scholarly journals High prevalence and genetic diversity of porcine bocaviruses in pigs in the USA, and identification of multiple novel porcine bocaviruses

2014 ◽  
Vol 95 (2) ◽  
pp. 453-465 ◽  
Author(s):  
Yong-Hou Jiang ◽  
Chao-Ting Xiao ◽  
Shuang-Hui Yin ◽  
Priscilla F. Gerber ◽  
Patrick G. Halbur ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequencing Analysis ◽  
Structural Protein ◽  
High Genetic Diversity ◽  
Vp2 Gene ◽  
Wild Pigs ◽  
Faecal Samples ◽  
High Prevalence ◽  
Complete Genomes ◽  
The Usa

Viruses in the genus Bocavirus are associated with respiratory and enteric disease in dogs and cattle. In addition, novel porcine bocaviruses (PBoVs) have been identified in domestic and wild pigs in recent years, but are of unknown relevance to date. The objectives of this study were to determine the prevalence ra tes and genetic diversity of PBoVs in pigs in the USA. Using newly established multiplex real-time PCR assays, 385 lung, lymph node, serum and faecal samples from pigs with various disease conditions were investigated. A high PBoV prevalence rate ranging from 21.3 to 50.8 % was identified in the investigated samples and often two or more PBoV species were detected in the same sample. Cloning and sequencing analysis of the partial non-structural protein NS1 and the capsid proteins VP1 and VP2 of DNA samples positive for PBoV groups 1 (n = 6), 2 (n = 16) and 3 (n = 42), including subgroups 3A, 3B or 3C, revealed a high genetic diversity especially for the PBoV G3 VP2 gene, whereas the PBoV group 1 VP1 gene displayed a low nucleotide polymorphism. Using primer walking, 18 partial or nearly complete genomes of PBoVs were obtained and six of the 18 nearly complete genomes represented novel PBoV species. Recombination analysis using partial NS1, VP1 and VP2 genes and the nearly complete genomes indicated possible recombination events within and between PBoVs. Further studies will be required to reveal the possible pathogenic role of these diverse PBoVs.

scholarly journals Molecular Analysis of a Plum pox virus W Isolate in Plum Germplasm Hand Carried into the USA from the Ukraine Shows a Close Relationship to a Latvian Isolate

Plant Disease ◽  
2013 ◽  
Vol 97 (1) ◽  
pp. 44-52 ◽  
Author(s):  
Vessela Mavrodieva ◽  
Delano James ◽  
Karen Williams ◽  
Sarika Negi ◽  
Aniko Varga ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
The United States ◽  
Common Source ◽  
Plum Pox Virus ◽  
High Genetic Diversity ◽  
Close Relationship ◽  
The Usa ◽  
Sequence Identities ◽  
Germplasm Accessions

Four of 19 Prunus germplasm accessions hand carried from the Ukraine into the United States without authorization were found to be infected with Plum pox virus (PPV). Of the three isolates characterized, isolates UKR 44189 and UKR 44191 were confirmed to be isolates of PPV strain W, and UKR 44188 was confirmed to be an isolate of PPV strain D. UKR 44189 and UKR 44191 are very closely related to the PPV strain W isolate LV-145bt (HQ670748) from Latvia. Nucleotide and amino acid sequence identities between these three isolates were greater than 99%. This indicates that the isolates are very closely related and likely originated from a common source. The high genetic diversity among PPV-W strain isolates allowed the identification of potential recombination events between PPV isolates. It appears also that GF 305 peach and Prunus tomentosa are not hosts for the PPV isolate UKR 44189.

Season of birth interacts with measures of inbreeding in multiplex schizophrenia pedigrees: evidence from genetic isolates in Daghestan

Open Medicine ◽  
2006 ◽  
Vol 1 (4) ◽  
pp. 392-398
Author(s):  
Kazima Bulayeva ◽  
John McGrath
Keyword(s):  
Genetic Diversity ◽  
Family History ◽  
Age Of Onset ◽  
Population Genetic Study ◽  
Season Of Birth ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
High Prevalence ◽  
History Of ◽  
Genetic Isolates

AbstractWhile the season-of-birth effect is one of the most consistent epidemiological features of schizophrenia, there is a lack of consistency with respect to the interaction between season of birth and family history of schizophrenia. Apart from family history, measures related to consanguinity can be used as proxy markers of genomic heterogeneity. Thus, these measures may provide an alternate, indirect index of genetic susceptibility. We had the opportunity to explore the interaction between season of birth and measure of consanguinity in well-described genetic isolates in Daghestan, some of which are known for their relatively high prevalence of schizophrenia. Our previous population-genetic study showed Daghestan has an extremely high genetic diversity between the ethnic populations and a low genetic diversity within them. The isolates selected for this study include some with more than 200 and some with less than 100 generations of demographical history since their founding. Based on pedigrees of multiply-affected families, we found that among individuals with schizophrenia, the measure of consanguinity was significantly higher in the parents of those born in winter/spring compared to those born in summer/autumn. Furthermore, compared to summer/autumn born, winter/spring born individuals with schizophrenia had an earlier age-of-onset, and more prominent auditory hallucinations. Our results suggest that the offspring of consanguineous marriages, and thus those with reduced allelic heterogeneity, may be more susceptible to the environmental factor(s) underpinning the season-of-the effect in schizophrenia.

scholarly journals Microsatellite genotyping from faeces of Lontra longicaudis from southern Brazil

2009 ◽  
Vol 99 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Laura I. Weber ◽  
Cintia G. Hildebrand ◽  
Anderson Ferreira ◽  
Gustavo Pedarassi ◽  
José A. Levy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Significant Degree ◽  
Southern Brazil ◽  
High Genetic Diversity ◽  
Low Degree ◽  
Faecal Samples ◽  
High Level ◽  
Degree Of Differentiation ◽  
Lontra Longicaudis

A genetic study of the neotropical river otter Lontra longicaudis (Olfers, 1818), which has an unknown conservation status, was carried out at the Taim Ecological Station and the margins of the Vargas stream, Rio Grande do Sul, southern Brazil. Faecal samples were collected, and DNA was extracted using a silica-guanidine method. Five microsatellite loci were amplified using PCR with heterologous primers previously described for Lutra lutra (Linnaeus, 1758). Sixteen faecal samples out of 29 from Taim and 11 out of 14 from Vargas stream margins contained enough DNA for genetic analysis. A total of 49 different alleles were found at both localities, from which 18 were exclusively found in individuals from Taim and 17 were exclusives from Vargas individuals. The most common allele was the same at both locations for three loci (Lut715, Lut733, and Lut818). A high level of genetic diversity was found at both sites (NeTaim=4.1, HoTaim=0.299, HeTaim=0.681; NeVargas=4.9, HoVargas=0.355, HeVargas=0.724), being higher at the Vargas stream site. A high and significant level of heterozygote deficiency was observed at most loci according to the χ2 test. The homogeneity χ2 test (P<0.001) showed that there were significant differences in the allele frequencies between the two locations. Genotyping for more than one locus was possible in 81.5% of samples, from which only 37% were possible to genotype for more than three loci. A low degree of relatedness was found among individuals from Taim (R=0.055±0.310), but an even lower value of relatedness was found at the Vargas site (R= -0.285±0.440). The significant degree of differentiation (I=0.890; F ST=0.059) found between Taim and Vargas individuals suggests that there is more than one population of otters in the southern extreme of Brazil, which probably are associated with the water body systems found in this region, the Mirim and the Caiuvá/Flores/Mangueira Lagoons. The high genetic diversity and low relatedness found at the Vargas stream, lead us to believe that the Vargas stream may be acting as a corridor between these water bodies for otter dispersion.

scholarly journals Identification and characterization of novel porcine astroviruses (PAstVs) with high prevalence and frequent co-infection of individual pigs with multiple PAstV types

2013 ◽  
Vol 94 (3) ◽  
pp. 570-582 ◽  
Author(s):  
Chao-Ting Xiao ◽  
Luis G. Giménez-Lirola ◽  
Priscilla F. Gerber ◽  
Yong-Hou Jiang ◽  
Patrick G. Halbur ◽  
...  
Keyword(s):  
Zoonotic Potential ◽  
The Novel ◽  
Extraintestinal Manifestations ◽  
Faecal Samples ◽  
High Prevalence ◽  
The Usa ◽  
History Of ◽  
Identification And Characterization ◽  
Sequence Identities

Many astrovirus (AstV) species are associated with enteric disease, although extraintestinal manifestations in mammalian and avian hosts have also been described. In this study, the prevalence rates of porcine AstV types 1–5 (PAstV1–PAstV5) were investigated using faecal samples from 509 pigs of which 488 (95.9 %) came from farms with a history of diarrhoea. All of the five known PAstV types were found to circulate in pigs in the USA, and co-infection of a single pig with two or more PAstV types was frequently observed. A high overall prevalence of 64.0 % (326/509) of PAstV RNA-positive samples was detected, with 97.2 % (317/326) of the PAstV RNA-positive pigs infected with PAstV4. Further genomic sequencing and characterization of the selected isolates revealed low sequence identities (49.2–89.0 %) with known PAstV strains, indicating novel types or genotypes of PAstV2, PAstV4 and PAstV5. Some new features of the genomes of the PAstVs were also discovered. The first complete genome of a PAstV3 isolate was obtained and showed identities of 50.5–55.3 % with mink AstV and the novel human AstVs compared with 38.4–42.7 % with other PAstV types. Phylogenetic analysis revealed that PAstV1, PAstV2 and PAstV3 were more closely related to AstVs from humans and other animals than to each other, indicating past cross-species transmission and the zoonotic potential of these PAstVs.

scholarly journals Prevalence of bovine astroviruses and their genotypes in sampled Chinese calves with and without diarrhoea

2021 ◽  
Vol 102 (8) ◽  
Author(s):  
Jie Zhu ◽  
Mingpu Qi ◽  
Chuanwen Jiang ◽  
Yongchong Peng ◽  
Qingjie Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Binary Logistic Regression ◽  
Binary Logistic Regression Analysis ◽  
Strong Positive Correlation ◽  
High Genetic Diversity ◽  
Bovine Rotavirus ◽  
Calf Diarrhoea ◽  
Faecal Samples ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs

Bovine astrovirus (BoAstV) belongs to genus Mamastravirus (MAstV). It can be detected in the faeces of both diarrhoeal and healthy calves. However, its prevalence, genetic diversity, and association with cattle diarrhoea are poorly understood. In this study, faecal samples of 87 diarrhoeal and 77 asymptomatic calves from 20 farms in 12 provinces were collected, and BoAstV was detected with reverse transcription-polymerase chain reaction (RT-PCR). The overall prevalence rate of this virus in diarrhoeal and asymptomatic calves was 55.17 % (95 % CI: 44.13, 65.85 %) and 36.36 % (95 % CI: 25.70, 48.12 %), respectively, indicating a correlation between BoAstV infection and calf diarrhoea (OR=2.15, P=0.024). BoAstV existed mainly in the form of co-infection (85.53 %) with one to five of nine viruses, and there was a strong positive correlation between BoAstV co-infection and calf diarrhoea (OR=2.83, P=0.004). Binary logistic regression analysis confirmed this correlation between BoAstV co-infection and calf diarrhoea (OR=2.41, P=0.038). The co-infection of BoAstV and bovine rotavirus (BRV) with or without other viruses accounted for 70.77 % of all the co-infection cases. The diarrhoea risk for the calves co-infected with BoAstV and BRV was 8.14-fold higher than that for the calves co-infected with BoAstV and other viruses (OR=8.14, P=0.001). Further, the co-infection of BoAstV/BRV/bovine kobuvirus (BKoV) might increase the risk of calf diarrhoea by 14.82-fold, compared with that of BoAstV and other viruses (OR=14.82, P <0.001). Then, nearly complete genomic sequences of nine BoAstV strains were assembled by using next-generation sequencing (NGS) method. Sequence alignment against known astrovirus (AstV) strains at the levels of both amino acids and nucleotides showed a high genetic diversity. Four genotypes were identified, including two known genotypes MAstV-28 (n=3) and MAstV-33 (n=2) and two novel genotypes designated tentatively as MAstV-34 (n=1) and MAstV-35 (n=3). In addition, seven out of nine BoAstV strains showed possible inter-genotype recombination and cross-species recombination. Therefore, our results increase the knowledge about the prevalence and the genetic evolution of BoAstV and provide evidence for the association between BoAstV infection and calf diarrhoea.

scholarly journals High genetic diversity of the VP2 gene of a canine parvovirus strain detected in a domestic cat

Virology ◽  
2006 ◽  
Vol 352 (1) ◽  
pp. 22-26 ◽  
Author(s):  
Mara Battilani ◽  
Alessandra Scagliarini ◽  
Sara Ciulli ◽  
Luigi Morganti ◽  
Santino Prosperi
Keyword(s):  
Genetic Diversity ◽  
Canine Parvovirus ◽  
Domestic Cat ◽  
High Genetic Diversity ◽  
Vp2 Gene

scholarly journals Attenuation of Bluetongue Virus (BTV) in an in ovo Model Is Related to the Changes of Viral Genetic Diversity of Cell-Culture Passaged BTV

Viruses ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 481 ◽  
Author(s):  
Fabian Z. X. Lean ◽  
Matthew J. Neave ◽  
John R. White ◽  
Jean Payne ◽  
Teresa Eastwood ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cell Culture ◽  
Bluetongue Virus ◽  
Genomic Analysis ◽  
Sequencing Analysis ◽  
Structural Protein ◽  
In Ovo ◽  
Novel Approach ◽  
Amino Acid Mutations

The embryonated chicken egg (ECE) is routinely used for the laboratory isolation and adaptation of Bluetongue virus (BTV) in vitro. However, its utility as an alternate animal model has not been fully explored. In this paper, we evaluated the pathogenesis of BTV in ovo using a pathogenic isolate of South African BTV serotype 3 (BTV-3) derived from the blood of an infected sheep. Endothelio- and neurotropism of BTV-3 were observed by immunohistochemistry of non-structural protein 1 (NS1), NS3, NS3/3a, and viral protein 7 (VP7) antigens. In comparing the pathogenicity of BTV from infectious sheep blood with cell-culture-passaged BTV, including virus propagated through a Culicoides-derived cell line (KC) or ECE, we found virus attenuation in ECE following cell-culture passage. Genomic analysis of the consensus sequences of segments (Seg)-2, -5, -6, -7, -8, -9, and -10 identified several nucleotide and amino-acid mutations among the cell-culture-propagated BTV-3. Deep sequencing analysis revealed changes in BTV-3 genetic diversity in various genome segments, notably a reduction of Seg-7 diversity following passage in cell culture. Using this novel approach to investigate BTV pathogenicity in ovo, our findings support the notion that pathogenic BTV becomes attenuated in cell culture and that this change is associated with virus quasispecies evolution.

scholarly journals Phylogenetic diversity of two common Trypanosoma cruzi lineages in the Southwestern United States

2021 ◽  
Author(s):  
Carlos A Flores-Lopez ◽  
Elizabeth A Mitchell ◽  
Carolina E Reisenman ◽  
Sahotra Sarkar ◽  
Philip C Williamson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Single Copy ◽  
High Genetic Diversity ◽  
Genetic Lineages ◽  
Control Programs ◽  
The Usa

Trypanosoma cruzi is the causative agent of Chagas disease, a devastating parasitic disease endemic to Central and South America, Mexico, and the USA. We characterized the genetic diversity of T. cruzi circulating in five triatomine species (Triatoma gerstaeckeri, T. lecticularia, T. indictiva, T. sanguisuga and T. recurva) collected in Texas and Southern Arizona using nucleotide sequences from four single-copy loci (COII-ND1, MSH2, DHFR-TS, TcCLB.506529.310). All T. cruzi variants fall in two main genetic lineages: 75% of the samples corresponded to T. cruzi Discrete Typing Unit (DTU) I (TcI), and 25% to a North American specific lineage previously labelled TcIV-USA. Phylogenetic and sequence divergence analyses of our new data plus all previously published sequence data from those 4 genes collected in the USA, show that TcIV-USA is significantly different from any other previously defined T. cruzi DTUs. The significant level of genetic divergence between TcIV-USA and other T. cruzi lineages should lead to an increased focus on understanding the epidemiological importance of this lineage, as well as its geographical range and pathogenicity in humans and domestic animals. Our findings further corroborate the fact that there is a high genetic diversity of the parasite in North America and emphasize the need for appropriate surveillance and vector control programs for Chagas disease in southern USA and Mexico.

scholarly journals Genetic diversity and molecular analysis of metallo beta lactamases among imipenem resistant clinical isolates of Pseudomonas aeruginosa from Peshawar, Pakistan

2021 ◽  
Vol 37 (7) ◽  
Author(s):  
Amjad Ali ◽  
Kafeel Ahmad ◽  
Shaista Rahat ◽  
Israr Ahmad
Keyword(s):  
Genetic Diversity ◽  
Pseudomonas Aeruginosa ◽  
Molecular Analysis ◽  
Opportunistic Pathogen ◽  
Clinical Isolates ◽  
High Genetic Diversity ◽  
Beta Lactamases ◽  
Creative Commons ◽  
High Prevalence ◽  
Control And Prevention

Objectives: Pseudomonas aeruginosa is an opportunistic pathogen with remarkable adaptation ability to thrive in diverse environmental conditions. This study aimed at phenotypic and molecular analysis of metallo beta lactamases (blaIMP, blaVIM, blaNDM-1 and blaSPM-1) and genetic diversity analysis among imipenem resistant clinical isolates of Pseudomonas aeruginosa. Methods: This study was conducted from May 2017 to June 2018. The study included 187 Pseudomonas aeruginosa isolates collected from different clinical specimens from Peshawar, Pakistan. The isolates were analyzed for resistance to imipenem. Combined disc test (CDT) was then performed for phenotypic detection of metallo beta lactamases among imipenem resistant isolates of Pseudomonas aeruginosa. Molecular detection of metallo beta lactamases genes i.e. blaIMP, blaVIM, blaNDM-1 and blaSPM-1 was analyzed through polymerase chain reaction. Genetic diversity was determined through RAPD-PCR. Results: MBL production was observed in 76% (n=19) isolates. The occurrence of MBL genes blaIMP, blaNDM-1 and blaVIM was 68% (n=17), 48% (n=12), and 4% (n=1) respectively. The blaSPM-1 gene was not detected. High genetic diversity was observed in current study. Out of 182 isolates 171 isolates showed different RAPD profiles (93.95% polymorphism); 160 were unique RAPD strains and based on similarity coefficient ≥ 80%, 22 isolates were clustered into 11 distinct clones. Conclusion: A high prevalence of blaIMP and blaNDM-1 among imipenem resistant isolates of Pseudomonas aeruginosa is alarming that calls for proper control and prevention strategies. RAPD technique was found to be a good genotyping technique when limited resources are available. doi: https://doi.org/10.12669/pjms.37.7.4303 How to cite this:Ali A, Ahmad K, Rahat S, Ahmad I. Genetic diversity and molecular analysis of metallo beta lactamases among imipenem resistant clinical isolates of Pseudomonas aeruginosa from Peshawar, Pakistan. Pak J Med Sci. 2021;37(7):---------.  doi: https://doi.org/10.12669/pjms.37.7.4303 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

scholarly journals PO 8249 SUBMICROSCOPIC PLASMODIUM FALCIPARUM INFECTIONS IN MATCHED PERIPHERAL, PLACENTAL AND UMBILICAL CORD BLOOD SAMPLES FROM CONGOLESE WOMEN AT DELIVERY

2019 ◽  
Vol 4 (Suppl 3) ◽  
pp. A23.2-A24
Author(s):  
Yvon Mbouamboua ◽  
Félix Koukouikila-Koussounda ◽  
Jacques Van Helden ◽  
Francine Ntoumi
Keyword(s):  
Genetic Diversity ◽  
Cord Blood ◽  
Cross Sectional Study ◽  
Sectional Study ◽  
High Genetic Diversity ◽  
Cross Sectional ◽  
Blood Samples ◽  
High Prevalence ◽  
Placental Blood ◽  
Submicroscopic Infection

BackgroundThis cross-sectional study was conducted to characterise P. falciparum infections matched in peripheral, placental and cord blood among Congolese women at delivery receiving 1, 2 or more doses of sulfadoxine-pyrimethamine. The cross-sectional study was conducted in a Southern district of Brazzaville, Republic of the Congo, between March 2014 and April 2015.MethodsPeripheral and placental blood samples were collected for P. falciparum infection investigation by microscopy and nested polymerase chain reaction (PCR), using P. falciparum merozoite surface protein-2 (msp2) gene as marker.ResultsOf the 370 pregnant women recruited, only 7.3% peripheral and 2.7% placental blood samples were found smear-positive for P. falciparum by microscopy. All isolates from cord blood were microscopy-negative. However, the prevalences of submicroscopic P. falciparum infections (detectable only by PCR) were 25.4%, 16.7% and 9.4% in peripheral, placental and cord blood respectively. The frequency of 3D7 msp2 alleles was the highest (>60%) whatever the blood considered. We found a high prevalence of submicroscopic infection in pregnant women associated with a high genetic diversity of P. falciparum isolates. The multiplicity of infection ranged between 1.2 and 1.4 irrespective of the blood compartment, and it showed no significant association with maternal age (p=0.3), gravidity (p=0.1) or sulfadoxine-pyrimethamine (p=0.3).ConclusionIn summary, this study showed that there is a high prevalence of submicroscopic infection and a high genetic diversity of Plasmodium falciparum strains in Congo. This diversity varies according to maternal, placental and umbilical cord blood. Age, gravidity and doses of preventive treatment based on sulfadoxine-pyrimethamine do not interfere with the multiplicity of infections.

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