Atypical Severe Puumala Hantavirus Infection and Virus Sequence Analysis of the Patient and Regional Reservoir Host

2012 ◽  
Vol 59 ◽  
pp. 110-115 ◽  
Author(s):  
I. Eckerle ◽  
E. Jakob ◽  
J. Hofmann ◽  
A. Schmidt-Bacher ◽  
J. Ettinger ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Reservoir Host ◽  
Hantavirus Infection ◽  
Virus Sequence

scholarly journals Use of short tandem repeat fingerprinting to validate sample origins in hepatitis C virus molecular epidemiology studies

2014 ◽  
Vol 95 (1) ◽  
pp. 66-70 ◽  
Author(s):  
Victoria C. Edwards ◽  
C. Patrick McClure ◽  
Richard J. P. Brown ◽  
Emma Thompson ◽  
William L. Irving ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Sequence Analysis ◽  
Molecular Epidemiology ◽  
Alternative Explanation ◽  
Sequence Analyses ◽  
Distinct Virus ◽  
Virus Sequence ◽  
Epidemiology Studies ◽  
Short Tandem

Sequence analysis is used to define the molecular epidemiology and evolution of the hepatitis C virus. Whilst most studies have shown that individual patients harbour viruses that are derived from a limited number of highly related strains, some recent reports have shown that some patients can be co-infected with very distinct variants whose frequency can fluctuate greatly. Whilst co-infection with highly divergent strains is possible, an alternative explanation is that such data represent contamination or sample mix-up. In this study, we have shown that DNA fingerprinting techniques can accurately assess sample provenance and differentiate between samples that are truly exhibiting mixed infection from those that harbour distinct virus populations due to sample mix-up. We have argued that this approach should be adopted routinely in virus sequence analyses to validate sample provenance.

scholarly journals RNA2 of grapevine fanleaf virus: sequence analysis and coat protein cistron location

1990 ◽  
Vol 71 (7) ◽  
pp. 1433-1441 ◽  
Author(s):  
M. A. Serghini ◽  
M. Fuchs ◽  
M. Pinck ◽  
J. Reinbolt ◽  
B. Walter ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Coat Protein ◽  
Grapevine Fanleaf Virus ◽  
Virus Sequence

Puumala hantavirus infection alters the odour attractiveness of its reservoir host

Oecologia ◽  
2014 ◽  
Vol 176 (4) ◽  
pp. 955-963 ◽  
Author(s):  
Nelika K. Hughes ◽  
Sanne Helsen ◽  
Katrien Tersago ◽  
Herwig Leirs
Keyword(s):  
Reservoir Host ◽  
Hantavirus Infection

scholarly journals ImputeCoVNet: 2D ResNet Autoencoder for Imputation of SARS-CoV-2 Sequences

2021 ◽  
Author(s):  
Ahmad Pesaranghader ◽  
Justin Pelletier ◽  
Jean-Christophe Grenier ◽  
Raphaël Poujol ◽  
Julie Hussin
Keyword(s):  
Deep Learning ◽  
Sequence Analysis ◽  
Genetic Variants ◽  
Hamming Distance ◽  
Imputation Accuracy ◽  
Computation Time ◽  
Allele Frequencies ◽  
Learning Approach ◽  
Efficient Manner ◽  
Virus Sequence

We describe a new deep learning approach for the imputation of SARS-CoV-2 variants. Our model, ImputeCoVNet, consists of a 2D ResNet Autoencoder that aims at imputing missing genetic variants in SARS-CoV-2 sequences in an efficient manner. We show that ImputeCoVNet leads to accurate results at minor allele frequencies as low as 0.0001. When compared with an approach based on Hamming distance, ImputeCoVNet achieved comparable results with significantly less computation time. We also present the provision of geographical metadata (e.g., exposed country) to decoder increases the imputation accuracy. Additionally, by visualizing the embedding results of SARS-CoV-2 variants, we show that the trained encoder of ImputeCoVNet, or the embedded results from it, recapitulates viral clade's information, which means it could be used for predictive tasks using virus sequence analysis.

Sign in / Sign up

Export Citation Format

Share Document