predominant genotype
Recently Published Documents


TOTAL DOCUMENTS

103
(FIVE YEARS 43)

H-INDEX

20
(FIVE YEARS 4)

2021 ◽  
Author(s):  
Noemi Navarro-Lleó ◽  
Cristina Santiso-Bellón ◽  
Susana Vila-Vicent ◽  
Noelia Carmona-Vicente ◽  
Roberto Gozalbo-Rovira ◽  
...  

Noroviruses are the leading cause of sporadic cases and outbreaks of viral gastroenteritis. For more than 20 years most norovirus infections have been caused by the pandemic genotype GII.4, yet recent studies have reported the emergence of recombinant strains in many countries. In the present study, 4,950 stool samples collected between January 2016 and April 2020 in Valencia (Spain) from patients with acute gastroenteritis were analyzed to investigate the etiological agent. Norovirus was the most frequently detected enteric virus with a positive rate of 9.5% (471/4,950). Among 224 norovirus strains characterized, 175 belonged to genogroup GII and 49 to genogroup GI. Using dual genotyping based on sequencing the ORF1/ORF2 junction region we detected 25 different capsid-polymerase type associations. The most common GII capsid genotype was GII.4 Sydney 2012, followed by GII.2, GII.3, GII.6 and GII.17. A high prevalence of recombinant strains (90.4%) was observed among GII infections between 2018 and 2020. GII.4 Sydney[P16] was the predominant genotype from 2019 to 2020. In addition, GII.P16 polymerase was found harboring within six different capsid genes. A new subcluster of GII.4 Sydney associated with the P31 polymerase was identified by phylogenetic analysis. GI.4 and GI.3 were the predominant genotypes in genogroup GI, in which recombinant strains were also found, such as GI.3[P10], GI.3[P13] and GI.5[P4]. Interestingly, the GI.3[P10] strain could represent a new capsid genotype. This study shows the extensive diversity of recombinant noroviruses circulating in Spain and highlights the role of recombination events in the spread of noroviruses.


Author(s):  
Akeel Beigh ◽  
Mohmommad Darzi ◽  
Samina Bashir ◽  
Parvaiz Dar ◽  
Nazir Ganai ◽  
...  

Background: Cystic Echinococcosis (CE) is an emergent or re-emergent zoonosis and remains a public health and economic problem all over the world. Methods:  The present study was carried on the prevalence and genotypes of Echinococcus present in small ruminants in Kashmir valley. A total of 2100, sheep (2052) and goats (48), slaughtered or spontaneously dead, from various areas of Kashmir valley were screened for the presence of hydatidosis. In case of goat none of the cases were found positive for hydatidosis, whereas, all the positive cases (85) were recorded in sheep only. The overall prevalence of hydatidosis was 4.04%. The prevalence was higher in female sheep (5.46%) compared to males (2.83%). Season-wise highest prevalence was in summer (4.55%), followed by autumn (4.1%), spring (3.89%) and winter (2.5%).The liver was observed to be the most frequently infected organ with relative prevalence of 61.17% followed by lungs (38.82%).The rDNA-ITS1 fragment of positive samples was amplified with BD1 / 4S primers. Results: The length of amplified fragment for all isolated samples was 1000bps. The products obtained on PCR were digested with four restriction enzymes (Rsa 1, Alu 1, Msp 1 and Taq1). Rsa 1, Alu 1, Msp 1 yielded identical fragments, 300 and 700 bp in sheep. TaqI restriction enzyme had no effect on PCR product and after digestion; intact 1000bps fragment was seen. Conclusion: Phylogenetic analysis of ITS1 gene revealed that the common sheep strain (G1) is the predominant genotype in sheep in Kashmir valley.


Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1724
Author(s):  
Sylvia Kahwage Sarmento ◽  
Juliana da Silva Ribeiro de Andrade ◽  
Marize Pereira Miagostovich ◽  
Tulio Machado Fumian

Noroviruses are considered an important cause of acute gastroenteritis (AGE) across all age groups. Here, we investigated the incidence of norovirus, genotypes circulation, and norovirus shedding in AGE stool samples from outpatients in Brazil. During a two-year period, 1546 AGE stool samples from ten Brazilian states were analyzed by RT-qPCR to detect and quantify GI and GII noroviruses. Positive samples were genotyped by dual sequencing using the ORF1/2 junction region. Overall, we detected norovirus in 32.1% of samples, with a massive predominance of GII viruses (89.1%). We also observed a significant difference between the median viral load of norovirus GI (3.4×105 GC/g of stool) and GII (1.9×107 GC/g). The most affected age group was children aged between 6 and 24 m old, and norovirus infection was detected throughout the year without marked seasonality. Phylogenetic analysis of partial RdRp and VP1 regions identified six and 11 genotype combinations of GI and GII, respectively. GII.4 Sydney[P16] was by far the predominant genotype (47.6%), followed by GII.2[P16], GII.4 Sydney[P31], and GII.6[P7]. We detected, for the first time in Brazil, the intergenogroup recombinant genotype GIX.1[GII.P15]. Our study contributes to the knowledge of norovirus genotypes circulation at the national level, reinforcing the importance of molecular surveillance programs for future vaccine designs.


2021 ◽  
Vol 3 (4) ◽  
pp. 133-136
Author(s):  
Pankaj Kumar Gadhia ◽  
Monika Patel ◽  
Khushboo Daryani ◽  
Salil Vaniawala

Introduction: Hepatitis C virus is known to cause liver inflammation, which may progress to liver cirrhosis and hepatocellular carcinoma. The genomes of HCV display sequence heterogenicity, thus, are classified in different genotypes and subtypes. Genotyping aids in understanding the epidemiology, biological features of the virus and inspecting the outbreak of the viral infection. Materials and Methods: In the present study, HCV viral RNA was isolated and quantified by RT-PCR technique followed by determining its genotype by Sanger sequencing method from the blood samples of infected patients. Results: Out of 40 samples, 25 showed positive results and 15 samples showed copy number lower than detection limit (< 35 IU/ml). Of 25 patients, the predominant genotype was 3 (a, b, g, i, k) followed by genotype 1 (a, b, g) and 4(a, c). Conclusion: The results revealed that genotype 3b accounted for the highest number of cases with positive HCV viral load as compared to genotype 1 and 4. The higher prevalence of genotype 3 shows that the needful measure and timely treatment should be conducted.


Author(s):  
Wei Li ◽  
Lu-Yan Chen ◽  
Ran Tao ◽  
Shi-Qiang Shang

Abstract Objective This study aimed to investigate characteristics of human cytomegalovirus (HCMV) glycoprotein H (gH) genotypes in urine, throat swab, and serum from children and breast milk from children's mothers. Methods Fresh urine samples, throat swabs, or serum samples from children and breast milk samples from children's mothers were collected for HCMV DNA detection. The positive samples of HCMV DNA were further detected by fluorescent quantitative polymerase chain reaction (PCR) with gH typing. Results Of 1,703 HCMV DNA-positive samples, the highest proportion (83.3%, 85/102) of children aged between 21 days and 3 months was detected positive in breast milk samples (p = 0.002), and the highest proportion (70.5%, 110/156) of children aged above 3 months was detected positive in throat swab samples (p = 0.002). HCMV in throat swab specimens is mainly high copy (p < 0.0001), and low-copy HCMV is prevalent in breast specimens (p < 0.0001). Among them, 1,059 samples were identified as gH1 genotype, 530 samples were gH2, and 114 samples were coinfection (gH1/2). There had the highest gH2 rates (32.3%) and lowest gH1 (61.0%) rates in urine samples (p = 0.041), whereas the highest gH1 rates (71.6%) and lowest gH2 rates (19.6%) were found in breast milk samples (p = 0.032). Concerning age groups, patients aged between 21 days and 3 months had the highest gH1 proportion (p = 0.017), while patients aged above 3 months had the highest gH1 and gH2 HCMV coinfection proportion (p = 0.002). Among 43 pairs of maternal and child samples corresponding to positive samples, gH genotype of 35 pairs of samples was consistent with a rate of 81.4%. Conclusion gH1 is the predominant genotype of HCMV in each kind of sample in China. However, the distribution of the HCMV gH genotype is different among different samples.


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.


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.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Saeed Shahabi ◽  
Bahador Sarkari ◽  
Afshin Barazesh

Abstract Background Different genotypes of Echinococcus granulosus sensu stricto (s.s.) isolated from livestock and humans have been identified based on cox1 and nad1 genomic fragments. The present study was performed to differentiate the G1/G3 genotypes of Echinococcus granulosus (s.s.) isolated from humans and livestock (sheep and cattle) from Azerbaijan in northwestern Iran, Fars Province in southern Iran, and Van province in Eastern Turkey, using the nad5 gene fragment as a suitable marker to distinguish these two genotypes. Methods A total of 60 pathologically confirmed human hydatid cysts and 90 hydatid cyst samples from livestock were collected from Turkey and Iran. PCR was performed on all of the samples, targeting the nad5 gene. Based on PCR product quality, host type, and the geographical area where the samples were obtained, 36 of the samples were sequenced and were used in the phylogenetic analysis. Results Out of 36 evaluated samples, 26 (72.2%) samples belonged to G1, and 10 (27.8%) samples belonged to the G3 genotype. Out of 21 samples from Turkey, 16 (76.2%) were G1 and 5 (23.8%) were G3, while out of 15 samples from Iran, 10 (66.7%) were G1 and 5 (33.3%) were the G3 genotype. None of the samples isolated from humans in Iran or from sheep in Turkey were G3. Overall, between the two countries, 18.18% of E. granulosus isolates in cattle, 41.66% of isolates in sheep, and 23.07% of human samples were identified as G3, and the others as the G1 genotype. The G3 genotype was not detected in human samples from Iran or sheep samples from Turkey. Conclusion The findings of the study revealed that the G1 genotype of E. granulosus s.s. is the predominant genotype in humans and livestock, both in Turkey and Iran. The ratio of the E. granulosus s.s. G1 to G3 genotype was 3.2 in Turkey and 2 in Iran. The study also further confirmed that the nad5 gene properly differentiated the G1/G3 isolates of E. granulosus from both humans and livestock. Graphical Abstract


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yulian Fang ◽  
Zhaoying Dong ◽  
Yan Liu ◽  
Wei Wang ◽  
Mengzhu Hou ◽  
...  

Abstract Background Norovirus (NoV) is a major cause of viral acute gastroenteritis (AGE) in children worldwide. Epidemiological analysis with respect to the virus strains is limited in China. This study aimed to investigate the prevalence, patterns, and molecular characteristics of NoV infection among children with AGE in China. Methods A total 4848 stool samples were collected from children who were admitted with AGE in Tianjin Children’s Hospital from August 2018 to July 2020. NoV was preliminarily detected using real-time reverse transcription polymerase chain reaction (RT-PCR). Partial sequences of the RNA-dependent RNA polymerase (RdRp) and capsid genes of positive samples were amplified by conventional RT-PCR and then sequenced. The NoV genotype was determined by online Norovirus Typing Tool Version 2.0, and phylogenetic analysis was conducted using MEGA 6.0. Results The prevalence of NoV was 26.4% (1280/4848). NoV was detected in all age groups, with the 7–12 months group having the highest detection rate (655/2014, 32.5%). NoV was detected during most part of the year with higher frequency in winter than other seasons. Based on the genetic analysis of RdRp, GII. Pe was the most predominant genotype detected at 70.7% (381/539) followed by GII.P12 at 25.4% (137/539). GII.4 was the most predominant capsid genotype detected at 65.3% (338/518) followed by GII.3 at 26.8% (139/518). Based on the genetic analysis of RdRp and capsid sequences, the strains were clustered into 10 RdRp–capsid genotypes: GII.Pe-GII.4 Sydney 2012 (65.5%), GII.P12-GII.3 (27.2%), GII.P16-GII.2 (1.8%), GII.P12-GII.2 (0.2%), GII.P17-GII.17 (1.1%), GII.Pe-GII.3 (1.8%), GII.Pe-GII.2 (1.1%), GII.Pe-GII.1 (0.4%), GII.16-GII.4 Sydney 2012 (0.7%), and GII.P7-GII.6 (0.2%). The predominant NoV genotypes changed from GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 between August 2018 and July 2019 to GII.Pe-GII.4 Sydney 2012 and GII.P16-GII.2 between August 2019 and July 2020. The patients with GII.Pe-GII.4 Sydney 2012 genotype were more likely to suffer from vomiting symptom than those with GII.P12-GII.3. Conclusions NoV is an important pathogen responsible for viral AGE among children in China. GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 were major recombinant genotypes. Knowledge of circulating genotypes and seasonal trends is of great importance for disease prevention and surveillance.


2021 ◽  
Author(s):  
Jose Arturo Molina-Mora

Emerging mutations and genotypes of the SARS-CoV-2 virus, responsible for the COVID-19 pandemic, have been reported globally. In Costa Rica during the year 2020, a predominant genotype carrying the mutation T1117I in the spike (S:T1117I) was previously identified. To investigate the possible effects of this mutation on the function of the spike, i.e. the biology of the virus, different bioinformatic pipelines based on phylogeny, natural selection and co-evolutionary models, molecular docking and epitopes prediction were implemented. Results of the phylogeny of sequences carrying the S:T1117I worldwide showed a polyphyletic group, with the emergency of local lineages. In Costa Rica, the mutation is found in the lineage B.1.1.389 and it is suggested to be a product of positive/adaptive selection. Different changes in the function of the spike protein and more stable interaction with a ligand (nelfinavir drug) were found. Only one epitope out 742 in the spike was affected by the mutation, with some different properties, but suggesting scarce changes in the immune response and no influence on the vaccine effectiveness. Jointly, these results suggest a partial benefit of the mutation for the spread of the virus with this genotype during the year 2020 in Costa Rica, although possibly not strong enough with the introduction of new lineages during early 2021 which became predominant later. In addition, the bioinformatics pipeline offers an integrative and exhaustive in silico strategy to eventually study other mutations of interest for the SARS-CoV-2 virus and other pathogens.


Sign in / Sign up

Export Citation Format

Share Document