Novel patterns of the Epstein-Barr nuclear antigen (EBNA-1) V-Val subtype in EBV-associated nasopharyngeal carcinoma from Vietnam

LD Thuan; ND Kha; NT Minh; LHA Thuy

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Novel patterns of the Epstein-Barr nuclear antigen (EBNA-1) V-Val subtype in EBV-associated nasopharyngeal carcinoma from Vietnam

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| Aug 28, 2019

Balkan Journal of Medical Genetics

Volume 22 (2019): Issue 1 (June 2019)

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Published Online: Aug 28, 2019

Page range: 61 - 68

DOI: https://doi.org/10.2478/bjmg-2019-0011

Keywords
Epstein-Barr nuclear antigen (EBNA-1), Epstein-Barr virus (EBV), V-val, Variation

© 2019 Thuan LD, Kha ND, Minh NT, Thuy LHA, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Schematic of the EBNA-1 gene and position of primers aligned with B95-8 strain (V10555). Primer 1: EBNA-1-1; primer 2: EBNA-1-2; primer 3: EBNA-1-3 and primer 4: EBNA-1-4.

Electrophoresis of nested-PCR products of the represented NPC biopsy samples. T91, T92, T93, T94, T95, T96: clinical biopsy samples; N: negative control; MW: molecular weight 100 bp.

Represented sequence identification of EBNA-1 subtype based on the amino acid at position 487. A) T91: V-Val subtype; B) V-Leu subtype; C) P-Thr subtype; D) P-Ala subtype.

Represented nucleotide substitution consensus changes indicated by T5. Amino acid at position: A) codon 497; B) codon 499; C) codon 502; D) codon 520; E) codon 524; F) codon 553; G) codon 594.

Represented nucleotide/amino acid additional changes: A) codon 585 by T6; B) codons 528 and 529 by T77; C) codon 588 by T77; D) codon 492 by T75.

The sequence of primers used in two stages nested-PCR.

Stage	Primers	Sequences	Temperature
1	EBNA-1-1	5'-TAG TCA GTC ATC ATC ATC CG-3'	55 °C
	EBNA-1-2	5'-GGG ATT TAT TCT TTA GTG CG-3'

2	EBNA-1-3	5'-GCC ATT TTT CCA CCC TGT AG-3'
	EBNA-1-4	5'-ATT GAG GGC GTC TCC TAA CA-3'	60 °C

The comparison between the patterns of the current study and the previous sequences.

Codon		487	492	499	502	520	524	528	529	533	553	585	588	594
Pattern 1	T5	Val	Ser	Glu	Asn	Leu	Ile	Val	Pro	Ile	Pro	Thr	Ala	Lys
Pattern 2	T6	⋅	·	·	·	⋅	⋅	⋅	⋅	⋅	⋅	Ile	⋅	⋅
Pattern 3	T77	⋅	⋅	⋅	⋅	⋅	⋅	Ile	Gin	Leu	⋅	Ile	Pro	⋅
Pattern 4	T70	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	Ile	Pro	⋅
Pattern 5	T75	⋅	•/Cys	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	Ile	Pro	⋅
Study 1	GC4	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅
Study 2		⋅	⋅	⋅	Thr	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅

Nucleotide and amino acid substitution in EBNA-1 C-terminal domain compared to B95-8B sequence.

B95-8	109408	109409	109410	109423	109424	109425	109444	109445	109446	109447	109448	109449	109453	109454	109455	109507	109508	109509	109519	109520	109521
	487			492			499			500			502			520			524
	G	C	T	A	G	T	G	A	C	G	A	A	A	C	T	C	T	A	A	C	T
	Ala			Ser			Asp			Glu			Thr			Leu			Thr
T5	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	C	⋅	T	⋅
T5	Val			*			Glu			*			Asn			+			Ile
T6	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	C	⋅	T	⋅
T6	Val			*			Glu			*			Asn			+			Ile
T77	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T77	Val			*			Glu			*			Asn			+			Ile
T70	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T70	Val			*			Glu			*			Asn			+			Ile
T75	⋅	T	⋅	T	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T75	Val			Cys			Glu			*			Asn			+			Ile

eISSN:: 1311-0160
Language:: English

Publication timeframe:: 2 times per year
Journal Subjects:: Medicine, Basic Medical Science, other

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Novel patterns of the Epstein-Barr nuclear antigen (EBNA-1) V-Val subtype in EBV-associated nasopharyngeal carcinoma from Vietnam

Article Category: Original Article

Published Online: Aug 28, 2019

Page range: 61 - 68

DOI: https://doi.org/10.2478/bjmg-2019-0011

Keywords
Epstein-Barr nuclear antigen (EBNA-1), Epstein-Barr virus (EBV), V-val, Variation

© 2019 Thuan LD, Kha ND, Minh NT, Thuy LHA, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

The sequence of primers used in two stages nested-PCR.

The comparison between the patterns of the current study and the previous sequences.

Nucleotide and amino acid substitution in EBNA-1 C-terminal domain compared to B95-8B sequence.

B95-8	109408	109409	109410	109423	109424	109425	109444	109445	109446	109447	109448	109449	109453	109454	109455	109507	109508	109509	109519	109520	109521
	487			492			499			500			502			520			524
	G	C	T	A	G	T	G	A	C	G	A	A	A	C	T	C	T	A	A	C	T
	Ala			Ser			Asp			Glu			Thr			Leu			Thr
T5	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	C	⋅	T	⋅
T5	Val			*			Glu			*			Asn			+			Ile
T6	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	C	⋅	T	⋅
T6	Val			*			Glu			*			Asn			+			Ile
T77	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T77	Val			*			Glu			*			Asn			+			Ile
T70	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T70	Val			*			Glu			*			Asn			+			Ile
T75	⋅	T	⋅	T	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T75	Val			Cys			Glu			*			Asn			+			Ile

B95-8	109408	109409	109410	109423	109424	109425	109444	109445	109446	109447	109448	109449	109453	109454	109455	109507	109508	109509	109519	109520	109521
	487			492			499			500			502			520			524
	G	C	T	A	G	T	G	A	C	G	A	A	A	C	T	C	T	A	A	C	T
	Ala			Ser			Asp			Glu			Thr			Leu			Thr
T5	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	C	⋅	T	⋅
T5	Val			*			Glu			*			Asn			+			Ile
T6	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	C	⋅	T	⋅
T6	Val			*			Glu			*			Asn			+			Ile
T77	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T77	Val			*			Glu			*			Asn			+			Ile
T70	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T70	Val			*			Glu			*			Asn			+			Ile
T75	⋅	T	⋅	T	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T75	Val			Cys			Glu			*			Asn			+			Ile

Novel patterns of the Epstein-Barr nuclear antigen (EBNA-1) V-Val subtype in EBV-associated nasopharyngeal carcinoma from Vietnam

Article Category: Original Article

Published Online: Aug 28, 2019

Page range: 61 - 68

DOI: https://doi.org/10.2478/bjmg-2019-0011

KeywordsEpstein-Barr nuclear antigen (EBNA-1), Epstein-Barr virus (EBV), V-val, Variation

© 2019 Thuan LD, Kha ND, Minh NT, Thuy LHA, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

The sequence of primers used in two stages nested-PCR.

The comparison between the patterns of the current study and the previous sequences.

Nucleotide and amino acid substitution in EBNA-1 C-terminal domain compared to B95-8B sequence.

Keywords
Epstein-Barr nuclear antigen (EBNA-1), Epstein-Barr virus (EBV), V-val, Variation

B95-8	109408	109409	109410	109423	109424	109425	109444	109445	109446	109447	109448	109449	109453	109454	109455	109507	109508	109509	109519	109520	109521
	487			492			499			500			502			520			524
	G	C	T	A	G	T	G	A	C	G	A	A	A	C	T	C	T	A	A	C	T
	Ala			Ser			Asp			Glu			Thr			Leu			Thr
T5	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	C	⋅	T	⋅
T5	Val			*			Glu			*			Asn			+			Ile
T6	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	C	⋅	T	⋅
T6	Val			*			Glu			*			Asn			+			Ile
T77	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T77	Val			*			Glu			*			Asn			+			Ile
T70	⋅	T	⋅	⋅	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T70	Val			*			Glu			*			Asn			+			Ile
T75	⋅	T	⋅	T	⋅	⋅	⋅	⋅	G	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	c	⋅	T	⋅
T75	Val			Cys			Glu			*			Asn			+			Ile