Emergence Of New Genotypes Research Articles

Genetic Diversity of Schistosoma haematobium in Qena Governorate, Upper Egypt.

IntroductionSchistosomiasis is an important neglected tropical disease (NTD) in several developing countries. Praziquantel is the principle and efficacious chemotherapeutic agent that has been used to treat schistosomiasis for decades. Unfortunately, emerging resistance to praziquantel with accompanying reduced efficacy is reported in some localities. Hence, genetic diversity among parasite populations is of significant interest in assessing the effects of selective pressure generated by praziquantel therapy that might result in encouraging the emergence of new genotypes that are either non-susceptible or drug-resistant. The present study aimed to investigate the genetic diversity of Schistosoma haematobium among human populations using the RAPD technique to help clarify disease epidemiology and transmission.Materials and MethodsS. haematobium eggs were isolated from 50 of 134 patients from four different localities in Qena Governorate, Upper Egypt. These patients complained of terminal hematuria and burning micturition. Samples were used for molecular analysis using RAPD-PCR primers (A02, A07, A09, A10).ResultsTwenty S. haematobium isolates (40%) were amplified using the selected RAPD primers. Amplification patterns of these isolates showed distinct variation in the size and number of amplified fragments, indicating high genetic variation among these isolates.ConclusionTo the best of our knowledge, this study is the first to characterize the genetic diversity of S. haematobium in human populations in Upper Egypt. Future studies on a larger geographic scale involving many districts in Upper Egypt should be encouraged. Information from such a study would provide better insight into clonal lineages of S. haematobium in this endemic area. In turn, understanding transmission of the parasite may have a major role in establishing control strategies for urogenital schistosomiasis in Upper Egypt.

New Insights into the Effect of Residue Mutations on the Rotavirus VP1 Function Using Molecular Dynamic Simulations.

Rotavirus group A remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious questions. Thirteen VP1 structures with mutations mapping to the RNA entry site were analyzed using molecular dynamics simulations, and the results were combined with the experimental findings reported previously. The results revealed structural fluctuations in the protein-protein recognition sites and in the bottleneck of the RNA entry site that may affect the interaction of different proteins and delay the initiation of the viral replication, respectively. Altogether, the structural analysis of VP1 in the region crucial for the initiation of the viral replication, mainly the bottleneck site, may boost efforts to develop antivirals, as they might complement the available vaccines.

Evidence for zoonotic transmission of species A rotavirus from goat and cattle in nomadic herds in Morocco, 2012-2014.

Species A rotaviruses (RVAs) are a leading cause of diarrhea in children and in the young of a large variety of mammalian and avian host species. The purpose of this study was to identify RVA in nomadic goats and calves during severe diarrhea outbreaks in 2012 and 2014 in Bouaarfa, Morocco, and to characterize the complete genomic constellation of two bovine and caprine strains (S18 and S19) and their genetic relatedness with the human strain ma31 detected in 2011 in Morocco. Partial nucleotide sequencing of VP4 and VP7 genes for the twenty-two positive samples revealed three circulating genotypes: G6P[14], G10P[14], and G10P[5] with predominance of G6P[14] genotype. Full-genome sequencing for both strains S18 and S19 presented, respectively, the following genomic constellations: G6-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3 and G10-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3. Phylogenetic analyses and the analysis of the VP8* antigenic epitopes for S18, S19 and ma31 revealed a shared similarity with bovine, caprine, ovine and human strains from Morocco and other countries. The VP2 and NSP1 genes of the S19 strain were closely related to those of the cognate genes of the human ma31 strain, while the VP4 gene of S18 strain was closely related to the cogent gene of the ma31 strain. Our findings revealed cases of zoonotic transmission and confirmed the risk of emergence of new genotypes in some environments such as nomadic regions, where close physical proximity between human and livestock is common. The present study is novel in reporting whole-genome analyses of RVA isolates obtained from nomadic livestock in Morocco.Electronic supplementary materialThe online version of this article (10.1007/s11262-020-01778-w) contains supplementary material, which is available to authorized users.

Epidemiological implications of the genetic diversification of dengue virus (DENV) serotypes and genotypes in Mexico

Variation and clade shifts in dengue virus (DENV) genotypes are responsible for numerous dengue fever outbreaks throughout Latin America in the past decade. Molecular analyses of dengue serotypes have revealed extensive genetic diversification and the emergence of new genotypes in Brazil (DENV-4 genotype I) and elsewhere in tropical and subtropical America. The goal of the present study is to assess the extent to which the adventitious introduction of DENV genotypes and their increasing genetic diversity affects dengue epidemiology in Mexico. A nuanced sequence inspection and phylogenetic analysis of the C-prM nucleotide region of DENV was performed for specimens collecting in 2009 from the Veracruz State, Mexico. Findings were contrasted with specimens collected in adjacent years and analysed based on the epidemiological patterns reported between 1990 and 2019. Additionally, the identification process of various DENV genotypes was assessed, including: (1) DENV-1, genotype V, (2) the DENV-2 Asian/American and Asian II genotypes (3) DENV-3, genotype III, and (4) DENV-4, genotype I. This resulted in the discovery of a distinct genetic cladistic pattern for serotype DENV-2. Lastly, study findings suggest that a correlation exists between the emergence of novel genotypes and genetic diversification, with the increasing incidence of DENV infections in Mexico in 2009.

Co-circulation of multiple reassortant H6 subtype avian influenza viruses in wild birds in eastern China, 2016\u20132017

BackgroundH6 subtype influenza viruses were prevalent in domestic poultry and wild birds, which also could pose potential threat to humans. However, little is known about the prevalence of H6 subtype viruses in wild birds in eastern China, a crucial stopover or wintering site for migratory wild birds along the East Asian-Australasian Flyway.MethodsDuring the routine surveillance in 2016–2017, H6 subtype AIVs positive samples were identified, and the representative strains were selected for further sequence and phylogenetic analysis and the pathogenicity in mice were evaluated.ResultsAmong the 30 H6 positive samples, there were at least four subtypes H6N1, H6N2, H6N5 and H6N8 co-circulated in Shanghai, China. Genetic analysis showed the 8 representative isolates shared homology with different AIV sub-lineages isolated from domestic ducks or wild birds in different countries along the East Asian-Australasian flyways, and were classified into 7 new genotypes. The pathogenicity to mice showed that these H6 viruses could replicate efficiently in the lungs without prior adaptation, but could not cause mice death.ConclusionsEight novel strains belonged to H6N1, H6N2, H6N5 and H6N8 subtypes were isolated. Phylogenetic analyses revealed multiple origins of internal genes indicative of robust reassortment events and frequent wild birds-poultry interaction encouraging the evolution and emergence of new genotypes. The pathogenicity to mammals should be closely monitored to prevent the emergence of novel pandemic viruses.

INFLUENCE OF GENOTYPIC VARIABILITY OF M. TUBERCULOSIS ON THE COURSE OF TUBERCULOSIS WITH MULTIPLE DRUG RESISTANCE

Tuberculosis is infectious and socially dependent disease, being now one of the most pressing issues in practical health care. As well the usual types of tuberculosis infection, chemoresistant tuberculosis is spreading rapidly in the world. The WHO estimates that about 500,000 people on the planet are infected with M. tuberculosis, which is resistant to standard anti−tuberculosis drugs. The probability of successful treatment decreases with emergence of new genotypes of M. tuberculosis with total resistance. In the modern epidemiology of tuberculosis, it is important to identify genotypes on certain signs, allowing to address issues such as their origin, identification of the infection source, possible routes and factors of transmission, as well as to reveal cases and spread of resistance to anti−tuberculosis drugs. To evaluate the therapy efficiency of multidrug−resistant tuberculosis patients with revealed genotypic variability during treatment, 10 patients with chemoresistant pulmonary tuberculosis having M. tuberculosis genotypic variability were treated. In these patients, the clinical, laboratory and radiological dynamics of disease in intensive phase of treatment were studied. Analysis of treatment results for patients with chemoresistant tuberculosis with genotypic variability of M. tuberculosis was evaluated by the intoxication syndrome dynamics of, the timing of closure of the decay cavities and cessation of bacterial excretion. The study found that the genotypic variability of M. tuberculosis is characterized by the change of less virulent genotypes of M. tuberculosis to more virulent. Signs of intoxication have been shown to change from less virulent M. tuberculosis genotypes to M. tuberculosis Beijing genotypes. Genotypic variability of mycobacteria in hospital suggests that hospitalization in tuberculosis facilities is a risk of exogenous tuberculosis superinfection. Studying the influence of genotypic variability of M. tuberculosis on the course of multidrug−resistant tuberculosis requires more extensive research, being a very relevant and promising area in phthisiology. Key words: Mycobacterium tuberculosis, genotypic variability, VNTR−genotyping, treatment.

Colletotrichum: species complexes, lifestyle, and peculiarities of some sources of genetic variability.

The genus Colletotrichum comprises species with different lifestyles but is mainly known for phytopathogenic species that infect crops of agronomic relevance causing considerable losses. The fungi of the genus Colletotrichum are distributed in species complexes and within each complex some species have particularities regarding their lifestyle. The most commonly found and described lifestyles in Colletotrichum are endophytic and hemibiotrophic phytopathogenic. Several of these phytopathogenic species show wide genetic variability, which makes long-term maintenance of resistance in plants difficult. Different mechanisms may play an important role in the emergence of genetic variants but are not yet fully understood in this genus. These mechanisms include heterokaryosis, a parasexual cycle, sexual cycle, transposable element activity, and repeat-induced point mutations. This review provides an overview of the genus Colletotrichum, the species complexes described so far and the most common lifestyles in the genus, with a special emphasis on the mechanisms that may be responsible, at least in part, for the emergence of new genotypes under field conditions.

Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach.

Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription.

Early antibody responses map to non-protective, PCV2 capsid protein epitopes

Porcine circovirus type 2 (PCV2) is an economically important cause of post-weaning multisystemic wasting syndrome (PMWS) in weanling piglets. Current commercial vaccines against PCV2 are highly effective. Yet, a recurring emergence of new genotypes in vaccinated herds necessitates a better understanding of protective immunity. The study objectives were to identify previously unrecognized decoy epitopes in the PCV2 capsid and test the hypothesis that early antibody responses would map to decoy epitopes and vice versa. Using a peptide library spanning the PCV2a capsid and weekly sera collections from PCV2a infected animals, three major immunodominant regions mapping the early responses to decoy epitopes were identified. Regions with potential decoy activity were mapped using peptide blocking fluorescent focus inhibition assays to residues 55 YTVKATTVRTPSWAVDMM 72, 106 WPCSPITQGDRGVGSTAV 123 and 124 ILDDNFVTKATALTYDPY 141. Post-vaccination responses largely recognized these same three identified regions and dominated the antibody responses to PCV2 in both infection and vaccination.

New molecular evolutionary characteristics of H9N2 avian influenza virus in Guangdong Province, China

To understand the evolution of H9N2 avian influenza virus genotype and its molecular evolution rate, we systematically analyzed 72 H9N2 avian influenza virus sequences isolated from Guangdong province from 2014 to 2018. We found three genotypes (G57, G68, and G118) of the H9N2 avian influenza virus, of which G118 is a newly discovered genotype and G57 is the dominant genotype. The internal gene cassette of the G57 genotype H9N2 avian influenza virus is a stable combination that can easily transport internal genes to other novel avian influenza viruses, and the internal gene cassettes of the G68 and G118 are identical to those of G57.In addition, we estimated the nucleotide substitution rate of the HA and NA genes of the H9N2 influenza virus from 2014 to 2018.The nucleotide substitution rate of HA and NA genes showed an upward trend in 2015 and 2016. In the past two years, H9N2 avian influenza virus recombination has produced genotype G68, which disappeared in 2014 for one year. And very coincidentally, in 2015, there was a new genotype G118. We observed that the emergence of new genotypes was accompanied by a slight increase in overall nucleotide substitution rate. Therefore we hypothesize that the emergence of new genotypes could accelerate the molecular evolution rate of genes. Our research shows that the H9N2 avian influenza virus in Guangdong province has been undergoing intense evolution, demonstrating the need to strengthen influenza surveillance in the region.

Progress in norovirus research and vaccine development

Norovirus is one of the leading causes of acute non-bacterial gastroenteritis. Emergence of new genotypes due to frequent genetic recombination and antigenic drift increases the prevalence of norovirus infection worldwide. Norovirus infection has become a global public health concern. This review focused on disease burden, vaccine research, cell culture and animal models regarding norovirus infection. Key words: Norovirus; Gastroenteritis; Vaccine

Emergence of new genotypes and lineages of dengue viruses during the 2012–15 epidemics in southern India

ObjectivesTo genotypically characterize dengue virus (DENV) isolates among dengue-infected children from 2012–13/2014–15 outbreaks in southern India. MethodsChildren hospitalized with suspected dengue were tested for dengue RT-PCR targeting Capsid-preMembrane (C-prM) and Envelope (Env) regions. Following virologic confirmation (n=612), a representative selection of DENV isolates (n=99) were sequenced for C-prM, aligned using ClustalW and subjected to phylogenetic analysis by maximum-likelihood method in MEGA6. ResultsIn 2012–13 (n=113), DENV-3 (44, 38.9%) and DENV-2 (43, 38.1%) predominated; DENV-1 (22, 19.5%) and DENV-4 (1, 0.9%) were less common. The pattern changed in 2014–15 (n=499), when DENV-1 (329, 65.7%) predominated, followed by DENV-2 (97, 21.2%), DENV-3 (36, 6.7%) and DENV-4 (10, 2.0%). Multiple-serotype co-infections occurred in 2.7% and 5.4% in 2012–13 and 2014–15, respectively. Genotype III (GIII) of DENV-1 predominated (85.7%) in 2012–13, ceding to GI predominance (80.8%) in 2014–15. Among DENV-2, 71.9% (23/32) showed distinct clustering suggesting a new lineage, ‘GIVc’. All tested DENV-4 were GIC, whose clustering pattern showed the emergence of two distinct clades. ConclusionsNew genotypic/lineage variations in DENV-1 and DENV-2 may have influenced the magnitude and severity of dengue epidemics in southern India during this period. These findings emphasize the role of active surveillance of DENV serotypes/genotypes in aiding outbreak control and vaccine studies.

Main directions and results of researches of phytoinvasion

The aim of this work is to generalize the main trends and the research results related to the expansion of invasive plant species. The main hypotheses that explain the success of invasive species are reviewed. The hypotheses are: absence of natural enemies in the secondary area, influence of hybridization and allelopathy on the processes of invasion, the hypothesis of vacant niches, the emergence of new genotypes with expressive adaptive features, the rapid development of genetic traits associated with the pressure of natural selection in new environmental conditions, the importance of bioecological features of invasive species – by morphological and biomorphological plasticity, ecological versatility, ecological-phytocoenic strategies, features of reproduction, etc. Invasion of non-native species is primarily caused by anthropogenic transformation of the natural environment, which is aggravated by climate change. The increasing level of transformation of the environment leads to an increase in the degree of naturalization of non-native species, and as a consequence to modification of types of habitats and to a loss of individual populations of natural species. Processes of naturalization of invasive species are supported by a set of specific various systematic groups of factors. The lack of an effective monitoring system and information tools prevents effective control of invasive non-native species. The necessity to construct models of the behavior of invasive species and to check the predictions of their invasive activity is substantiated.

Emergence of a virulent genotype VIIi of Newcastle disease virus in Iran

ABSTRACTNewcastle disease (ND) is a contagious viral disease affecting numerous avian species, particularly domestic poultry, and causes devastating outbreaks. In spite of its endemicity and importance in Iran, data on the genetic characterization of ND virus (NDV) are scarce. An alarming issue that has just been raised is the occurrence of ND outbreaks with unexpected high mortality and severe clinical signs. The present study was conducted to characterize the emerging NDV genetically. An NDV strain, isolated in 2017 from commercial broilers showing severe nervous and enteric signs, was completely sequenced and found to be 15,192 nucleotides in length. The phylogenetic analysis demonstrated that the virus belonged to subgenotype VIIi, a subgenotype with potential panzootic features which has recently emerged in the Middle East and Asia. The supporting genetic pattern obtained from the complete genome, fusion and haemagglutinin gene analysis showed close relationship of the isolate with Pakistani VIIi NDVs. The analysis of the F protein showed a polybasic amino acid motif and a phenylalanine at position 117 at the cleavage site, which is a characteristic of virulent strains. The isolate showed significant differences from the previously characterized NDV strains from commercial and rural chickens in Iran. This may describe the importance of the illegal trade of pet birds from neighbouring countries leading to the emergence of new genotypes. This study introduces a newly emerging NDV VIIi subgenotype in Iran. This investigation emphasizes the necessity of effective control strategies.

Pathogenesis of infectious bronchitis virus (IBV) and laboratory test methods available to detect IBV in chickens

Infectious bronchitis is a high contagious disease of chicken caused by gamma coronavirus. The disease was characterized by respiratory, renal, urogenital, and alimentary infections. Different strains of IBV may show variable tissue tropisms. For example, the classical strains of Massachussetts serotype (M41) targeted in respiratory and reproductive system while variant serotypes including QX, 793/B, D388 have been detected in respiratory, reproductive, alimentary system and kidney. Because the evolution and mutation of IBV have contributed to the emergence of new genotypes of IBV, the outbreak of IB still occurred in the vaccinated flocks. Therefore, diagnosis of IB plays an important role for limiting the effects caused by IBV infection. Available laboratory tests for diagnosis of IBV include virus isolation, electron microscope, immunohistochemistry, serological tests (virus neutralization, haemagglutination inhibition, enzyme-linked immunosorbent assay –ELISA-, agar gel immunodiffusion), genotype identification (RT-PCR, genome sequencing [using NGS Miseq]).

Relative Contribution of Seed Tuber- and Soilborne Inoculum to Potato Disease Development and Changes in the Population Genetic Structure of Rhizoctonia solani AG 3-PT under Field Conditions in South Africa.

Understanding the contribution of seed tuber- and soilborne inocula of Rhizoctonia solani AG 3-PT in causing potato disease epidemics is an important step in implementing effective management strategies for the pathogen. A 2-year study was conducted to evaluate the contribution of each source of inoculum using an integrative experimental approach combining field trials and molecular techniques. Two distinct sets of genetically marked isolates were used as seed tuberborne and soilborne inocula in a mark-release-recapture experiment. Disease assessments were done during tuber initiation and at tuber harvest. Both inoculum sources were found to be equally important in causing black scurf disease, whereas soilborne inocula appeared to be more important for root and stolon infection, and seedborne inocula contributed more to stem canker. However, seed tuber-transmitted genotypes accounted for 60% of the total recovered isolates when genotyped using three polymerase chain reaction restriction fragment length polymorphism markers. The changes in population structure of the experimental R. solani population over the course of the growing season and across two growing seasons were investigated using eight microsatellite markers. The populations at different sampling times were somewhat genetically differentiated, as indicated by Nei's gene diversity (0.24 to 0.27) and the fixation index (FST). The proportion of isolates with genotypes that differed from the inoculants ranged from 13 to 16% in 2013 and 2014, respectively, suggesting the possibility of emergence of new genotypes in the field. Because both soilborne and tuberborne inocula are critical, it is important to ensure the use of pathogen-free seed tubers to eliminate seed tuberborne inoculum and the introduction of new genotypes of R. solani for sustainable potato production in South Africa.

Co-circulation of multiple subtypes of enterovirus A71 (EV- A71) genotype C, including novel recombinants characterised by use of whole genome sequencing (WGS), Denmark 2016.

In Europe, enterovirus A71 (EV-A71) has primarily been associated with sporadic cases of neurological disease. The recent emergence of new genotypes and larger outbreaks with severely ill patients demonstrates a potential for the spread of new, highly pathogenic EV-A71 strains. Detection and characterisation of these new emerging EV variants is challenging as standard EV assays may not be adequate, necessitating the use of whole genome analysis.

Genotype 1 of human parvovirus B19 in clinical cases.

Virus surveillance strategies and genetic characterization of human parvovirus B19 (B19V) are important tools for regional and global control of viral outbreak. In São Paulo, Brazil, we performed a study of B19V by monitoring the spread of this virus, which is an infectious agent and could be mistakenly reported as a rash and other types of infection. Serum samples were subjected to enzyme immunoassay, real time polymerase chain reaction, and sequencing. From the 462 patients with suspected cases of exanthematic infections, the results of the 164 serum samples were positive for B19V immunoglobulin M. Among these cases, there were 38 patients with erythema infections and B19-associated with other infections such as encephalitis, hydrops fetalis, chronic anemia, hematological malignancies. These samples were sequenced and identified as genotype 1. This study showed patients with infections caused by B19V and sequencing genotype 1. Continuous monitoring is necessary to detect all known genotypes, and the emergence of new genotypes of these viruses for case management in public health control activities.

Phylogenetic analysis of S1 gene of infectious bronchitis virus reveals emergence of new genotype

In India the most common vaccine strain against infectious bronchitis (IB) virus (IBV) is Mass strain (M41). Most of the organized and unorganized poultry farms use Mass strain for vaccination of parent stock. But even after taking all precautions the incidences of IB outbreak are common in poultry population. IBV, a major pathogen of poultry flocks, circulates in the form of several genotypes and serotypes. Only a few amino acid changes in the S1 subunit of wild type proteins may results in mutants unaffected by current vaccine. In the year 2008 one strains of IBV was isolated from vaccinated chicken flocks. The results from sequencing of S1 gene showed that this strain was distinct from classic IBV strains of H120, M41 etc. Compared to H120 and M41 vaccine strain, point mutation occurred at many positions in the S1 protein of this field strain. The homology of the nucleotide and amino acid sequences of the S1 gene of this isolate was 79.0%-99.6% and 74.5%-98.8%, respectively with relation to major vaccine strains used worldwide. The results from this study indicate that different IBV strains cocirculate in the chicken population in India.

Emergence of new genotype and diversity of Theileria orientalis parasites from bovines in India

Bovine theileriosis is a serious threat to livestock worldwide. Uncertainty around species prevalence, antigenic diversity and genotypes of strains make it difficult to assess the impact of this parasite and to provide necessary treatment. We aimed to characterize genotypic diversity, phylogeny and prevalence of Theileria orientalis parasites from the states of Telangana and Andhra Pradesh, India by collecting bovine blood samples from the major districts of the two states. Bioinformatic analysis identified antigenic diversity among the prevalent parasite strains using major piroplasm surface protein (MPSP) gene. Our study revealed a prevalence rate of 4.8% (n=41/862) of T. orientalis parasites in bovine animals and a new genotype of T. orientalis parasite which was not previously reported in India. The emergence of these new genotypes could be an explanation for the frequent outbreaks of bovine theileriosis. Further, whole genome sequencing of T. orientalis strains will help to elucidate the genetic factors relevant for transmissibility and virulence as well as vaccine and new drug development.