scholarly journals Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6142
Author(s):  
Therese A. Catanach ◽  
Andrew D. Sweet ◽  
Nam-phuong D. Nguyen ◽  
Rhiannon M. Peery ◽  
Andrew H. Debevec ◽  
...  

Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.

2009 ◽  
Vol 170 (12) ◽  
pp. 1455-1463 ◽  
Author(s):  
W. M. van Ballegooijen ◽  
R. van Houdt ◽  
S. M. Bruisten ◽  
H. J. Boot ◽  
R. A. Coutinho ◽  
...  

2019 ◽  
Vol 30 (9) ◽  
pp. 902-910 ◽  
Author(s):  
Paula CR Frade ◽  
Nairis C Raiol ◽  
Luana M da Costa ◽  
Luiz ML Pinheiro ◽  
Gláucia C Silva-Oliveira ◽  
...  

In South America, the Amazon basin is considered an endemic area of hepatitis B virus (HBV) infection. However, epidemiological studies with vulnerable groups are scarce. Female sex workers (FSWs) are highly vulnerable to sexually transmitted infections due to a combination of their sexual behavior and socio-economic conditions. Thus, this study investigated the prevalence of HBV infections and HBV–hepatitis C virus, HBV–hepatitis D virus, HBV–HIV, and HBV–human T-lymphotropic virus co-infections among FSWs in the Marajó Archipelago, northern Brazil, as well as identifying the HBV genotypes circulating in this population. A total of 153 FSWs in 5 towns and 18 riverside communities were included in the study. The HBV infection and co-infections were diagnosed by enzyme-linked immunosorbent assay and real-time polymerase chain reaction. The HBV genotypes were detected by sequencing and were then analyzed phylogenetically. Most of the FSWs surveyed were single, young, heterosexual, and born locally, with low levels of education. Overall, 21 (13.7%) had been exposed to HBV, and HBV-DNA was detected in 13 (8.5%). Genotypes A (69.2%), D (23.1%), and F (7.7%) were detected. Seven cases of co-infections with other viruses were detected. These findings indicate a clear need for urgent measures to control the spread of HBV and other pathogens, and to promote the health of the local FSWs.


Hepatology ◽  
2020 ◽  
Author(s):  
Daryl T.Y. Lau ◽  
Lilia Ganova‐Raeva ◽  
Junyao Wang ◽  
Douglas Mogul ◽  
Raymond T. Chung ◽  
...  

2003 ◽  
Vol 38 ◽  
pp. 112
Author(s):  
R. Jardi ◽  
F. Rodriguez-Frias ◽  
M. Buti ◽  
X. Costa ◽  
A. Valdes ◽  
...  

2007 ◽  
Vol 4 (1) ◽  
pp. 74 ◽  
Author(s):  
Abdel-Rahman N Zekri ◽  
Mohamed M Hafez ◽  
Nahed I Mohamed ◽  
Zeinab K Hassan ◽  
Manal H El-Sayed ◽  
...  

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