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

	SAT2		O		A		Vaccine

	GenBank	WRL	GenBank	WRL	GenBank	WRL
2006	0	0	0	1	0	5
2007	0	0	0	8	0	3
2008	0	0	0	5	0	0
2009	5*	0	6	19	0	9
2010	0	0	2*	0	0	3
2011	0	0	0	3	1	4
2012	17	19	1	12	0	4	O, A, SAT2
2013	2*	0	1*	0	2	10	A
2014	1	6	4	21	3	4	O, A, SAT2
							O, SAT2
2015	0	0	0	6	3*	0	No vaccine
2016	0	1	9	12	3	1	O
							O, A, SAT2
2017	0	1	19	22	0	1	O, A
2018	0	6	0	1	2	2	O, A, SAT2

* – the serotype recorded in GenBank and missing in WRL

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 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 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

Table 2

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

	O serotype				A serotype				SAT2 serotype

	A	T/U	C	G	A	T/U	C	G	A	T/U	C	G
A	-				-				-
T/U	3.47	-			4.69	-			3.16	-
C	3.47	18.06	-		4.69	15.62	-		3.16	18.67	-
G	18.06	3.47	3.47	-	15.62	4.69	4.69	-	18.67	3.16	3.16	-

[i] Bold letters indicate transitional substitutions, italics indicate transversional substitutions

N.B. The substitution matrix covered the virus isolates from 1993 to 2018 for the O serotype, from 2009 to 2018 for the A serotype, and from 2012 to 2018 for the SAT2 serotype

Table 3

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

		O				A				SAT2
From/To	A	T	C	G	A	T	C	G	A	T	C	G
Mean evolutionary rates	0.03	0.25	0.82	2.90	0.01	0.11	0.61	3.28	-	3.16	3.16	18.67

Articles in this issue

DOI: https://doi.org/10.2478/jvetres-2020-0069 | Journal eISSN: 2450-8608 (formerly 2300-3235)

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Language: English

Page range: 487 - 493

Submitted on: Apr 8, 2020

Accepted on: Oct 6, 2020

Published on: Nov 6, 2020

Published by: National Veterinary Research Institute in Pulawy

In partnership with: Paradigm Publishing Services

Keywords:

disease,

vaccine,

Related subjects:

Microbiology and virology,

Life sciences, other,

Medicine,

Veterinary medicine

© 2020 Abeer F. El Nahas, Sayed A.H. Salem, published by National Veterinary Research Institute in Pulawy
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Volume 64 (2020): Issue 4 (December 2020)

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

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Fig. 1

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Table 2

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