Phylogenetic Analysis of Hepatitis E Virus

A blast analysis identified that the sequences most closely related to FR-HuHEVF3f were HEPAC-15, TLS09-3, SW8a24 Spain and JAO-SpaTok12. Alignments were performed with ClustalW using the complete or near-complete genome sequences of these HEV-3f sequences as well as the reference sequences of the different genotypes of HEV (HEV-1 to -8) and subtypes of HEV-3 [43 (link)]. A phylogenetic tree was then constructed by using the Maximum Likelihood method and Tamura-Nei model with a bootstrap of 1000 replicates. The initial tree was obtained using the Neighbor-Joining method. This analysis was conducted using the MEGA X software (http://www.megasoftware.net, accessed on 5 February 2021).

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Pellerin M., Hirchaud E., Blanchard Y., Pavio N, & Doceul V. (2021). Characterization of a Cell Culture System of Persistent Hepatitis E Virus Infection in the Human HepaRG Hepatic Cell Line. Viruses, 13(3), 406.

Publication 2021

MEGA X software

Genome Genotypes Tree

Corresponding Organization :

Other organizations : NeuroDiderot, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, École Nationale Vétérinaire d'Alfort, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail

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Variable analysis

independent variables

Complete or near-complete genome sequences of HEV-3f sequences
Reference sequences of the different genotypes of HEV (HEV-1 to -8) and subtypes of HEV-3

dependent variables

Phylogenetic relationships between the HEV-3f sequences and the reference sequences

control variables

Alignment method (ClustalW)
Phylogenetic tree construction method (Maximum Likelihood method and Tamura-Nei model with a bootstrap of 1000 replicates)
Initial tree construction method (Neighbor-Joining method)
Software used (MEGA X)

controls

No positive or negative controls were explicitly mentioned in the information provided.

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