Molecular Epidemiology and Genetic Diversity of Echovirus Type 30 (E30): Genotypes Correlate with Temporal Dynamics of E30 Isolation

1999 ◽  
Vol 37 (12) ◽  
pp. 3928-3933 ◽  
Author(s):  
M. Steven Oberste ◽  
Kaija Maher ◽  
Margery L. Kennett ◽  
Janice J. Campbell ◽  
Michael S. Carpenter ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Aseptic Meningitis ◽  
Temporal Dynamics ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
The United States ◽  
Molecular Techniques ◽  
Surveillance Data ◽  
Echovirus Type 30 ◽  
Echovirus Type

Echovirus type 30 (E30) (genus, Enterovirus; family,Picornaviridae) has caused large outbreaks of aseptic meningitis in many regions of the world in the last 40 years. U.S. enterovirus surveillance data for the period 1961 to 1998 indicated that the annual proportion of E30 isolations relative to total enterovirus isolations has fluctuated widely, from a low of 0% in 1966 to a high of 42% in 1998. Peaks of E30 isolations occurred in the years 1968 to 1969, 1981 to 1984, 1990 to 1993, and 1997 to 1998, coincident with large nationwide outbreaks of E30-associated aseptic meningitis. Analysis of the complete VP1 sequence (876 nucleotides) of 136 E30 strains isolated in geographically dispersed regions of the United States and nine other countries between 1956 and 1998 indicated that the currently circulating E30 strains are genetically distinct from those isolated 30 to 40 years ago. Phylogenetic reconstruction demonstrated the existence of at least four distinct genetic groups, three of which have not been isolated in North America since 1981. Two of the three groups disappeared during periods when E30 was isolated infrequently. All North American E30 strains isolated after 1988 were closely related to one another, and all post-1993 isolates were of the same lineage within this group. Surveillance data indicate that E30 causes large national outbreaks of 2- to 4-year durations, separated by periods of relative quiescence. Our results show that shifts in the overall genetic diversity of E30 and the predominant genetic type correlate temporally with the dynamics of E30 isolation. The sequence data also provide a basis for the application of molecular techniques for future epidemiologic investigations of E30 disease.

Molecular analysis of selected paramphistome isolates from cattle in southern Africa

2015 ◽  
Vol 90 (6) ◽  
pp. 784-788 ◽  
Author(s):  
S. Dube ◽  
M.S. Sibula ◽  
Z. Dhlamini
Keyword(s):  
Sequence Data ◽  
Animal Health ◽  
Phylogenetic Reconstruction ◽  
Morphological Characterization ◽  
Its2 Sequence ◽  
Molecular Techniques ◽  
Its2 Rdna ◽  
African Countries ◽  
Rdna Sequences ◽  
The Individual

AbstractParamphistomes are parasites of domestic and wild ruminants, the effects of which in animal health remain underestimated. Very few studies in Africa have been done using molecular techniques to resolve situations associated with taxonomical groupings and epidemiology of these parasites. In this study, the genetic variability of nine representative paramphistome isolates collected from southern African countries, namely Botswana, South Africa, Zambia and Zimbabwe, was assessed using both morphological and internal transcribed spacer 2 (ITS2) rDNA sequence data. Morphological characterization and identification were carried out using median sagittal sections of the paramphistomes. DNA of the individual paramphistomes was isolated, the ITS2 rDNA was amplified, purified and sequenced. The sequences were submitted to GenBank, which assigned them the following accession numbers: KP639631, KP639630, KP639632, KP639633, KP639634, KP639635, KP639636, KP639637 and KP639638. These sequences were used for phylogenetic analysis using MEGA 6. Morphological characterization revealed three species of paramphistomes belonging to three different sub-families: one Stephanopharynx compactus isolate, a member of the Stephanopharyngidae sub-family; one Carmyerius dollfusi isolate, a member of the Gastrothylacidae sub-family; and seven Calicophoron microbothrium isolates belonging to the Paramphistomidae sub-family. ITS2 sequence analysis using BlastN results indicated that this is the first report of S. compactus (KP639630) and C. dollfusi (KP639636). Phylogenetic reconstruction of the paramphistome isolates revealed three separate clades representing the three species. However, the clade with all the C. microbothrium isolates was the only one that was supported by a higher bootstrap value of 92%, although there was no differentiation of the isolates according to geographical locations. The low divergence values on the ITS2 sequences of the C. microbothrium isolates indicate that ITS rDNA sequences can be used as a molecular tool to infer knowledge for resolving taxonomic groupings.

Molecular Surveillance of HIV-1 Infection in Krasnoyarsk Region, Russia: Epidemiology, Phylodynamics and Phylogeography

2019 ◽  
Vol 17 (2) ◽  
pp. 114-125 ◽  
Author(s):  
Dmitry Neshumaev ◽  
Aleksey Lebedev ◽  
Marina Malysheva ◽  
Anatoly Boyko ◽  
Sergey Skudarnov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Temporal Dynamics ◽  
Phylogenetic Reconstruction ◽  
Viral Population ◽  
Recent Common Ancestor ◽  
Krasnoyarsk Region ◽  
Most Recent Common Ancestor ◽  
And Migration ◽  
Viral Lineage ◽  
Hiv 1

Background:The information about the dynamics of the viral population and migration events that affect the epidemic in different parts of the Russia is insufficient. Possibly, the huge size of the country and limited transport accessibility to certain territories may determine unique traits of the HIV-1 evolutionary history in different regions.Objective:The aim of this study was to explore the genetic diversity of HIV-1 in the Krasnoyarsk region and reconstruct spatial-temporal dynamics of the infection in the region.Methods:The demographic and virologic data from 281 HIV-infected individuals in Krasnoyarsk region collected during 2011-2016 were analyzed. The time to the most recent common ancestor, evolutionary rates, population growth, and ancestral geographic movements was estimated using Bayesian coalescent-based methods.Results:The study revealed moderate diversity of the HIV-1 subtypes found in the region, which included A6 (92.3%), CRF063_02A (4.3%), B (1.1%), and unique recombinants (2.5%). Phylogenetic reconstruction revealed that the A6 subtype was introduced into Krasnoyarsk region by one viral lineage, which arose around 1996.9 (1994.5-1999.5). The phylogeography analysis pointed to Krasnoyarsk city as the geographical center of the epidemic, which further spread to central neighboring districts of the region. At least two epidemic growth phases of subtype A6 were identified which included exponential growth in early-2000s followed by the decline in the mid/late 2010s.Conclusion:This study demonstrates a change in the genetic diversity of HIV-1 in the Krasnoyarsk region. At the beginning of the epidemic, subtype A6 prevailed, subtypes B and CRF063_02A appeared in the region later.

scholarly journals Clinical Study of an Outbreak of Aseptic Meningitis due to Echovirus Type 30 in Munakata City in 1997-1998

2000 ◽  
Vol 74 (3) ◽  
pp. 231-236
Author(s):  
Izumi KAJIWARA ◽  
Tomohiro KUSABA ◽  
Isao HAYASHIDA ◽  
Takeshi KAI ◽  
Akio OOSHIMA
Keyword(s):  
Clinical Study ◽  
Aseptic Meningitis ◽  
Echovirus Type 30 ◽  
Echovirus Type

scholarly journals Phylogenic Analysis of Echovirus Type 30 Isolated from a Large Epidemic of Aseptic Meningitis in Japan during 1997-1998

1999 ◽  
Vol 52 (4) ◽  
pp. 160-163 ◽  
Author(s):  
Hiromu Yoshida ◽  
Zheng Hong ◽  
Tetsuo Yoneyama ◽  
Kumiko Yoshii ◽  
Hiroyuki Shimizu ◽  
...  
Keyword(s):  
Aseptic Meningitis ◽  
Phylogenic Analysis ◽  
Echovirus Type 30 ◽  
Echovirus Type

An outbreak of Aseptic Meningitis due to echovirus type 30 in two cities of Turkey

2002 ◽  
Vol 18 (8) ◽  
pp. 823-826 ◽  
Author(s):  
E. Ozkaya ◽  
K. Hizel ◽  
G. Uysal ◽  
S. Akman ◽  
S. Terzioglu ◽  
...  
Keyword(s):  
Aseptic Meningitis ◽  
Two Cities ◽  
Echovirus Type 30 ◽  
Echovirus Type

Phylogeny of the Crepidula plana (Gastropoda: Calyptraeidae) cryptic species complex in North America

2000 ◽  
Vol 78 (8) ◽  
pp. 1500-1514 ◽  
Author(s):  
Rachel Collin
Keyword(s):  
North Carolina ◽  
North America ◽  
Species Complex ◽  
East Coast ◽  
Sequence Data ◽  
Single Species ◽  
The United States ◽  
Molecular Techniques ◽  
Dna Sequence Data ◽  
Cryptic Species Complex

The taxonomy of Crepidula species with flat white shells is particularly difficult. These animals from the east coast of North America have generally been classified as a single species, Crepidula plana Say, 1822. Based on allozyme and developmental data, however, Hoagland (K.E. Hoagland. 1984. Malacologia, 25: 607-628; K.E. Hoagland. 1986. Am. Malacol. Bull. 4: 173-183) concluded that two species of flat white-shelled Crepidula live along the east coast of the United States, but she did not apply any name to the second species. Herein I use molecular techniques to characterize populations of flat white-shelled Crepidula species from Texas, Florida, Georgia, North Carolina, and |Massachusetts, and describe their morphology and development. DNA-sequence data support the existence of three species. One species is readily distinguished on the basis of morphology and development, but the other two are very similar. To clarify the nomenclature of these species, I designate neotypes for C. plana Say, 1822 and Crepidula depressa Say, 1822, and describe Crepidula atrasolea sp.nov.

scholarly journals Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259531
Author(s):  
Mariana Kikuti ◽  
Juan Sanhueza ◽  
Carles Vilalta ◽  
Igor Adolfo Dexheimer Paploski ◽  
Kimberly VanderWaal ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Production Systems ◽  
Sequence Data ◽  
The United States ◽  
Respiratory Syndrome Virus ◽  
Viral Diversity ◽  
Wild Type ◽  
Routine Monitoring ◽  
Genotype 2

Porcine reproductive and respiratory syndrome virus genotype 2 (PRRSV-2) genetic diversity in the U.S. was assessed using a database comprising 10 years’ worth of sequence data obtained from swine production systems routine monitoring and outbreak investigations. A total of 26,831 ORF5 PRRSV-2 sequences from 34 production systems were included in this analysis. Within group mean genetic distance (i.e. mean proportion of nucleotide differences within ORF5) per year according to herd type was calculated for all PRRSV-2 sequences. The percent nucleotide difference between each sequence and the ORF5 sequences from four commercially available PRRSV-2 vaccines (Ingelvac PRRS MLV, Ingelvac PRRS ATP, Fostera PRRS, and Prevacent PRRS) within the same lineage over time was used to classify sequences in wild-type or vaccine-like. The mean ORF5 genetic distance fluctuated from 0.09 to 0.13, being generally smaller in years in which there was a relative higher frequency of dominant lineage. Vaccine-like sequences comprised about one fourth of sequences obtained through routine monitoring of PRRS. We found that lineage 5 sequences were mostly Ingelvac PRRS MLV-like. Lineage 8 sequences up to 2011 were 62.9% Ingelvac PRRS ATP-like while the remaining were wild-type viruses. From 2012 onwards, 51.9% of lineage 8 sequences were Ingelvac PRRS ATP-like, 45.0% were Fostera PRRS-like, and only 3.2% were wild-type. For lineage 1 sequences, 0.1% and 1.7% of the sequences were Prevacent PRRS-like in 2009–2018 and 2019, respectively. These results suggest that repeated introductions of vaccine-like viruses through use of modified live vaccines might decrease within-lineage viral diversity as vaccine-like strains become more prevalent. Overall, this compilation of private data from routine monitoring provides valuable information on PRRSV viral diversity.

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