Complete genome analysis confirms that the pygmy marmoset adenovirus is a variant of the skunk adenovirus 1 – Short communication

AbstractThe complete genomic sequence along with phylogenetic analyses of an adenovirus (AdV), isolated from a dead captive pygmy marmoset (Callithrix pygmaea) from a Hungarian zoo is reported. Earlier, based on the phylogenetic analysis of the sequence of a PCR-amplified fragment from the DNA polymerase gene, the pygmy marmoset AdV (PMAdV) has been reported to cluster closest to certain chiropteran AdVs. In the following years similar AdVs were discovered in additional mammalian hosts, including a skunk (Mephitis mephitis), African pygmy hedgehogs (Atelerix albiventris), North American porcupines (Erethizon dorsatum) and grey fox (Urocyon cinereoargenteus). After the full genome analysis of the skunk adenovirus (SkAdV-1), a novel species Skunk mastadenovirus A (SkAdV-A) has been established. The AdVs, originating from the African pygmy hedgehogs, have been found to belong to virus species SkAdV-A. Partial gene sequences from the porcupine AdVs have also implied their very close genetic relatedness to SkAdV-A. The complete genomic sequence of PMAdV, examined in this study, was found to share 99.83% nucleotide identity with SkAdV-1, thus unequivocally represents a genomic variant of SkAdV-1. The observation that viruses classifiable as SkAdV-A are able to infect and cause diseases in several, distantly related mammals seems to deserve further studies to elucidate the infection biology of this intriguing AdV.

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Complete Genomic Sequence of Goose-Origin Reovirus from China

Journal of Virology ◽

10.1128/jvi.01692-12 ◽

2012 ◽

Vol 86 (18) ◽

pp. 10257-10257 ◽

Cited By ~ 20

Author(s):

Tao Yun ◽

Weicheng Ye ◽

Zheng Ni ◽

Liu Chen ◽

Bin Yu ◽

...

Keyword(s):

New Species ◽

Genomic Sequence ◽

Phylogenetic Analyses ◽

Full Genome Sequence ◽

Avian Reovirus ◽

Complete Genomic Sequence ◽

Full Genome ◽

Established Species ◽

A New Species ◽

Complete Genomic

We report the full-genome sequence of a goose-origin reovirus (GRV) strain 03G from Zhejiang Province, China. This is the first report of the complete genomic sequence (segments 1 to 10) of GRV. Phylogenetic analyses of the sequence suggest that GRV 03G represents a new species distinct from other established species within the avian reovirus (ARV) group of orthoreoviruses.

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Characterization of the complete genomic sequence of genotype II hepatitis A virus (CF53/Berne isolate)

Journal of General Virology ◽

10.1099/vir.0.80304-0 ◽

2004 ◽

Vol 85 (10) ◽

pp. 2943-2952 ◽

Cited By ~ 86

Author(s):

Ling Lu ◽

Karen Z. Ching ◽

Vanessa Salete de Paula ◽

Tatsunori Nakano ◽

Gunter Siegl ◽

...

Keyword(s):

Hepatitis A ◽

Genomic Sequence ◽

Hepatitis A Virus ◽

Phylogenetic Analyses ◽

Pairwise Comparison ◽

Complete Genomic Sequence ◽

Single Genotype ◽

Close Relationship ◽

Genomic Regions ◽

Complete Genomic

The complete genomic sequence of hepatitis A virus (HAV) CF53/Berne strain was determined. Pairwise comparison with other complete HAV genomic sequences demonstrated that the CF53/Berne isolate is most closely related to the single genotype VII strain, SLF88. This close relationship was confirmed by phylogenetic analyses of different genomic regions, and was most pronounced within the capsid region. These data indicated that CF53/Berne and SLF88 isolates are related more closely to each other than are subtypes IA and IB. A histogram of the genetic differences between HAV strains revealed four separate peaks. The distance values for CF53/Berne and SLF88 isolates fell within the peak that contained strains of the same subtype, showing that they should be subtypes within a single genotype. The complete genomic data indicated that genotypes II and VII should be considered a single genotype, based upon the complete VP1 sequence, and it is proposed that the CF53/Berne isolate be classified as genotype IIA and strain SLF88 as genotype IIB. The CF53/Berne isolate is cell-adapted, and therefore its sequence was compared to that of two other strains adapted to cell culture, HM-175/7 grown in MK-5 and GBM grown in FRhK-4 cells. Mutations found at nucleotides 3889, 4087 and 4222 that were associated with HAV attenuation and cell adaptation in HM175/7 and GMB strains were not present in the CF53/Berne strain. Deletions found in the 5′UTR and P3A regions of the CF53/Berne isolate that are common to cell-adapted HAV isolates were identified, however.

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West Nile virus isolates from India: evidence for a distinct genetic lineage

Journal of General Virology ◽

10.1099/vir.0.82403-0 ◽

2007 ◽

Vol 88 (3) ◽

pp. 875-884 ◽

Cited By ~ 116

Author(s):

Vijay P. Bondre ◽

R. S. Jadi ◽

A. C. Mishra ◽

P. N. Yergolkar ◽

V. A. Arankalle

Keyword(s):

West Nile Virus ◽

Genomic Sequence ◽

Phylogenetic Analyses ◽

Genomic Sequences ◽

Genetic Lineage ◽

Complete Genomic Sequence ◽

West Nile ◽

Human Patient ◽

Indian Isolates ◽

Complete Genomic

The complete genomic sequence of one human isolate of West Nile virus (WNV) and the partial genomic sequences of 14 other strains from India isolated in the period 1955–1982 from different hosts and geographical areas were determined. Phylogenetic analyses based on complete and partial genomic sequences (921 nt of the C–prM–E region) revealed that WNV could be classified into five distinct groups that differed from each other by 20–25 % at the complete genome level and by 20–26 % using partial sequences. Of the Indian isolates, 13 formed a distinct genetic lineage, lineage 5, whereas two isolates, one from a human patient (1967) and another from a bat (1968), were related closely to lineage 1 strains. The complete genomic sequence of the Indian isolate, 804994, showed 20–22 % genetic divergence from the previously proposed lineage 1 and 2 strains and 24–25 % divergence from isolates of the newly proposed lineages 3 (Rabensburg isolate 97-103 of 1997) and 4 (Russian isolate LEIV-Krnd88-190 of 1998). Similarly, the partial genomic sequences of the Indian isolates showed 21–26 % divergence from lineage 1 and 2 strains and from the Rabensburg (97-103) and Russian (LEIV-Krnd88-190) isolates. Cross-neutralization using strain-specific polyclonal antibodies against lineage 1 strain Eg-101 and representative Indian strains suggests substantial antigenic variation. This study documents circulation of WNV strains typical to India for 27 years and the introduction of lineage 1 strains during 1967–1968. These results indicate strongly that WNV should be classified into five genetic lineages, with Indian viruses constituting the distinct genetic lineage 5.

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Complete Genomic Sequence of Dengue virus 1, Isolated from Plasma Collected from a Haitian Child in 2014

Genome Announcements ◽

10.1128/genomea.00331-17 ◽

2017 ◽

Vol 5 (22) ◽

Cited By ~ 2

Author(s):

Maha Elbadry ◽

Sarah White ◽

Julia Loeb ◽

Massimiliano Tagliamonte ◽

Marco Salemi ◽

...

Keyword(s):

Dengue Virus ◽

Dengue Fever ◽

Genomic Sequence ◽

Phylogenetic Analyses ◽

South American ◽

Plasma Samples ◽

Complete Genomic Sequence ◽

Chikungunya Fever ◽

Genotype V ◽

Complete Genomic

ABSTRACT An outbreak of dengue fever followed a chikungunya fever outbreak in Haiti in 2014. We detected Dengue virus 1 (DENV-1) in plasma samples collected between May 2014 and February 2015. A representative isolate was fully sequenced, and phylogenetic analyses indicate that it groups within the genotype V South American and Caribbean DENV-1 clades.

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Special Issue: Genetic Basis of Phenotypic Variation in Drosophila and Other Insects

Genes ◽

10.3390/genes12081212 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1212

Author(s):

J. Spencer Johnston ◽

Carl E. Hjelmen

Keyword(s):

Next Generation Sequencing ◽

Genetic Basis ◽

Genomic Sequence ◽

Sequence Data ◽

Complete Genomic Sequence ◽

Special Issue ◽

Model Species ◽

Road Map ◽

Generation Sequencing ◽

Complete Genomic

Next-generation sequencing provides a nearly complete genomic sequence for model and non-model species alike; however, this wealth of sequence data includes no road map [...]

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