Update of the global distribution of human gammaherpesvirus 8 genotypes.
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ABSTRACT:
SUBMITTER: Lopes AO
PROVIDER: S-EPMC8026617 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Phylogenetic analysis of a collection of 103 E1 gene sequences from rubella viruses isolated from 17 countries from 1961 to 2000 confirmed the existence of at least two genotypes. Rubella genotype I (RGI) isolates, predominant in Europe, Japan, and the Western Hemisphere, segregated into discrete subgenotypes; international subgenotypes present in the 1960s and 1970s were replaced by geographically restricted subgenotypes after approximately 1980. Recently, active subgenotypes include one in the United States and Latin America, one in China, and a third that apparently originated in Asia and spread to Europe and North America, starting in 1997, indicating the recent emergence of an international subgenotype. A virus that potentially arose as a recombinant between two RGI subgenotypes was discovered. Rubella genotype II (RGII) showed greater genetic diversity than did RGI and may actually consist of multiple genotypes. RGII viruses were limited to Asia and Europe; RGI viruses were also present in most of the countries where RGII viruses were isolated.
| S-EPMC3034328 | biostudies-literature
Project description:UnlabelledHepatitis C virus (HCV) exhibits high genetic diversity, characterized by regional variations in genotype prevalence. This poses a challenge to the improved development of vaccines and pan-genotypic treatments, which require the consideration of global trends in HCV genotype prevalence. Here we provide the first comprehensive survey of these trends. To approximate national HCV genotype prevalence, studies published between 1989 and 2013 reporting HCV genotypes are reviewed and combined with overall HCV prevalence estimates from the Global Burden of Disease (GBD) project. We also generate regional and global genotype prevalence estimates, inferring data for countries lacking genotype information. We include 1,217 studies in our analysis, representing 117 countries and 90% of the global population. We calculate that HCV genotype 1 is the most prevalent worldwide, comprising 83.4 million cases (46.2% of all HCV cases), approximately one-third of which are in East Asia. Genotype 3 is the next most prevalent globally (54.3 million, 30.1%); genotypes 2, 4, and 6 are responsible for a total 22.8% of all cases; genotype 5 comprises the remaining <1%. While genotypes 1 and 3 dominate in most countries irrespective of economic status, the largest proportions of genotypes 4 and 5 are in lower-income countries.ConclusionAlthough genotype 1 is most common worldwide, nongenotype 1 HCV cases—which are less well served by advances in vaccine and drug development—still comprise over half of all HCV cases. Relative genotype proportions are needed to inform healthcare models, which must be geographically tailored to specific countries or regions in order to improve access to new treatments. Genotype surveillance data are needed from many countries to improve estimates of unmet need.
| S-EPMC4303918 | biostudies-literature
Project description:Development of next-generation sequencing and metagenomics has revolutionized detection of novel viruses. Among these viruses are 3 human protoparvoviruses: bufavirus, tusavirus, and cutavirus. These viruses have been detected in feces of children with diarrhea. In addition, cutavirus has been detected in skin biopsy specimens of cutaneous T-cell lymphoma patients in France and in 1 melanoma patient in Denmark. We studied seroprevalences of IgG against bufavirus, tusavirus, and cutavirus in various populations (n = 840), and found a striking geographic difference in prevalence of bufavirus IgG. Although prevalence was low in adult populations in Finland (1.9%) and the United States (3.6%), bufavirus IgG was highly prevalent in populations in Iraq (84.8%), Iran (56.1%), and Kenya (72.3%). Conversely, cutavirus IgG showed evenly low prevalences (0%-5.6%) in all cohorts, and tusavirus IgG was not detected. These results provide new insights on the global distribution and endemic areas of protoparvoviruses.
| S-EPMC6038761 | biostudies-literature
Project description:White spot disease, caused by infection with white spot syndrome virus (WSSV), is a serious panzootic affecting prawn aquaculture. The disease has spread rapidly around the prawn-culturing regions of the world through a number of previously identified mechanisms. The ability to distinguish and trace strains of WSSV is of great benefit to identify, and then limit, the translocation routes of the disease. Here, we describe a novel genotyping method using 34 short tandem repeat regions of the viral genome concurrently. This technique is highly sensitive to strain differences when compared to previous methods. The efficacy of the described method is demonstrated by testing WSSV isolates from around the globe, showing regional genotypic differences. The differences in the genotypes were used to create a global minimum spanning network, and in most cases the observed relationships were substantiated with verification of transboundary movement. This novel panel of STR markers will provide a valuable epidemiological tool for white spot disease. We have applied this to an outbreak of the disease in Queensland, Australia, that occurred in 2016. While the results indicate that the source of this outbreak currently remains cryptic, the analyses have provided valuable insights with which to further study the origins of the strains involved.
| S-EPMC6591196 | biostudies-literature
Project description:BackgroundSnail-borne parasitic diseases, such as angiostrongyliasis, clonorchiasis, fascioliasis, fasciolopsiasis, opisthorchiasis, paragonimiasis and schistosomiasis, pose risks to human health and cause major socioeconomic problems in many tropical and sub-tropical countries. In this review we summarize the core roles of snails in the life cycles of the parasites they host, their clinical manifestations and disease distributions, as well as snail control methods.Main bodySnails have four roles in the life cycles of the parasites they host: as an intermediate host infected by the first-stage larvae, as the only intermediate host infected by miracidia, as the first intermediate host that ingests the parasite eggs are ingested, and as the first intermediate host penetrated by miracidia with or without the second intermediate host being an aquatic animal. Snail-borne parasitic diseases target many organs, such as the lungs, liver, biliary tract, intestines, brain and kidneys, leading to overactive immune responses, cancers, organ failure, infertility and even death. Developing countries in Africa, Asia and Latin America have the highest incidences of these diseases, while some endemic parasites have developed into worldwide epidemics through the global spread of snails. Physical, chemical and biological methods have been introduced to control the host snail populations to prevent disease.ConclusionsIn this review, we summarize the roles of snails in the life cycles of the parasites they host, the worldwide distribution of parasite-transmitting snails, the epidemiology and pathogenesis of snail-transmitted parasitic diseases, and the existing snail control measures, which will contribute to further understanding the snail-parasite relationship and new strategies for controlling snail-borne parasitic diseases.
| S-EPMC5890347 | biostudies-literature
Project description:Cryptosporidiosis and giardiasis are recognized as significant enteric diseases due to their long-term health effects in humans and their economic impact in agriculture and medical care. Molecular analysis is essential to identify species and genotypes causing these infectious diseases and provides a potential tool for monitoring. This study uses information on species and genetic variants to gain insights into the geographical distribution and spatial patterns of Cryptosporidium and Giardia parasites. Here, we describe the population heterogeneity of genotypic groups within Cryptosporidium and Giardia present in New Zealand using gp60 and gdh markers to compare the observed variation with other countries around the globe. Four species of Cryptosporidium (C. hominis, C. parvum, C. cuniculus and C. erinacei) and one species of Giardia (G. intestinalis) were identified. These species have been reported worldwide and there are not unique Cryptosporidium gp60 subtype families and Giardia gdh assemblages in New Zealand, most likely due to high gene flow of historical and current human activity (travel and trade) and persistence of large host population sizes. The global analysis revealed that genetic variants of these pathogens are widely distributed. However, genetic variation is underestimated by data biases (e.g. neglected submission of sequences to genetic databases) and low sampling. New genotypes are likely to be discovered as sampling efforts increase according to accumulation prediction analyses, especially for C. parvum. Our study highlights the need for greater sampling and archiving of genotypes globally to allow comparative analyses that help understand the population dynamics of these protozoan parasites. Overall our study represents a comprehensive overview for exploring local and global protozoan genotype diversity and advances our understanding of the importance for surveillance and potential risk associated with these infectious diseases.
| S-EPMC5526614 | biostudies-literature
Project description:Subspecies in the global human gut microbiome
| PRJEB17632 | ENA
Project description:DNA was extracted from saliva samples and genotyping was performed on Illumina Infinium Global Screening Array.
| EGAD00010002374 | EGA
Project description:BackgroundGroup A rotavirus (RVA) mainly causes acute gastroenteritis, exclusively in young children in developing countries. The prevalence and determination of the molecular epidemiology of rotavirus genotypes will determine the dominant rotavirus genotypes in the region and provide a strategy for the development of appropriate vaccines.MethodsA total of 100 fecal samples were collected from children below five years with acute gastroenteritis who referred to Aboozar Children’s Hospital of Ahvaz city during October 2015 to March 2016. All samples were screened by latex agglutination for the presence of rotavirus antigen. Rotavirus-positive samples were further analyzed by the semi-multiplex RT-PCR, and the sequencing was performed for G/P genotyping.ResultsFindings showed that 32% of the specimens were RVA-positive. Among the 32 VP7 genotyped strains, the predominant G genotype was G9 (37.5%), followed by G2 (21.9%), G1 (12.5%), G12 (9.4%), G4 (9.4%), G2G9 (6.3%), and G3 (3.1%). Among the 31 VP4 genotyped strains, P[8] genotype was the dominant (62.5%), followed by P[4] (31.3%) and P[4] P[8] (3.1%). The genotypes for G and P were identified for 31 rotaviruses (96.87%), but only one strain, G9, remained non-typeable for the P genotype. The most prevalent G/P combination was G9P[8] (28.5%), followed by G2P[4] (18.8%), G1P[8] (9.4%), G12P[8] (9.4%), G4P[8] (9.4%), G2G9P[4] (6.3%), G9P[4] P[8] (3.1%), G3P[8] (3.1%), G9P[4] (3.1%), G2P[8] (3.1%), and G9P[non-typeable] (3.1%).ConclusionA novel rotavirus strain, G12, was detected, for the first time, in patients from the southwest of Iran. Comprehensive investigations are required to evaluate the emergence of this strain.
| S-EPMC5786656 | biostudies-literature
Project description:BackgroundHuman Papillomavirus (HPV) causes various types of cancer in both men and women. Woman with HPV infection has a risk of developing invasive cervical cancer. Globally, HPV 16 and 18 were predominant. This study aims to find the distribution of various HPV types in South Andaman.MethodsA cross-sectional study was conducted among women in South Andaman, where cervical scrapes were collected after collecting written informed consent. Detection of HPV genotypes was carried out by using a PCR assay. Further, sequencing analysis was performed using MEGA11 to identify various genotypes in this territory.ResultOf these 1000 samples, 32 were positive for HR-HPV 16, and four were positive for HR-HPV 18. Fifteen HPV genotypes were detected using molecular evolutionary analysis. Six cases were identified with multiple genotypes. The most prevalent genotype is HPV 16 which belongs to Lineage-A and sub-lineage A2. HPV 18 identified in South Andaman belonged to the lineage A1 to A5.DiscussionVarious HPV types were identified among women in South Andaman. Global burden of cervical cancer associated with various HPV sub-lineages. HPV-16 A1 sub-lineage was globally widespread, whereas sub-lineages A1, A2 and D1 prevailed in South Andaman.ConclusionsHR-HPV identified in this study enlightens the importance of HPV vaccination among women in remote places. These findings will help to strengthen public health awareness programs and prevention strategies for women in remote areas.
| S-EPMC10486394 | biostudies-literature