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Meta-analysis of genetic diversity of the VP1 gene among the circulating O, A, and SAT2 serotypes and vaccine strains of FMD virus in Egypt

Abeer F. El Nahas
Abeer F. El Nahas
 and 
Sayed A.H. Salem
Sayed A.H. Salem
   | Nov 06, 2020
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Published Online: Nov 06, 2020
Page range: 487 - 493
Received: Apr 08, 2020
Accepted: Oct 06, 2020
DOI: https://doi.org/10.2478/jvetres-2020-0069
Keywords
© 2020 A.F. El Nahas et al. published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Fig. 1

Maximum likelihood phylogenetic tree of the VP1 gene nucleotide sequences of FMDV serotype O genotypes circulating in Egypt from 1993 to 2018. Numbers at nodes indicate the bootstrap values based on the maximum likelihood analysis of 1,000 replicates. The scale bar (0.05) represents substitutions per nucleotide position. * – Vaccine strains. The rectangles contain the amino acid substitutions per year
Maximum likelihood phylogenetic tree of the VP1 gene nucleotide sequences of FMDV serotype O genotypes circulating in Egypt from 1993 to 2018. Numbers at nodes indicate the bootstrap values based on the maximum likelihood analysis of 1,000 replicates. The scale bar (0.05) represents substitutions per nucleotide position. * – Vaccine strains. The rectangles contain the amino acid substitutions per year

Fig. 2

Maximum likelihood phylogenetic tree of the VP1 gene nucleotide sequences of FMDV serotype A genotypes circulating in Egypt from 2011 to 2018. Numbers at nodes indicate the bootstrap values based on the maximum likelihood analysis of 1,000 replicates. The scale bar (0.01) represents substitutions per nucleotide position. The rectangles contain the amino acid substitutions per year
Maximum likelihood phylogenetic tree of the VP1 gene nucleotide sequences of FMDV serotype A genotypes circulating in Egypt from 2011 to 2018. Numbers at nodes indicate the bootstrap values based on the maximum likelihood analysis of 1,000 replicates. The scale bar (0.01) represents substitutions per nucleotide position. The rectangles contain the amino acid substitutions per year

Fig. 3

Maximum likelihood phylogenetic tree of the VP1 gene nucleotide sequences of FMDV serotypes SAT2 genotypes circulating in Egypt from 2012 to 2018. Numbers at nodes indicate the bootstrap values based on the maximum likelihood analysis of 1,000 replicates. The scale bar (0.01) represents substitutions per nucleotide position. *– Vaccine strains. The rectangles contain the amino acid substitutions per year
Maximum likelihood phylogenetic tree of the VP1 gene nucleotide sequences of FMDV serotypes SAT2 genotypes circulating in Egypt from 2012 to 2018. Numbers at nodes indicate the bootstrap values based on the maximum likelihood analysis of 1,000 replicates. The scale bar (0.01) represents substitutions per nucleotide position. *– Vaccine strains. The rectangles contain the amino acid substitutions per year

Mean evolutionary rates of the O, A, and SAT2 serotypes

OASAT2
From/ToATCGATCGATCG
Mean evolutionary rates0.030.250.822.900.010.110.613.28-3.163.1618.67

Year distribution of O, A, and SAT2 serotypes of FMDV and vaccine strains in Egypt based on the data in GenBank and WRLFMD

SAT2OAVaccine
GenBankWRLGenBankWRLGenBankWRL
2006000105
2007000803
2008000500
20095

– the serotype recorded in GenBank and missing in WRL

061909
2010002

– the serotype recorded in GenBank and missing in WRL

003
2011000314
2012171911204O, A, SAT2
20132

– the serotype recorded in GenBank and missing in WRL

01

– the serotype recorded in GenBank and missing in WRL

0210A
20141642134O, A, SAT2
O, SAT2
201500063

– the serotype recorded in GenBank and missing in WRL

0No vaccine
20160191231O
O, A, SAT2
201701192201O, A
2018060122O, A, SAT2

Maximum likelihood estimate of substitution matrix-A among O, A, and SAT2 serotypes circulating in Egypt

O serotypeA serotypeSAT2 serotype
AT/UCGAT/UCGAT/UCG
A---
T/U3.47-4.69-3.16-
C3.4718.06-4.6915.62-3.1618.67-
G18.063.473.47-15.624.694.69-18.673.163.16-
eISSN:
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Language:
English
Publication timeframe:
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Journal Subjects:
Life Sciences, Molecular Biology, Microbiology and Virology, other, Medicine, Veterinary Medicine
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