scholarly journals Surveillance of Human Rotavirus in Wuhan, China (2011–2019): Predominance of G9P[8] and Emergence of G12

Pathogens ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 810
Author(s):  
Xuan Zhou ◽  
Yuan-Hong Wang ◽  
Bei-Bei Pang ◽  
Nan Chen ◽  
Nobumichi Kobayashi
Keyword(s):  
Etiologic Agent ◽  
Genetic Characteristics ◽  
Predominant Genotype ◽  
Rotavirus A ◽  
Epidemic Season ◽  
Human Rotavirus ◽  
Stool Specimens ◽  
Virus Strains ◽  
Nsp3 Gene ◽  
Infants And Young Children

Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children worldwide. To learn the shift of genotypes and genetic characteristics of Rotavirus A (RVA) causing diarrhea in children and adults, a hospital-based surveillance of rotavirus was conducted in Wuhan, China from June 2011 through May 2019, and representative virus strains were phylogenetically analyzed. Among a total of 6733 stool specimens collected from both children and adults with acute gastroenteritis, RVA was detected in 25.5% (1125/4409) and 12.3% (285/2324) of specimens, respectively. G9P[8] was the most common genotype (74.5%), followed by G1P[8] (8.7%), G2P[4] (8.4%), and G3P[8] (7.3%), with G9P[8] increasing rapidly during the study period. The predominant genotype shifted from G1P[8] to G9P[8] in 2012–2013 epidemic season. G12P[6] strain RVA/Human-wt/CHN/Z2761/2019/G12P[6] was detected in April 2019 and assigned to G12-P[6]-I1-R1-C1-M1-A1-N1-T2-E1-H1 genotypes. Phylogenetic analysis revealed that VP7, VP4, VP6, VP3, NSP1, NSP2, and NSP5 genes of Z2761 clustered closely with those of Korean G12P[6] strain CAU_214, showing high nucleotide identities (98.0–98.8%). The NSP3 gene of Z2761 was closely related to those of G2P[4] and G12P[6] rotaviruses in Asia. All the eleven gene segments of Z2761 kept distance from those of cocirculating G9P[8], G1P[8], and G3P[8] strains detected in Wuhan during this study period. This is the first identification of G12 rotavirus in China. It is deduced that Z2761 is a reassortant having DS-1-like NSP3 gene in the background of G12P[6] rotavirus genetically close to CAU_214.

scholarly journals Reference Human Rotavirus A Genome Sequence from a Previously Vaccinated Child with Diarrhea in Nigeria

2020 ◽  
Vol 9 (5) ◽  
Author(s):  
T. O. C. Faleye ◽  
U. E. George ◽  
C. Simsek ◽  
O. A. Arowolo ◽  
O. M. Adewumi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Reverse Transcription ◽  
Rapid Test ◽  
Etiologic Agent ◽  
Rt Pcr ◽  
Rotavirus A ◽  
Reverse Transcription Pcr ◽  
Human Rotavirus ◽  
A Genome ◽  
Genotype Constellation

In 2018, a 26-month-old girl, fully vaccinated with Rotarix in 2016, presented with fever, diarrhea, and vomiting. A rapid test showed that her feces contained rotavirus A (RVA). VP7 reverse transcription-PCR (RT-PCR) and Illumina sequencing showed that a G1P[8] strain with a Wa-like genotype constellation was the etiologic agent. This is the first near-complete RVA genome sequence from Nigeria.

scholarly journals Generation of Simian Rotavirus Reassortants with VP4- and VP7-Encoding Genome Segments from Human Strains Circulating in Africa Using Reverse Genetics

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 201 ◽  
Author(s):  
Alexander Falkenhagen ◽  
Corinna Patzina-Mehling ◽  
Ashish K. Gadicherla ◽  
Amy Strydom ◽  
Hester G. O’Neill ◽  
...  
Keyword(s):  
Cell Culture ◽  
Disease Burden ◽  
Reverse Genetics ◽  
Sub Saharan Africa ◽  
Rotavirus A ◽  
Virus Particles ◽  
Rotavirus Vaccines ◽  
Human Rotavirus ◽  
Sub Saharan ◽  
Infants And Young Children

Human rotavirus A (RVA) causes acute gastroenteritis in infants and young children. The broad use of two vaccines, which are based on RVA strains from Europe and North America, significantly reduced rotavirus disease burden worldwide. However, a lower vaccine effectiveness is recorded in some regions of the world, such as sub-Saharan Africa, where diverse RVA strains are circulating. Here, a plasmid-based reverse genetics system was used to generate simian RVA reassortants with VP4 and VP7 proteins derived from African human RVA strains not previously adapted to cell culture. We were able to rescue 1/3 VP4 mono-reassortants, 3/3 VP7 mono-reassortants, but no VP4/VP7 double reassortant. Electron microscopy showed typical triple-layered virus particles for the rescued reassortants. All reassortants stably replicated in MA-104 cells; however, the VP4 reassortant showed significantly slower growth compared to the simian RVA or the VP7 reassortants. The results indicate that, at least in cell culture, human VP7 has a high reassortment potential, while reassortment of human VP4 from unadapted human RVA strains with simian RVA seems to be limited. The characterized reassortants may be useful for future studies investigating replication and reassortment requirements of rotaviruses as well as for the development of next generation rotavirus vaccines.

CLINICAL AND PARACLINICAL CHARACTERISTITICS OF ROTAVIRUS DIARRHEA IN CHILDREN LESS THAN 5 YEARS OLD IN PEDIATRIC DEPARTMENT OF BINH DINH GENERAL HOSPITAL

2013 ◽  
pp. 50-56
Author(s):  
Quoc Tinh Nguyen ◽  
Thi Cu Nguyen
Keyword(s):  
General Hospital ◽  
Acute Diarrhea ◽  
White Blood Cells ◽  
Blood Calcium ◽  
Pediatric Department ◽  
Rotavirus A ◽  
Initial Symptoms ◽  
Stool Specimens ◽  
The Mean ◽  
Rotavirus Diarrhea

Background: Diarrhea is a leading cause of morbidity and mortality in children in developing countries. Rotavirus is the most important factor cause of severe diarrhea and mortality in children, especially under 2 years. Objective: To study Clinical and paraclinical characteristitics of rotavirus diarrhea in children less than 5 years old in the Pediatric Department of Binh Dinh General Hospital. Methods: Cross observational study, 417 children from 2 months to 5 years old who were hospitalized for acute diarrhea without blood in stool in Pediatric Department of Binh Dinh general hospital, from 15/3/2012 to 14/3/2013. There were 228 patients with rotavirus - positive stool specimens and 189 patients with rotavirus - negative stool specimens. Tested for rotavirus A classification by agglutination techniques. Results: Percentage of Rotavirus diarrhea in children <5 years was 54.7%. The mean age of rotavirus diarrhea was 14.83 ± 9.08 tháng months. Ages with the highest cases of rotavirus diarrhea are 2 - 12 months: 48.2%. Rotavirrus diarrhea is experienced in every month but, the highest prevalence is experienced in the spring - summer) with 71,5%. Clinical characteristitics of rotavirus diarrhea: Vomit presents in 91,7% of cases. 32.9% of the initial symptoms of the disease is vomiting. Mean number of vomiting episodes per day: 7 ± 3.57 times, significantly higher compared with non-rotavirus acute diarrhea (p <0,01). Mean number of bowel movement per day: 10.61±4.18 times, mean duration of diarrhea: 6.66 ± 2.52 days. Younger children have higher frequency and duration of diarrhea compared to older children. Paraclinical characteristitics of rotavirus diarrhea: the mean number leukocyte: 9.74 ±3.61 (x 109/l). 2.2% with low blood sodium status; 8.8% with reduction in serum potassium concentration. 26.3% with low blood calcium and glucose status. Laboratory characteristics of stool: 8.8% with white blood cells in stool, 41.7% with carbohydrate in stool. Conclusion: Rotavirus accounting for 54.7% of the causes of diarrhea in children. Rotavirus diarrhea is experienced throughout the year but the highest prevalence is in the spring-summer. Prominent symptoms of the disease are vomiting and watery stool. Children <24 months experience higher frequency and duration of diarrhea compared to older age groups. Key words: Diarrhea, Rotavirus.

scholarly journals MOLECULAR AND GENETIC CHARACTERISTICS OF SURFACE AND NONSTRUCTURE PROTEINS OF PANDEMIC INFLUENZA VIRUSES A(H1N1)PDM09 IN 2015-2016 EPIDEMIC SEASON

2016 ◽  
Vol 72 (2) ◽  
pp. 44-48
Author(s):  
O. Smutko ◽  
L. Radchenko ◽  
A. Mironenko
Keyword(s):  
Amino Acid ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Phylogenetic Trees ◽  
Influenza Viruses ◽  
Amino Acid Substitutions ◽  
Ns1 Protein ◽  
Genetic Characteristics ◽  
Epidemic Season ◽  
Influenza A H1n1

The aim of the present study was identifying of molecular and genetic changes in hemaglutinin (HA), neuraminidase (NA) and non-structure protein (NS1) genes of pandemic influenza A(H1N1)pdm09 strains, that circulated in Ukraine during 2015-2016 epidemic season. Samples (nasopharyngeal swabs from patients) were analyzed using real-time polymerase chain reaction (RTPCR). Phylogenetic trees were constructed using MEGA 7 software. 3D structures were constructed in Chimera 1.11.2rc software. Viruses were collected in 2015-2016 season fell into genetic group 6B and in two emerging subgroups, 6B.1 and 6B.2 by gene of HA and NA. Subgroups 6B.1 and 6B.2 are defined by the following amino acid substitutions. In the NS1 protein were identified new amino acid substitutions D2E, N48S, and E125D in 2015-2016 epidemic season. Specific changes were observed in HA protein antigenic sites, but viruses saved similarity to vaccine strain. NS1 protein acquired substitution associated with increased virulence of the influenza virus.

scholarly journals Molecular Epidemiology of Rotavirus A Strains Pre- and Post-Vaccine (Rotarix®) Introduction in Mozambique, 2012–2019: Emergence of Genotypes G3P[4] and G3P[8]

Pathogens ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 671 ◽  
Author(s):  
Eva D. João ◽  
Benilde Munlela ◽  
Assucênio Chissaque ◽  
Jorfélia Chilaúle ◽  
Jerónimo Langa ◽  
...  
Keyword(s):  
Acute Diarrhea ◽  
Sentinel Site ◽  
Predominant Genotype ◽  
Post Vaccination ◽  
Rotavirus A ◽  
Strain Diversity ◽  
Monovalent Vaccine ◽  
Group A ◽  
Expanded Program On Immunization ◽  
First Time

Group A rotavirus (RVA) remains the most important etiological agent associated with severe acute diarrhea in children. Rotarix® monovalent vaccine was introduced into Mozambique’s Expanded Program on Immunization in September 2015. In the present study, we report the diversity and prevalence of rotavirus genotypes, pre- (2012–2015) and post-vaccine (2016–2019) introduction in Mozambique, among diarrheic children less than five years of age. Genotyping data were analyzed for five sentinel sites for the periods indicated. The primary sentinel site, Mavalane General Hospital (HGM), was analyzed for the period 2012–2019, and for all five sites (country-wide analyses), 2015–2019. During the pre-vaccine period, G9P[8] was the most predominant genotype for both HGM (28.5%) and the country-wide analysis (46.0%). However, in the post-vaccine period, G9P[8] was significantly reduced. Instead, G3P[8] was the most common genotype at HGM, while G1P[8] predominated country-wide. Genotypes G9P[4] and G9P[6] were detected for the first time, and the emergence of G3P[8] and G3P[4] genotypes were observed during the post-vaccine period. The distribution and prevalence of rotavirus genotypes were distinct in pre- and post-vaccination periods, while uncommon genotypes were also detected in the post-vaccine period. These observations support the need for continued country-wide surveillance to monitor changes in strain diversity, due to possible vaccine pressure, and consequently, the effect on vaccine effectiveness.

Full genome characterization of human Rotavirus A strains isolated in Cameroon, 2010–2011: Diverse combinations of the G and P genes and lack of reassortment of the backbone genes

2014 ◽  
Vol 28 ◽  
pp. 537-560 ◽  
Author(s):  
Valentine Ngum Ndze ◽  
Mathew Dioh Esona ◽  
Eric Akum Achidi ◽  
Kamga Hortense Gonsu ◽  
Renáta Dóró ◽  
...  
Keyword(s):  
Full Genome ◽  
Genome Characterization ◽  
Rotavirus A ◽  
Human Rotavirus

scholarly journals Molecular-Genetic Characterization of Human Rotavirus A Strains Circulating in Moscow, Russia (2009–2014)

2018 ◽  
Vol 33 (4) ◽  
pp. 304-313 ◽  
Author(s):  
Victoria Kiseleva ◽  
Evgeny Faizuloev ◽  
Elena Meskina ◽  
Anna Marova ◽  
Alexey Oksanich ◽  
...  
Keyword(s):  
Genetic Characterization ◽  
Molecular Genetic ◽  
Rotavirus A ◽  
Human Rotavirus ◽  
Molecular Genetic Characterization

scholarly journals Genomic Characterization of Urethritis-Associated Neisseria meningitidis Shows that a Wide Range of N. meningitidis Strains Can Cause Urethritis

2017 ◽  
Vol 55 (12) ◽  
pp. 3374-3383 ◽  
Author(s):  
Kevin C. Ma ◽  
Magnus Unemo ◽  
Samo Jeverica ◽  
Robert D. Kirkcaldy ◽  
Hideyuki Takahashi ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Etiologic Agent ◽  
Factor H ◽  
Urogenital Tract ◽  
Genetic Characteristics ◽  
Content Type ◽  
Nitrite Reductase Gene ◽  
Reductase Gene ◽  
Wide Range ◽  
Genomic Characterization

ABSTRACTNeisseria meningitidis, typically a resident of the oro- or nasopharynx and the causative agent of meningococcal meningitis and meningococcemia, is capable of invading and colonizing the urogenital tract. This can result in urethritis, akin to the syndrome caused by its sister species,N. gonorrhoeae, the etiologic agent of gonorrhea. Recently, meningococcal strains associated with outbreaks of urethritis were reported to share genetic characteristics with the gonococcus, raising the question of the extent to which these strains contain features that promote adaptation to the genitourinary niche, making them gonococcus-like and distinguishing them from otherN. meningitidisstrains. Here, we analyzed the genomes of 39 diverseN. meningitidisisolates associated with urethritis, collected independently over a decade and across three continents. In particular, we characterized the diversity of the nitrite reductase gene (aniA), the factor H-binding protein gene (fHbp), and the capsule biosynthetic locus, all of which are loci previously suggested to be associated with urogenital colonization. We observed notable diversity, including frameshift variants, inaniAandfHbpand the presence of intact, disrupted, and absent capsule biosynthetic genes, indicating that urogenital colonization and urethritis caused byN. meningitidisare possible across a range of meningococcal genotypes. Previously identified allelic patterns in urethritis-associatedN. meningitidisstrains may reflect genetic diversity in the underlying meningococcal population rather than novel adaptation to the urogenital tract.

scholarly journals Multicenter Evaluation of the BioFire FilmArray Gastrointestinal Panel for Etiologic Diagnosis of Infectious Gastroenteritis

2015 ◽  
Vol 53 (3) ◽  
pp. 915-925 ◽  
Author(s):  
Sarah N. Buss ◽  
Amy Leber ◽  
Kimberle Chapin ◽  
Paul D. Fey ◽  
Matthew J. Bankowski ◽  
...  
Keyword(s):  
Simultaneous Detection ◽  
Turnaround Time ◽  
Stool Culture ◽  
Content Type ◽  
Rotavirus A ◽  
E Coli ◽  
Infectious Gastroenteritis ◽  
Wide Range ◽  
Stool Specimens ◽  
Etiologic Diagnosis

The appropriate treatment and control of infectious gastroenteritis depend on the ability to rapidly detect the wide range of etiologic agents associated with the disease. Clinical laboratories currently utilize an array of different methodologies to test for bacterial, parasitic, and viral causes of gastroenteritis, a strategy that suffers from poor sensitivity, potentially long turnaround times, and complicated ordering practices and workflows. Additionally, there are limited or no testing methods routinely available for most diarrheagenicEscherichia colistrains, astroviruses, and sapoviruses. This study assessed the performance of the FilmArray Gastrointestinal (GI) Panel for the simultaneous detection of 22 different enteric pathogens directly from stool specimens:Campylobacterspp.,Clostridium difficile(toxin A/B),Plesiomonas shigelloides,Salmonellaspp.,Vibriospp.,Vibrio cholerae,Yersinia enterocolitica, enteroaggregativeE. coli, enteropathogenicE. coli, enterotoxigenicE. coli, Shiga-like toxin-producingE. coli(stx1andstx2) (including specific detection ofE. coliO157),Shigellaspp./enteroinvasiveE. coli,Cryptosporidiumspp.,Cyclospora cayetanensis,Entamoeba histolytica,Giardia lamblia, adenovirus F 40/41, astrovirus, norovirus GI/GII, rotavirus A, and sapovirus. Prospectively collected stool specimens (n= 1,556) were evaluated using the BioFire FilmArray GI Panel and tested with conventional stool culture and molecular methods for comparison. The FilmArray GI Panel sensitivity was 100% for 12/22 targets and ≥94.5% for an additional 7/22 targets. For the remaining three targets, sensitivity could not be calculated due to the low prevalences in this study. The FilmArray GI Panel specificity was ≥97.1% for all panel targets. The FilmArray GI Panel provides a comprehensive, rapid, and streamlined alternative to conventional methods for the etiologic diagnosis of infectious gastroenteritis in the laboratory setting. The potential advantages include improved performance parameters, a more extensive menu of pathogens, and a turnaround time of as short as 1 h.

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