Analysis of nad2 and nad5 enables reliable identification of genotypes G6 and G7 within the species complex Echinococcus granulosus sensu lato

Laurimäe, Teivi; Kinkar, Liina; Römig, Thomas; Umhang, Gérald; Casulli, Adriano; Omer, Rihab Ali; Sharbatkhori, Mitra; Mirhendi, Hossein; Ponce-Gordo, Francisco; Lazzarini, Lorena Evelina; Soriano, Silvia Viviana; Varcasia, Antonio; Rostami-Nejad, Mohammad; Andresiuk, Vanessa; Maravilla, Pablo; González, Luís Miguel; Dybicz, Monika; Gawor, Jakub; Šarkūnas, Mindaugas; Šnábel, Viliam; Kuzmina, Тetiana А.; Kia, Eshrat Beigom; Saarma, Urmas

doi:10.1016/j.meegid.2019.103941

Cited by 18 publications

(22 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, comparison of the complete cox 2 gene sequences from this study with the partial cox 2 gene sequences of the G6 genotype previously isolated from sheep in the Tibet Autonomous Region (GenBank: KC692991, KC692992) showed similar nucleotide sequences without variation. However, the G6 genotype from this study, confirmed by comparing the complete mitochondrial genome sequences with reference G6 and G7 genotypes available in GenBank and the phylogenetic network of the nad 2- nad 5 gene sequences [24], possessed the G6 peculiar nucleotide bases at the defining positions for E. granulosus ( s.l. ) genotypes G6 and G7 as previously described [24].…”

Section: Discussionmentioning

confidence: 69%

“…However, the G6 genotype from this study, confirmed by comparing the complete mitochondrial genome sequences with reference G6 and G7 genotypes available in GenBank and the phylogenetic network of the nad 2- nad 5 gene sequences [24], possessed the G6 peculiar nucleotide bases at the defining positions for E. granulosus ( s.l. ) genotypes G6 and G7 as previously described [24].…”

Section: Discussionmentioning

confidence: 69%

“…Median-joining networks for E. granulosus ( s.s .) and E. canadensis G6 were constructed based on the nucleotide sequences of the mitochondrial nad 5 [20] and concatenated nad 2- nad 5 [24] genes, respectively using PopART software [25]. Using DnaSP v6 [23], the population neutrality indices, Tajima’s D [26] and Fu’s Fs [27], and pairwise fixation index (F ST ), were calculated.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Genetic variation of Echinococcus spp. in yaks and sheep in the Tibet Autonomous Region of China based on mitochondrial DNA

Ohiolei¹,

Xia

Li³

et al. 2019

Parasites Vectors

View full text Add to dashboard Cite

BackgroundCystic echinococcosis (CE) in humans and livestock is caused by Echinococcus granulosus (sensu lato). In China where CE is endemic, a number of studies have shown that Echinococcus granulosus (sensu stricto) is majorly responsible for CE. However, E. canadensis (G6) which is the second leading cause of CE is now being detected in most parts of the country. In this study, the species diversity and genetic variation of Echinococcus granulosus (s.l.) in four counties in Tibet Autonomous Region of China were investigated.MethodsInfection with Echinococcus granulosus (s.s.) in yaks and sheep was identified using NADH dehydrogenase subunit 1 and 5 (nad1 and nad5) mitochondrial genes while the genotype G6 of E. canadensis initially diagnosed with NADH dehydrogenase subunit 1 (nad1) was further confirmed by analysis of the complete mitochondrial genome and a phylogenetic network constructed based on the nad2 and nad5 genes.ResultsOut of 85 hydatid cyst samples collected from slaughtered sheep (n = 54) and yaks (n = 31), 83 were identified as E. granulosus (s.s.) G1 (n = 77), G3 (n = 6) and 2 were identified as E. canadensis G6. Analysis of the nad1/nad5 genes revealed 16/17 mutations with 9/14 parsimony informative sites resulting in 15/14 haplotypes, respectively. Haplotype diversity (Hd) and nucleotide diversity (π) of E. granulosus (s.s.) population were 0.650 and 0.00127 for nad1 and 0.782 and 0.00306 for nad5, respectively, with an overall negative Tajima’s D and Fu’s Fs. A low FST indicated no genetic difference between isolates from sheep and yaks.ConclusionPockets of infection with E. canadensis (G6, G7, G8 and G10) have been previously reported in sheep, goats, yaks and/or humans in different parts of China. While the G6 genotype has been previously reported in sheep in the Tibet Autonomous Region, the detection in a yak in the present study represents the first to the best of our knowledge. Therefore, we recommend future surveys and control efforts to comprehensively investigate other potential intermediate hosts for the prevalence and genetic diversity of the E. canadensis group (G6, G7, G8 and G10) across the country and their inclusion into the existing CE control programme.

show abstract

Section: Discussionmentioning

confidence: 69%

Section: Discussionmentioning

confidence: 69%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Genetic variation of Echinococcus spp. in yaks and sheep in the Tibet Autonomous Region of China based on mitochondrial DNA

Ohiolei¹,

Xia

Li³

et al. 2019

Parasites Vectors

View full text Add to dashboard Cite

show abstract

“…Even though the three assays, especially SNP 758, seemed able to separately distinguish G1 from G3, we cannot exclude the existence of rare genetic variants characterized by the absence of the diagnostic polymorphism examined in this study. For this reason, as already pointed out by other authors [17,33], the targeting of the single SNP cannot be sufficient to reliably distinguish G1 from G3 but the use of all three SNPs is highly recommended.…”

Section: Discussionmentioning

confidence: 95%

Identification of Echinococcus granulosus Genotypes G1 and G3 by SNPs Genotyping Assays

et al. 2021

View full text Add to dashboard Cite

Echinococcus granulosus sensu lato (s.l.) is the causative agent of cystic echinococcosis in animals and humans. Different E. granulosuss.l. genotypes exhibit great diversity in their life cycle, host selectivity and pathogenicity. For this reason, the study of genetic variation within Echinococcus species is of importance for their epidemiological implication. We employed two SNP genotyping technologies to distinguish G1 and G3 E. granulosus sensu stricto (s.s.). genotypes. The genotypes of DNA samples (n = 28) extracted from hydatid cysts of different animal species were identified by amplification and sequencing of a fragment of the mitochondrial nad5 gene. Two SYBR green and three TaqMan real time PCR assays were developed for targeting of three nad5 informative positions (SNP758, 1123, and 1380) known to be able to discriminate G1 from G3. Genotyping by SYBR Green PCR based on cycle threshold (Ct) with melting temperature (Tm) analysis and performed on SNP1123 and SNP1380 failed to identify one DNA sample. TaqMan assays for SNP758, 1123 and 1380 effectively confirmed genotype identification obtained by Sanger sequencing. Our results demonstrated that the combination of the three Taqman assays developed in this study represents a valuable and cost effective tool alternative to DNA sequencing for E. granulosus s.s. genotyping.

show abstract

“…Until now, the diversity and population structure of E. shiquicus has been largely investigated by partial mitochondrial gene sequences of cox1 and/or nad1 (Ma et al, 2012(Ma et al, , 2015Wang et al, 2018;Han et al, 2019), and recently by mtDNA sequences of up to 2505 bp (Fan et al, 2016;Zhu et al, 2020). Moreover, studies have shown that by analysing longer DNA sequences or certain genes with higher resolution power, a better understanding of the intraspecies variation and phylogenetic resolution of Echinococcus species is realised (Laurimäe et al, 2018(Laurimäe et al, , 2019Ohiolei et al, 2020). In this report, analyses of the concatenated mitochondrial cox1 and nad1 gene sequences were used to infer the population structure of E. shiquicus collected from the plateau in contrast to most previous studies that utilized partial gene sequences.…”

Section: Discussionmentioning

confidence: 99%

Echinococcus shiquicus in Qinghai–Tibet plateau: population structure and confirmation of additional endemic areas

Yan

et al. 2021

Parasitology

View full text Add to dashboard Cite

show abstract

Analysis of nad2 and nad5 enables reliable identification of genotypes G6 and G7 within the species complex Echinococcus granulosus sensu lato

Cited by 18 publications

References 50 publications

Genetic variation of Echinococcus spp. in yaks and sheep in the Tibet Autonomous Region of China based on mitochondrial DNA

Genetic variation of Echinococcus spp. in yaks and sheep in the Tibet Autonomous Region of China based on mitochondrial DNA

Identification of Echinococcus granulosus Genotypes G1 and G3 by SNPs Genotyping Assays

Echinococcus shiquicus in Qinghai–Tibet plateau: population structure and confirmation of additional endemic areas

Contact Info

Product

Resources

About