Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based PAirwise Sequence Comparison (PASC) Analysis

2017 ◽  
pp. 43-53
Author(s):  
Yīmíng Bào ◽  
Jens H. Kuhn
Keyword(s):  
Sequence Comparison ◽  
Hemorrhagic Fever ◽  
Pairwise Sequence Comparison ◽  
Preliminary Classification

scholarly journals PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses

Viruses ◽  
2012 ◽  
Vol 4 (8) ◽  
pp. 1318-1327 ◽  
Author(s):  
Yiming Bao ◽  
Vyacheslav Chetvernin ◽  
Tatiana Tatusova
Keyword(s):  
Sequence Comparison ◽  
Pairwise Sequence Comparison

scholarly journals Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1476
Author(s):  
Lester J. Perez ◽  
Gavin A. Cloherty ◽  
Michael G. Berg
Keyword(s):  
Genetic Diversity ◽  
Sequence Comparison ◽  
Complete Resolution ◽  
Pairwise Distance ◽  
Pairwise Sequence Comparison ◽  
Double Stranded Rna ◽  
Phylogenetic Marker ◽  
High Degree ◽  
Phylogenetic Noise

Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We demonstrate here that this phylogenetic marker is saturated, affected by homoplasy, and has high phylogenetic noise, resulting in 34% unsolved topologies. By contrast, full-length RdRp sequences provide reliable topologies that allow ancestralism of members to be correctly inferred. MAFFT alignment and maximum likelihood trees were established as the optimal methods to determine phylogenetic relationships, providing complete resolution of PBV RdRp and capsid taxa, each into three monophyletic groupings. Pairwise distance calculations revealed these lineages represent three species. For RdRp, the application of cutoffs determined by theoretical taxonomic distributions indicates that there are five genotypes in species 1, eight genotypes in species 2, and three genotypes in species 3. Capsids were also divided into three species, but sequences did not segregate into statistically supported subdivisions, indicating that diversity is lower than RdRp. We thus propose the adoption of a new nomenclature to indicate the species of each segment (e.g., PBV-C1R2).

scholarly journals Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
He-Teng Zhang ◽  
Hao Wang ◽  
Hai-Sheng Wu ◽  
Jian Zeng ◽  
Yan Yang
Keyword(s):  
Human Papillomavirus ◽  
Bacterial Community ◽  
Pregnant Women ◽  
Sequence Comparison ◽  
Pairwise Sequence Comparison ◽  
Vaginal Secretion ◽  
The Family ◽  
Complete Genomes ◽  
Different Types ◽  
Vaginal Tract

Abstract Background Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. Methods To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. Results Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. Conclusion Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.

scholarly journals Canine Malignant Mammary Tumours II. Adenocarcinomas, Solid Carcinomas and Spindle Cell Carcinomas

1972 ◽  
Vol 9 (6) ◽  
pp. 447-470 ◽  
Author(s):  
W. Misdorp ◽  
E. Cotchin ◽  
J. F. Hampe ◽  
Anne G. Jabara ◽  
J. von Sandersleben
Keyword(s):  
Spindle Cell ◽  
Clinical Signs ◽  
Subjective Assessment ◽  
Simple Type ◽  
Well Differentiated ◽  
The Times ◽  
Lymphatic Permeation ◽  
Preliminary Classification ◽  
Mammary Adenocarcinomas

A preliminary classification of 130 canine mammary adenocarcinomas, 76 solid carcinomas, and nine spindle cell carcinomas, together with several subtypes, was constructed from pooled, selected (metastasized) material. Each tumour in this series was classified by subjective assessment of its quantitatively predominant histological picture. Many adenocarcinomas and solid carcinomas of simple type were infiltrative, and lymphatic permeation was often found. The complex types of adenocarcinomas and of solid carcinomas were expansive, and lymphatic permeation was rare. Some metastasized adenocarcinomas were well differentiated. The clinical signs, distribution of metastases and some preliminary data on the times of survival of dogs with various types of carcinomas are discussed.

Sign in / Sign up

Export Citation Format

Share Document