Molecular Epidemiology of Human Sapovirus Among Children with Acute Gastroenteritis in Western Canada

Author(s):  
Ran Zhuo ◽  
Xiaofeng Ding ◽  
Stephen B. Freedman ◽  
Bonita E. Lee ◽  
Samina Ali ◽  
...  

Objectives: Sapovirus is increasingly recognized as an important cause of acute gastroenteritis (AGE) worldwide, however studies of prevalence, genetic diversity and strain-specific clinical implications have been scarce. Methods: To fill this knowledge gap, we used reverse transcription real-time PCR and sequencing of the partial major capsid protein VP1 gene to analyze stool specimens and rectal swabs obtained from 3347 children with AGE and 1355 asymptomatic controls (all <18 years old) collected between December 2014 and August 2018 in Alberta, Canada. Results: Sapovirus was identified in 9.5% (317/3347) of the children with AGE and 2.9% of controls. GI.1 (36%) was the predominant genotype identified, followed by GI.2 (18%), GII.5 (8%) and GII.3 (6%). Rare genotypes GII.1, GII.2, GV.1, GII.4, GIV.1, GI.3 and GI.7 were also seen. Sapovirus was detected year-round, peaking during the winter months of November to January. The exception was the 2016-2017 season when GI.2 overtook GI.1 as the predominant strain with a high detection rate persisting into April. We did not observe significant difference in the severity of gastroenteritis by genogroup or genotype. Repeated infection by sapovirus of different genogroups occurred in three controls who developed AGE later. Conclusions: Our data suggests that sapovirus is a common cause of AGE in children with high genetic diversity.

2017 ◽  
Vol 146 (1) ◽  
pp. 11-18 ◽  
Author(s):  
P. R. PATIL ◽  
N. N. GANORKAR ◽  
V. GOPALKRISHNA

SUMMARYHuman parechoviruses (HPeVs) are known to cause various clinical manifestations including acute gastroenteritis. Although HPeV infections and their genotypes have been detected in human patients worldwide, no such reports are available from India to ascertain the association of HPeVs in acute gastroenteritis. The present study was conducted to determine the clinical features and genetic diversity of HPeVs detected in children hospitalised for acute gastroenteritis. Stool specimens (n= 979) collected from children aged ⩽5 years hospitalised for acute gastroenteritis in Pune, western India during January 2006–December 2010 were included. HPeV RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) (5′UTR) followed by genotyping using VP1 gene-based PCR and phylogenetic analysis. HPeV was detected in 13·9% (136/979) of the cases, co-infections with other enteric viruses were found in 43·4%. HPeV was more frequent in children ⩽1 year age with infections reported throughout the year. A total of 102/136 (75%) HPeV strains were genotyped, which comprised 13 different HPeV genotypes. Of these, HPeV1 was the most predominant genotype detected and phylogenetically clustered with the Harris strain which is rarely reported. The study documents circulation of heterogeneous HPeV genotypes. Two variant strains of HPeV4 and ‘RGD absent’ HPeV5 and 6 strains were also detected. This is the first report of HPeV with diversified genotypes identified in acute gastroenteritis patients from India.


2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Taveesak Janetanakit ◽  
Supassama Chaiyawong ◽  
Kamonpan Charoenkul ◽  
Ratanaporn Tangwangvivat ◽  
Ekkapat Chamsai ◽  
...  

Abstract Background Enterovirus G (EV-G) causes subclinical infections and is occasionally associated with diarrhea in pigs. In this study, we conducted a cross-sectional survey of EV-G in pigs from 73 pig farms in 20 provinces of Thailand from December 2014 to January 2018. Results Our results showed a high occurrence of EV-Gs which 71.6 % of fecal and intestinal samples (556/777) and 71.2 % of pig farms (52/73) were positive for EV-G by RT-PCR specific to the 5’UTR. EV-Gs could be detected in all age pig groups, and the percentage positivity was highest in the fattening group (89.7 %), followed by the nursery group (89.4 %). To characterize the viruses, 34 EV-G representatives were characterized by VP1 gene sequencing. Pairwise sequence comparison and phylogenetic analysis showed that Thai-EV-Gs belonged to the EV-G1, EV-G3, EV-G4, EV-G8, EV-G9 and EV-G10 genotypes, among which the EV-G3 was the predominant genotype in Thailand. Co-infection with different EV-G genotypes or with EV-Gs and porcine epidemic diarrhea virus (PEDV) or porcine deltacoronavirus (PDCoV) on the same pig farms was observed. Conclusions Our results confirmed that EV-G infection is endemic in Thailand, with a high genetic diversity of different genotypes. This study constitutes the first report of the genetic characterization of EV-GS in pigs in Thailand.


PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246598
Author(s):  
Paksathorn Kietsiri ◽  
Chonchanok Muangnapoh ◽  
Woradee Lurchachaiwong ◽  
Paphavee Lertsethtakarn ◽  
Ladaporn Bodhidatta ◽  
...  

Arcobacter butzleri is an emerging zoonotic food-borne and water-borne pathogen that can cause diarrhea in humans. The global prevalence of A. butzleri infection is underestimated, and little is known about their phenotypic and genotypic characterization. The aim of this study was to determine antimicrobial susceptibility (AST) profiles, detect related virulence genes, and classify sequence type (ST) of A. butzleri isolates obtained from human stool and food samples. A total of 84 A. butzleri isolates were obtained from human diarrheal (n = 25), non-diarrheal (n = 24) stool, and food (n = 35) samples in Thailand. They were evaluated for phenotypic identification by conventional microbiological procedures and AST by Kirby-Bauer disc diffusion method as well as virulence genes detection. Representative isolates from each origin were selected based on the presence of virulence genes and AST profiles to analyze genetic diversity by multilocus sequence typing (MLST). All isolates showed resistance to nalidixic acid 40.5% (34/84), ciprofloxacin 11.9% (10/84), azithromycin 8.3% (7/84), and erythromycin 3.6% (3/84). Regarding the ten virulence genes detected, cj1349, mviN and pldA had the highest prevalence 100% (84/84), followed by tlyA 98.8% (83/84), cadF 97.6% (82/84), ciaB 71.4% (60/84), hecA and hecB 22.6% (19/84), iroE 15.5% (13/84) and irgA 10.7% (9/84), respectively. Three virulence genes were present among A. butzleri isolates of human diarrheal stool and food samples, with a significant difference observed among isolates; hecB [36% (9/25) and 8.6% (3/35)], hecA [36% (9/25) and 5.7% (2/35)], and irgA [24% (6/25) and 2.9% (1/35)] (p < 0.05), respectively. The hecA and hecB virulence genes functions are related to the mechanism of hemolysis, while irgA supports a bacterial nutritional requirement. MLST analysis of 26 A. butzleri isolates revealed that 16 novel STs exhibited high genetic diversity. The results of this study is useful for understanding potentially pathogenic and antimicrobial-resistant A. butzleri in Thailand. The pathogenic virulence markers hecB, hecA, and irgA have the potential to be developed for rapid diagnostic detection in human diarrheal stool. No significant relationships among STs and sources of origin were observed. Little is known about A. butzleri, the mechanism of action of these virulence genes, is a topic that needs further investigation.


2021 ◽  
Author(s):  
Andrezza Nascimento ◽  
Alberto José da Silva Duarte ◽  
Patricia Bianca Clissa ◽  
Sabri Saeed Sanabani

Norovirus (NoV) has been recognized as the most common etiological agent of acute gastroenteritis (AGE) in various epidemiological settings worldwide. The virus displays a high genetic diversity that can be classified into genogroups, genotypes, and recombinant strains. Only genogroups I, II, and IV have been found to infect humans. Variants of genogroup II genotype 4 are the most widely circulating strains and have been responsible for all NoV outbreaks globally since the mid-1990s. Several studies from different Brazilian regions have been conducted to detect and genetically characterize NoV from sporadic AGE cases and outbreaks. In this chapter, we have summarized the data that focused on the genetic variabilities of NoVs and thus highlight the value of a surveillance system in assessing not only the true burden of the disease, but also the detection and characterization of emerging novel variants.


2021 ◽  
Vol 12 ◽  
Author(s):  
Tuuli-Marjaana Koski ◽  
Sanne de Jong ◽  
Anne Muola ◽  
Daniel B. Amby ◽  
Erik Andreasson ◽  
...  

The transition toward more sustainable plant protection with reduced pesticide use is difficult, because there is no “silver bullet” available among nonchemical tools. Integrating several plant protection approaches may thus be needed for efficient pest management. Recently, increasing the genetic diversity of plantations via cultivar mixing has been proposed as a possible method to reduce pest damage. However, previous studies have not addressed either the relative efficiency of exploiting cultivar mixing and intrinsic plant herbivore resistance or the potential utility of combining these approaches to increase cropping security. Here, using a full factorial experiment with 60 woodland strawberry plots, we tested for the relative and combined effect of cultivar mixing and intrinsic plant resistance on herbivore damage and yield. The experiment comprised two levels of diversity (“high” with 10 varieties and “low” with two varieties) and three levels of resistance (“resistant” comprising only varieties intrinsically resistant against strawberry leaf beetle Galerucella tenella; “susceptible” with susceptible varieties only; and “resistance mixtures” with 50:50 mixtures of resistant and susceptible varieties). The experiment was carried out over two growing seasons. Use of resistant varieties either alone or intermixed with susceptible varieties in “resistance mixtures” reduced insect herbivory. Interestingly, resistant varieties not only reduced the mean damage in “resistance mixtures” by themselves being less damaged, but also protected intermixed susceptible varieties via associational resistance. The effect of higher genetic diversity was less evident, reducing herbivory only at the highest level of herbivore damage. In general, herbivory was lowest in plots with high diversity that included at least some resistant varieties and highest in low diversity plots consisting only of susceptible varieties. Despite this, no significant difference in yield (fruit biomass) was found, indicating that strawberry may be relatively tolerant. Our results demonstrate that combined use of high genetic diversity and resistant varieties can help reduce pest damage and provide a useful tool for sustainable food production. “Resistance mixtures” may be particularly useful for sensitive food crops where susceptible varieties are high yielding that could not be completely replaced by resistant ones.


Viruses ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 32
Author(s):  
Matías Castells ◽  
Estefany Bertoni ◽  
Rubén Darío Caffarena ◽  
María Laura Casaux ◽  
Carlos Schild ◽  
...  

Viral infections affecting cattle lead to economic losses to the livestock industry worldwide, but little is known about the circulation, pathogenicity and genetic diversity of enteric bovine astrovirus (BoAstV) in America. The aim of this work was to describe the prevalence and genetic diversity of enteric BoAstV in dairy cattle in Uruguay. A total of 457 fecal and 43 intestinal contents from dairy calves were collected between July 2015 and May 2017 and tested by RT-PCR, followed by sequencing and phylogenetic analyses of the polymerase and capsid regions. Twenty-six percent (128/500) of the samples were positive. Three different species within the Mamastrovirus genus were identified, including Mamastrovirus 28, Mamastrovirus 33 (3 samples each) and an unclassified Mamastrovirus species (19 samples). The unclassified species was characterized as a novel Mamastrovirus species. BoAstV circulates in Uruguayan dairy cattle with a high genetic diversity. The eventual clinicopathological significance of enteric BoAstV infection in cattle needs further investigation.


Author(s):  
Shuvra Kanti Dey ◽  
Nadim Sharif ◽  
Baki Billah ◽  
Tanjir Tarek Ibn Siddique ◽  
Tarequl Islam ◽  
...  

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