC109-216 ,Pandemics ,Vero Cells ,business.industry ,SARS-CoV-2 ,Research ,lcsh:R ,Outbreak ,COVID-19 ,biology.organism_classification ,medicine.disease ,Virology ,United States ,zoonoses ,Pneumonia ,Viral Tropism ,novel coronavirus disease 2019 ,Tissue tropism ,Vero cell ,business - Abstract
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.
- Published
- 2020
16. Variability in Colletotrichum infecting chilli plants of Andaman and Nicobar Islands, India
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B. Shalini, K. Sakthivel, Pawan K. Singh, V.K. Pandey, M.M. Das, Rashi Gautam, S. Sawhney, and K. Manigundan
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Veterinary medicine ,Environmental Engineering ,Colletotrichum ,biology ,Health, Toxicology and Mutagenesis ,Toxicology ,biology.organism_classification - Published
- 2020
17. Gastrointestinal Tract Infections: Viruses
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Mathew D. Esona, Rashi Gautam, Preeti Chhabra, Jan Vinjé, Michael D. Bowen, and Rachel M. Burke
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- 2022
18. Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016-2018
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Jijoho Michel Agbla, Mathew D. Esona, Jose Jaimes, Rashi Gautam, Alidéhou Jerrold Agbankpé, Eric Katz, Tamegnon Victorien Dougnon, Annick Capo-Chichi, Nafissatou Ouedraogo, Osseni Razack, Honoré Sourou Bankolé, and Michael D. Bowen
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Rotavirus ,Cancer Research ,Vaccines ,Infectious Diseases ,Genotype ,Virology ,Child, Preschool ,Benin ,Humans ,Genome, Viral ,Child ,Phylogeny ,Rotavirus Infections - Abstract
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.
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- 2021
19. Incidence, Etiology, and Severity of Acute Gastroenteritis Among Prospectively Enrolled Patients in 4 Veterans Affairs Hospitals and Outpatient Centers, 2016–2018
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Aron J. Hall, Neha Balachandran, Rashi Gautam, Rebecca M. Dahl, Jan Vinjé, Mark Holodniy, David O. Beenhouwer, Sheldon T. Brown, Cynthia Lucero-Obusan, Umesh D. Parashar, Adrienne Perea, Blanca Vargas, Karen V. Evangelista, Michael D. Bowen, Anita Kambhampati, Cristina V. Cardemil, Scott Grytdal, Kathryn L Meagley, Maria C. Rodriguez-Barradas, Hannah Browne, and Vincent C. Marconi
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0301 basic medicine ,Microbiology (medical) ,Adult ,Rotavirus ,medicine.medical_specialty ,Hospitals, Veterans ,030106 microbiology ,Population ,medicine.disease_cause ,Article ,law.invention ,03 medical and health sciences ,Feces ,0302 clinical medicine ,fluids and secretions ,law ,Internal medicine ,Outpatients ,medicine ,Humans ,030212 general & internal medicine ,Prospective Studies ,education ,Veterans Affairs ,Aged ,Caliciviridae Infections ,Veterans ,education.field_of_study ,business.industry ,Clostridioides difficile ,Incidence (epidemiology) ,Incidence ,virus diseases ,Infant ,Clostridium difficile ,Intensive care unit ,United States ,Gastroenteritis ,Infectious Diseases ,Norovirus ,Etiology ,business - Abstract
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.
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- 2021
20. Development of a Real-Time Reverse Transcription-PCR Assay To Detect and Quantify Group A Rotavirus Equine-Like G3 Strains
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Rashi Gautam, Michael D. Bowen, Mathew D. Esona, and Eric M Katz
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Microbiology (medical) ,Rotavirus ,Genotype ,Reverse Transcription ,Biology ,medicine.disease_cause ,Real-Time Polymerase Chain Reaction ,Group A ,Virology ,Rotavirus Infections ,Reverse transcription polymerase chain reaction ,Feces ,Real-time polymerase chain reaction ,TaqMan ,medicine ,Animals ,Humans ,RNA, Viral ,Horses ,Forward primer ,Viral load ,Phylogeny - Abstract
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.
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- 2021
21. Rotavirus Vaccination Coverage During a Rotavirus Outbreak Resulting in a Fatality at a Subacute Care Facility
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Rashi Gautam, Debra A. Wadford, Umesh D. Parashar, George Han, Rebecca Quenelle, Michael D. Bowen, Rachel M Burke, and Jacqueline E. Tate
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Male ,Rotavirus ,Pediatrics ,medicine.medical_specialty ,medicine.disease_cause ,Article ,Rotavirus Infections ,Disease Outbreaks ,Feces ,03 medical and health sciences ,0302 clinical medicine ,030225 pediatrics ,Intensive care ,medicine ,Humans ,Subacute care ,030212 general & internal medicine ,Child ,Skilled Nursing Facilities ,business.industry ,Rotavirus Vaccines ,Infant ,Outbreak ,General Medicine ,Rotavirus vaccine ,United States ,Vaccination ,Diarrhea ,Infectious Diseases ,Immunization ,Child, Preschool ,Pediatrics, Perinatology and Child Health ,Female ,medicine.symptom ,business ,Subacute Care - Abstract
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.
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- 2019
22. Comparative genomic analysis of genogroup 1 and genogroup 2 rotaviruses circulating in seven US cities, 2014–2016
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Daniel C. Payne, Christopher J. Harrison, Jose Jaime, Jan Englund, Rashi Gautam, Natasha B. Halasa, Naga S. Betrapally, Geoffrey A. Weinberg, James D. Chappell, Mary E Wikswo, Umesh D. Parashar, Michael D. Bowen, Julie A. Boom, Mary Allen Staat, Eileen J. Klein, Eric M Katz, Rangaraj Selvarangan, Slavica M Rustempasic, M Leanne Ward, Mathew D. Esona, and Monica M. McNeal
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Whole genome sequencing ,Genetics ,Phylogenetic tree ,Reassortment ,Biology ,medicine.disease_cause ,Microbiology ,Virology ,Rotavirus ,Genotype ,medicine ,ORFS ,Allele ,Gene ,Research Article - Abstract
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.
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- 2021
23. Additive main effects and multiplicative interaction analyses of yield performance in rice genotypes for general and specific adaptation to salt stress in locations in India
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S. Thirumeni, V. K. Mishra, G. Padmavathi, Parbodh C. Sharma, M. Prakash, Raman Gill, D. K. Sharma, K. D. Patil, Pawan K. Singh, D. Burman, Rashi Gautam, B. C. Marandi, A. H. Khan, B. J. Roy, Subhasis Mandal, B. Maji, P. B. Vanve, S.N. Tiwari, R. K. Singh, O. P. Verma, K. K. Manohara, Krishnendu Chattopadhyay, S. L. Krishnamurthy, S. Geetha, Annamalai Anandan, Abdelbagi M. Ismail, Justine Bonifacio, V. K. Yadav, Sukanta K. Sarangi, and Y. P. Singh
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0106 biological sciences ,biology ,Kharif crop ,Ammi ,04 agricultural and veterinary sciences ,Plant Science ,Horticulture ,biology.organism_classification ,01 natural sciences ,Yield (chemistry) ,Mega environment ,Genotype ,040103 agronomy & agriculture ,Genetics ,0401 agriculture, forestry, and fisheries ,Multiplicative interaction ,Adaptation ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
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.
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- 2021
24. Detection of diarrhoea associated rotavirus and co-infection with diarrhoeagenic pathogens in the Littoral region of Cameroon using ELISA, RT-PCR and Luminex xTAG GPP assays
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François-Xavier Etoa, Rashi Gautam, Maurice Boda, Rahinatou N. Ghapoutsa, Akongnwi E. Mugyia, Mathew D. Esona, Michael D. Bowen, and Valantine N Ndze
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0301 basic medicine ,Diarrhea ,Male ,Rotavirus ,medicine.medical_specialty ,Childhood diarrhoea ,RT-PCR ,Enzyme-Linked Immunosorbent Assay ,Infectious and parasitic diseases ,RC109-216 ,medicine.disease_cause ,Vaccines, Attenuated ,Rotavirus Infections ,03 medical and health sciences ,0302 clinical medicine ,Medical microbiology ,Epidemiology ,Genotype ,medicine ,Prevalence ,Humans ,Shigella ,030212 general & internal medicine ,Cameroon ,Genotyping ,Antigens, Viral ,xTAG GPP ,business.industry ,Coinfection ,Reverse Transcriptase Polymerase Chain Reaction ,Research ,Rotarix ,Vaccination ,Rotavirus Vaccines ,Infant ,Virology ,Co-infection ,030104 developmental biology ,Infectious Diseases ,Parasitology ,Immunization ,Child, Preschool ,Biological Assay ,Capsid Proteins ,Female ,business ,Child, Hospitalized - Abstract
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.
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- 2021
25. Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient
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Jennifer Harcourt, Azaibi Tamin, Xiaoyan Lu, Shifaq Kamili, Senthil Kumar. Sakthivel, Janna Murray, Krista Queen, Ying Tao, Clinton R. Paden, Jing Zhang, Yan Li, Anna Uehara, Haibin Wang, Cynthia Goldsmith, Hannah A. Bullock, Lijuan Wang, Brett Whitaker, Brian Lynch, Rashi Gautam, Craig Schindewolf, Kumari G. Lokugamage, Dionna Scharton, Jessica A. Plante, Divya Mirchandani, Steven G. Widen, Krishna Narayanan, Shinji Makino, Thomas G. Ksiazek, Kenneth S. Plante, Scott C. Weaver, Stephen Lindstrom, Suxiang Tong, Vineet D. Menachery, and Natalie J. Thornburg
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0303 health sciences ,Isolation (health care) ,030306 microbiology ,business.industry ,viruses ,Outbreak ,medicine.disease_cause ,medicine.disease ,Virology ,Virus ,Article ,3. Good health ,03 medical and health sciences ,Pneumonia ,Cell culture ,medicine ,Vero cell ,business ,Tropism ,030304 developmental biology ,Coronavirus - Abstract
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.
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- 2020
26. Additional file 1 of Molecular characteristics of rotavirus genotypes circulating in the south of Benin, 2016–2018
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Jijoho Michel Agbla, Esona, Mathew D., Alidehou Jerrold Agbankpe, Capo-Chichi, Annick, Rashi Gautam, Tamegnon Victorien Dougnon, Osseni Razack, Bowen, Michael D., and Honore Sourou Bankole
- Abstract
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.
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- 2020
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27. Bioefficacy of antimicrobial peptide biosynthesis-gene-linked antagonistic Lysinibacillus sphaericus strains for management of bacterial plant diseases in Andaman and Nicobar Islands, India
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K. Sakthivel, T. Subramani, K. Manigundan, Yogeshwari, Sushil K. Sharma, Rashi Gautam, R. Khande, and Pawan K. Singh
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Environmental Engineering ,biology ,Health, Toxicology and Mutagenesis ,Peptide Biosynthesis ,Lysinibacillus sphaericus ,Toxicology ,biology.organism_classification ,Antimicrobial ,Gene ,Microbiology - Published
- 2018
28. Detection of antimicrobial peptide genes from antagonistic Bacillus subtilis (Bs_Ane) isolated from Neil Islands of Andaman, India
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K. Sakthivel, K. Manigundan, Reena Singh, Rashi Gautam, Sushil K. Sharma, S. Dam Roy, and I. Jaisankar
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0301 basic medicine ,chemistry.chemical_classification ,Environmental Engineering ,Health, Toxicology and Mutagenesis ,Peptide ,Bacillus subtilis ,Biology ,Toxicology ,Antimicrobial ,biology.organism_classification ,Microbiology ,03 medical and health sciences ,030104 developmental biology ,chemistry ,Gene - Published
- 2017
29. Outbreak of diarrhoea in piglets caused by novel rotavirus genotype G4P[49] in north-western district of Bangladesh, February 2014
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Mustafizur Rahman, Warda Haque, Umesh D. Parashar, Emily S. Gurley, Rashi Gautam, Christina J. Castro, Erin D. Kennedy, Mohammed Ziaur Rahman, Salah Uddin Khan, Michael D. Bowen, Mathew D. Esona, Terry Fei Fan Ng, Shamim Sarkar, and Mohammad Enayet Hossain
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Diarrhea ,Rotavirus ,Veterinary medicine ,Genotype ,040301 veterinary sciences ,Swine ,animal diseases ,Attack rate ,Genome, Viral ,Biology ,medicine.disease_cause ,Genetic analysis ,Rotavirus Infections ,Disease Outbreaks ,0403 veterinary science ,03 medical and health sciences ,symbols.namesake ,Case fatality rate ,medicine ,Animals ,Humans ,Phylogeny ,030304 developmental biology ,Sanger sequencing ,Swine Diseases ,0303 health sciences ,Bangladesh ,General Veterinary ,General Immunology and Microbiology ,Reverse Transcriptase Polymerase Chain Reaction ,Outbreak ,High-Throughput Nucleotide Sequencing ,04 agricultural and veterinary sciences ,General Medicine ,Herd ,symbols - Abstract
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.
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- 2019
30. Distribution of rotavirus genotypes in the postvaccine introduction era in Ashaiman, Greater Accra Region, Ghana, 2014-2016
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Belinda Lartey, Francis E. Dennis, Michael D. Bowen, Osbourne Quaye, Susan Damanka, George Armah, Mathew D. Esona, Naga S. Betrapally, Victor Letsa, and Rashi Gautam
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Rotavirus ,Veterinary medicine ,Genotype ,Biology ,medicine.disease_cause ,Ghana ,Rotavirus Infections ,03 medical and health sciences ,Feces ,0302 clinical medicine ,Virology ,Zoonoses ,medicine ,Prevalence ,Animals ,Humans ,030212 general & internal medicine ,Genotyping ,Phylogeny ,High prevalence ,Infant ,Sequence Analysis, DNA ,Acute gastroenteritis ,Gastroenteritis ,Infectious Diseases ,Child, Preschool ,Group A rotaviruses ,Etiology ,RNA, Viral ,030211 gastroenterology & hepatology - Abstract
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.
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- 2019
31. Infectious Causes of Acute Gastroenteritis in US Children Undergoing Allogeneic Hematopoietic Cell Transplant: A Longitudinal, Multicenter Study
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Michael D. Bowen, Bhinnata Piya, Mary E Wikswo, Daniel C. Payne, Jan Vinjé, Hannah Browne, Parvin H. Azimi, Jennifer E. Schuster, Rendie McHenry, Daniel E. Dulek, Natasha B. Halasa, Samantha H. Johnston, Rashi Gautam, Janet A. Englund, and Rangaraj Selvarangan
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Male ,medicine.medical_specialty ,Adolescent ,medicine.disease_cause ,Asymptomatic ,03 medical and health sciences ,Immunocompromised Host ,0302 clinical medicine ,Internal medicine ,Rotavirus ,Epidemiology ,medicine ,Prevalence ,Infection control ,Humans ,030212 general & internal medicine ,Longitudinal Studies ,Prospective Studies ,Child ,0303 health sciences ,biology ,030306 microbiology ,business.industry ,Hematopoietic Stem Cell Transplantation ,Infant ,Sapovirus ,General Medicine ,biology.organism_classification ,United States ,Gastroenteritis ,Vaccination ,Diarrhea ,Infectious Diseases ,Child, Preschool ,Pediatrics, Perinatology and Child Health ,Acute Disease ,Norovirus ,Female ,medicine.symptom ,business - Abstract
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.
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- 2019
32. Analysis of Stability and G × E Interaction of Rice Genotypes across Saline and Alkaline Environments in India
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V. K. Mishra, S. Thirumeni, R. K. Singh, Shashi Kant Tiwari, S. K. Sharma, Pankaj Singh, Glenn B. Gregorio, B. C. Marandi, S. L. Krishnamurthy, Parbodh C. Sharma, Padmavathi G, B.K. Bandyopadhyay, Rashi Gautam, Abdelbagi M. Ismail, Subhasis Mandal, A. H. Khan, Yash Pal Singh, P. B. Vanve, Sukanta K. Sarangi, M. Shakila, D. P. Singh, D. K. Sharma, D. Burman, K. D. Patil, K. K. Manohara, O. P. Verma, and B. Maji
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0106 biological sciences ,Biplot ,biology ,Physiology ,business.industry ,Ammi ,04 agricultural and veterinary sciences ,biology.organism_classification ,Interaction ,01 natural sciences ,Biotechnology ,Salinity ,Agriculture ,Genotype ,040103 agronomy & agriculture ,Genetics ,0401 agriculture, forestry, and fisheries ,Multiplicative interaction ,business ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
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...
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- 2016
33. Diversity of Ralstonia solanacearum Strains on the Andaman Islands in India
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C Devendrakumar, Aundy Kumar, S. Neelam, Koushi Kumar, S. Dam Roy, Boris A. Vinatzer, Rashi Gautam, K. Sakthivel, and M. Vibhuti
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0106 biological sciences ,0301 basic medicine ,Phylotype ,Ralstonia solanacearum ,biology ,Biovar ,fungi ,food and beverages ,Virulence ,Plant Science ,Ribosomal RNA ,biology.organism_classification ,16S ribosomal RNA ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Botany ,Multilocus sequence typing ,Solanum ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
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.
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- 2016
34. Evaluation of an Alternative Recombinant Thermostable Thermus thermophilus (r Tth )-Based Real-Time Reverse Transcription-PCR Kit for Detection of Rotavirus A
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Eric M Katz, Rashi Gautam, and Michael D. Bowen
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0301 basic medicine ,Microbiology (medical) ,biology ,030106 microbiology ,Rotavirus Infections ,Thermus thermophilus ,biology.organism_classification ,medicine.disease_cause ,Virology ,law.invention ,Reverse transcription polymerase chain reaction ,03 medical and health sciences ,Real-time polymerase chain reaction ,law ,Rotavirus ,medicine ,Recombinant DNA ,Molecular diagnostic techniques ,Letter to the Editor - Published
- 2017
35. Three Rotavirus Outbreaks in the Postvaccine Era - California, 2017
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Carly Bock, Michael D. Bowen, Rachel M Burke, Thalia Huynh, John Holguin, Chao-Yang Pan, Rebecca Quenelle, Cindy Torres, Rashi Gautam, David Chang, Nora Barin, Umesh D. Parashar, Debra A. Wadford, Catherine Sallenave, Jacqueline E. Tate, and George Han
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0301 basic medicine ,Adult ,Pediatrics ,medicine.medical_specialty ,Health (social science) ,Adolescent ,Epidemiology ,viruses ,Health, Toxicology and Mutagenesis ,030106 microbiology ,Prevalence ,Rotavirus Infections ,medicine.disease_cause ,California ,Disease Outbreaks ,03 medical and health sciences ,Young Adult ,fluids and secretions ,Health Information Management ,Assisted Living Facilities ,Rotavirus ,medicine ,Humans ,Full Report ,Young adult ,Child ,Aged ,Aged, 80 and over ,Tetanus ,business.industry ,Diphtheria ,Rotavirus Vaccines ,virus diseases ,Outbreak ,Infant ,General Medicine ,Child Day Care Centers ,Middle Aged ,medicine.disease ,Rotavirus vaccine ,Child, Preschool ,Health Facilities ,business - Abstract
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.
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- 2018
36. Molecular characterization of a human G20P[28] rotavirus a strain with multiple genes related to bat rotaviruses
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Sunando Roy, Michael D. Bowen, Kunchala Rungsrisuriyachai, Mathew D. Esona, Gloria Rey-Benito, Sandra Hermelijn, and Rashi Gautam
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0301 basic medicine ,Microbiology (medical) ,Rotavirus ,Genotype ,viruses ,030106 microbiology ,Genome, Viral ,Biology ,medicine.disease_cause ,Microbiology ,Article ,Rotavirus Infections ,03 medical and health sciences ,Open Reading Frames ,Phylogenetics ,Chiroptera ,Genetics ,medicine ,Animals ,Humans ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,NSP1 ,Strain (biology) ,virus diseases ,Sequence Analysis, DNA ,Virology ,Open reading frame ,030104 developmental biology ,Infectious Diseases ,Child, Preschool ,Multilocus sequence typing ,Female ,Multilocus Sequence Typing - Abstract
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.
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- 2017
37. 652. What Is Blood Got to Do with It? Genetic Susceptibility to Norovirus and Rotavirus Infection: Results From the SUPERNOVA Network
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Vincent C. Marconi, Anita Kambhampati, Frederick H. Neill, Aleksandra Poteshkina, Cristina V. Cardemil, Adrienne Perea, Kathryn L Meagley, Scott Grytdal, David O. Beenhouwer, Michael D. Bowen, Sheldon T. Brown, Jan Vinjé, Aron J. Hall, Blanca Vargas, Robert L. Atmar, Umesh D. Parashar, Maria C. Rodriguez-Barradas, Hannah Browne, and Rashi Gautam
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business.industry ,viruses ,Rotavirus Infections ,virus diseases ,Stool specimen ,medicine.disease_cause ,Virology ,Rotavirus infection ,Abstracts ,Infectious Diseases ,fluids and secretions ,Oncology ,B. Poster Abstracts ,Rotavirus ,Genotype ,medicine ,Norovirus ,Genetic predisposition ,business - Abstract
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.
- Published
- 2018
38. Multiplexed one-step RT-PCR VP7 and VP4 genotyping assays for rotaviruses using updated primers
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Ka Ian Tam, Rashi Gautam, Mathew D. Esona, Alice Williams, Michael D. Bowen, and Slavica Mijatovic-Rustempasic
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Rotavirus ,Genotyping Techniques ,viruses ,Biology ,medicine.disease_cause ,Sensitivity and Specificity ,Article ,Virus ,fluids and secretions ,Virology ,Genotype ,Multiplex polymerase chain reaction ,medicine ,Humans ,Antigens, Viral ,Genotyping ,DNA Primers ,Reverse Transcriptase Polymerase Chain Reaction ,virus diseases ,Amplicon ,Molecular biology ,Real-time polymerase chain reaction ,Capsid Proteins ,Multiplex Polymerase Chain Reaction - Abstract
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.
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- 2015
39. Molecular genotyping and quantitation assay for rotavirus surveillance
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Gibson S. Kibiki, Kate Lurain, Jie Liu, Shihab U. Sobuz, Michael D. Bowen, Denise Toney, Rashidul Haque, Eric R. Houpt, Sharmin Begum, Rashi Gautam, Happiness Kumburu, Jean Gratz, and William A. Petri
- Subjects
Rotavirus ,Genotyping Techniques ,Concordance ,Biology ,Real-Time Polymerase Chain Reaction ,medicine.disease_cause ,Sensitivity and Specificity ,Tanzania ,Article ,Rotavirus Infections ,Virology ,Genotype ,Multiplex polymerase chain reaction ,medicine ,Humans ,Genotyping ,Bangladesh ,Molecular Epidemiology ,Molecular epidemiology ,Coinfection ,Reverse Transcriptase Polymerase Chain Reaction ,Infant, Newborn ,Virginia ,Infant ,Viral Load ,Molecular biology ,Diarrhea ,Child, Preschool ,Epidemiological Monitoring ,medicine.symptom ,Multiplex Polymerase Chain Reaction - Abstract
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.
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- 2015
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40. Path and association analysis and stress indices for salinity tolerance traits in promising rice (Oryza sativaL.) genotypes
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Rashi Gautam, S. L. Krishnamurthy, V. Kumar, and S. K. Sharma
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Soil salinity ,Oryza sativa ,Yield (engineering) ,Physiology ,Kharif crop ,Randomized block design ,food and beverages ,Biology ,Salinity ,Agronomy ,Path coefficient ,Genetics ,Agronomy and Crop Science ,Panicle - Abstract
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...
- Published
- 2014
41. EVENTRATION OF DIAPHRAGM COMPLICATED BY GASTRIC VOLVULUS IN ELDERLY FEMALE : A CASE REPORT
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Rashi Gautam, Shraddha Sahu, Reena Sinha, Ashok Kumar, and Kedarnath Arya
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Abdominal pain ,medicine.medical_specialty ,Gastric volvulus ,business.industry ,medicine.medical_treatment ,Stomach ,Perforation (oil well) ,Diaphragmatic breathing ,medicine.disease ,Epigastric pain ,digestive system diseases ,Diaphragm (structural system) ,Surgery ,Gastropexy ,medicine.anatomical_structure ,Medicine ,medicine.symptom ,business - Abstract
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.
- Published
- 2014
42. 2322. Etiology, Severity of Illness, and Risk Factors for Patients Hospitalized with Acute Gastroenteritis from Multi-Site Veteran’s Affairs (VA) Surveillance, 2016–2018: Results from SUPERNOVA
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Neha Balachandran, Sheldon T. Brown, Anita Kambhampati, Jan Vinjé, Karen V. Evangelista, Scott Grytdal, Mark Holodniy, Cristina V. Cardemil, Kathryn L Meagley, Blanca Vargas, Cynthia Lucero-Obusan, Adrienne Perea, David O. Beenhouwer, Aron J. Hall, Vincent C. Marconi, Michael D. Bowen, Maria C. Rodriguez-Barradas, Hannah Browne, Umesh D. Parashar, and Rashi Gautam
- Subjects
Pediatrics ,medicine.medical_specialty ,business.industry ,Multi site ,Acute gastroenteritis ,medicine.disease_cause ,Hiv seropositivity ,Causality ,Intensive care unit ,law.invention ,Abstracts ,Infectious Diseases ,Oncology ,law ,Severity of illness ,Poster Abstracts ,Norovirus ,medicine ,Etiology ,business - Abstract
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.
- Published
- 2019
43. 1648. Incidence of Norovirus and Rotavirus From Multisite Active Surveillance in Veteran’s Affairs Hospitals, December 2016–February 2018: Results From the SUPERNOVA Network
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Scott Grytdal, Maria C. Rodriguez-Barradas, Cynthia A. Lucero, Mark Holodniy, Hannah Browne, Vincent Marconi, Karen V. Evangelista, Aron J. Hall, Michael D. Bowen, Rashi Gautam, Blanca Vargas, David O. Beenhouwer, Adrienne Perea, Umesh D. Parashar, Jan Vinjé, Anita Kambhampati, Cristina V. Cardemil, Kathryn L Meagley, and Sheldon T. Brown
- Subjects
0301 basic medicine ,Pediatrics ,medicine.medical_specialty ,viruses ,medicine.medical_treatment ,030106 microbiology ,Stool specimen ,medicine.disease_cause ,Abstracts ,03 medical and health sciences ,fluids and secretions ,0302 clinical medicine ,A. Oral Abstracts ,Rotavirus ,Genotype ,Cost of illness ,Medicine ,030212 general & internal medicine ,Genotype determination ,business.industry ,Incidence (epidemiology) ,virus diseases ,Infectious Diseases ,Oncology ,Norovirus ,business ,Watchful waiting - Abstract
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.
- Published
- 2018
44. Human G9P[8] rotavirus strains circulating in Cameroon, 1999–2000: Genetic relationships with other G9 strains and detection of a new G9 subtype
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Marcelle Figueira Marques da Silva, Kimberly Foytich, Krisztián Bányai, Osbourne Quaye, Nicola Page, Sunando Roy, George E. Armah, Valentine Ngum Ndze, M. Aminu, Mapaseka Seheri, Jon R. Gentsch, Slavica Mijatovic-Rustempasic, Rashi Gautam, Eduardo de Mello Volotão, James Nyangao, Mariela Martínez Gómez, Michael D. Bowen, J.C. Forbi, A. D. Steele, Ka Ian Tam, and Mathew D. Esona
- Subjects
Rotavirus ,Microbiology (medical) ,Molecular Sequence Data ,Genome, Viral ,Biology ,medicine.disease_cause ,Microbiology ,Genome ,Article ,Rotavirus Infections ,DNA sequencing ,Phylogenetics ,Genotype ,Genetics ,medicine ,Humans ,Amino Acid Sequence ,Cameroon ,Genetic variability ,Antigens, Viral ,Molecular Biology ,Gene ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Phylogenetic tree ,Infant ,Virology ,Infectious Diseases ,Child, Preschool ,Capsid Proteins ,Sequence Alignment - Abstract
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.
- Published
- 2013
45. Rotavirus Strain Trends During the Postlicensure Vaccine Era: United States, 2008-2013
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Slavica Mijatovic-Rustempasic, Daniel C. Payne, Parvin H. Azimi, Julie A. Boom, Janet A. Englund, Rangaraj Selvarangan, Kathryn M. Edwards, Elizabeth N. Teel, Leila C. Sahni, Rashi Gautam, Stephanie Donauer, Monica M. McNeal, Geoffrey A. Weinberg, Michael D. Bowen, Christopher J. Harrison, Marcia A. Rench, Mary E. Moffatt, Michele M Sturgeon, Natasha B. Halasa, Eileen J. Klein, Umesh D. Parashar, James D. Chappell, Samantha H. Johnston, Mathew D. Esona, Mary E Wikswo, Peter G. Szilagyi, Carol J. Baker, Mary Allen Staat, and David I. Bernstein
- Subjects
0301 basic medicine ,Male ,Rotavirus ,medicine.medical_specialty ,Genotype ,prevalence ,030106 microbiology ,Rotavirus Infections ,medicine.disease_cause ,Medical and Health Sciences ,Microbiology ,Article ,Vaccine Related ,03 medical and health sciences ,0302 clinical medicine ,Clinical Research ,vaccine ,Internal medicine ,medicine ,Immunology and Allergy ,Humans ,030212 general & internal medicine ,Preschool ,Child ,Genotyping ,Genotype determination ,Pediatric ,business.industry ,Prevention ,Rotavirus Vaccines ,Infant ,Biological Sciences ,Virology ,Disease control ,United States ,Good Health and Well Being ,Infectious Diseases ,Child, Preschool ,Epidemiological Monitoring ,surveillance ,Group A rotaviruses ,Immunization ,Female ,business - Abstract
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.
- Published
- 2016
46. One-step Quantitative RT-PCR Assays for Detecting, Genotyping and Differentiating Wild-Type Group a Rotaviruses and Vaccine (Rotarix® and RotaTeq®) Strains in Stool Samples
- Author
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Michael D. Bowen and Rashi Gautam
- Subjects
0301 basic medicine ,Immunology ,Wild type ,Biology ,medicine.disease_cause ,Omics ,Virology ,Molecular biology ,Article ,03 medical and health sciences ,030104 developmental biology ,Real-time polymerase chain reaction ,Rotavirus ,Drug Discovery ,medicine ,Group A rotaviruses ,Immunology and Allergy ,Genotyping - Published
- 2016
47. Rotavirus disease burden among children <5 years of age - Santa Rosa, Guatemala, 2007-2009
- Author
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Wences Arvelo, Lissette Reyes, Beatriz Lopez, Jennifer E. Cortes, Rashi Gautam, Tara Kerin, Manish M. Patel, Kim A. Lindblade, and Umesh D. Parashar
- Subjects
Gynecology ,medicine.medical_specialty ,Pediatrics ,business.industry ,Incidence (epidemiology) ,Office visits ,Public Health, Environmental and Occupational Health ,medicine.disease_cause ,Rotavirus disease ,Infectious Diseases ,Rotavirus ,medicine ,Cost of illness ,Parasitology ,business - Abstract
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
- Published
- 2011
48. First report of Colletotrichum plurivorum from the Andaman and Nicobar Islands causing anthracnose in chilli ( Capsicum annuum )
- Author
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K. Sakthivel, S. Neelam, K. Charishma, K. Manigundan, Rashi Gautam, A. K. Patel, S. Sneha, and Anil Kumar
- Subjects
0106 biological sciences ,0301 basic medicine ,biology ,Health, Toxicology and Mutagenesis ,Crop yield ,Plant Science ,030108 mycology & parasitology ,Fruit rot ,biology.organism_classification ,Pathogenicity ,01 natural sciences ,Crop ,03 medical and health sciences ,Capsicum annuum ,Horticulture ,Colletotrichum ,Pepper ,Fungal morphology ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Chilli pepper (Capsicum annuum) is an important spice crop worldwide, which is cultivated widely in the Andaman and Nicobar Islands and accounts for one-third of the solanaceous vegetables grown in India. During the first quarter of 2017, …
- Published
- 2018
49. Rotavirus
- Author
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Mathew D. Esona and Rashi Gautam
- Subjects
Rotavirus ,Virus Cultivation ,Genotyping Techniques ,Reverse Transcriptase Polymerase Chain Reaction ,Sequence Analysis, RNA ,Biochemistry (medical) ,Clinical Biochemistry ,High-Throughput Nucleotide Sequencing ,Real-Time Polymerase Chain Reaction ,Rotavirus Infections ,Gastroenteritis ,Immunoenzyme Techniques ,Agglutination Tests ,Humans - Abstract
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.
- Published
- 2015
50. Full genomic characterization and phylogenetic analysis of a zoonotic human G8P[14] rotavirus strain detected in a sample from Guatemala☆
- Author
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Beatriz Lopez, Michael D. Bowen, Rashi Gautam, Gloria Rey-Benito, Sunando Roy, Mathew D. Esona, Slavica Mijatovic-Rustempasic, and Yolanda Mencos
- Subjects
Microbiology (medical) ,Rotavirus ,Lineage (genetic) ,Genes, Viral ,Reassortment ,Genome, Viral ,Biology ,medicine.disease_cause ,Microbiology ,Genome ,Article ,Rotavirus Infections ,Open Reading Frames ,Phylogenetics ,Zoonoses ,Genotype ,Genetics ,medicine ,Animals ,Humans ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Phylogenetic tree ,Strain (biology) ,Genomics ,Guatemala ,Virology ,Infectious Diseases - Abstract
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.
- Published
- 2015
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