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

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

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.

Table 2

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	109531	109532	109533	109534	109535	109536	109546	109547	109548	109606	109607	109608	109702	109703	109704	109711	109712	109713	109729	109730	109731
	528			529			533			553			585			588			594
	A	T	T	C	C	A	C	T	T	C	C	G	A	C	A	G	C	T	A	G	G
	Ile			Pro			Leu			Pro			Thr			Ala			Arg
T5	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	⋅	⋅	⋅	A	⋅
T5	Val			*			Ile			+			*			*			Lys
T6	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	⋅	⋅	⋅	⋅	A	⋅
T6	Val			*			Ile			+			Ile			*			Lys
T77	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T77	*			Gin			*			+			Ile			Pro			Lys
T70	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T70	Val			*			Ile			+			Ile			Pro			Lys
T75	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T75	Val			*			Ile			+			Ile			Pro			Lys

[i] NB: The top four rows correspond to the nucleotide, amino acid position, nucleotide and amino acid of B95-8 prototype sequence. In each row, the upper character denoted the nucleotide that is different to the B95-8 prototype sequence. Conversely, the dot (•) denotes the same nucleotide compared to the referent sequence. The characters below indicate the amino acid written in the three letter code that is different to the reference sequence, while the asterisk (*) indicates the unchanged amino acid, and the plus sign (+) indicates the silent amino acid changes.

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.

Table 3

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	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅	⋅

[i] NB: The EBNA-1 sequence variants in study 1 [19] and study 2 [16]. The dot (•) denotes the same nucleotide compared to each of the sequences.

References

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Articles in this issue

DOI: https://doi.org/10.2478/bjmg-2019-0011 | Journal eISSN: 2199-5761 (formerly 1311-0160) | Journal ISSN: 1311-0160

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Language: English

Page range: 61 - 68

Published on: Aug 28, 2019

Published by: Macedonian Academy of Sciences and Arts

In partnership with: Paradigm Publishing Services

Keywords:

Epstein-Barr nuclear antigen (EBNA-1),

Epstein-Barr virus (EBV),

V-val,

Variation

Related subjects:

Medicine,

Basic medical science,

Basic medical science, other

© 2019 LD Thuan, ND Kha, NT Minh, LHA Thuy, published by Macedonian Academy of Sciences and Arts
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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

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

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Table 1

Figure 2

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Table 2

Figure 4

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Table 3

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B95-8	109531	109532	109533	109534	109535	109536	109546	109547	109548	109606	109607	109608	109702	109703	109704	109711	109712	109713	109729	109730	109731
	528			529			533			553			585			588			594
	A	T	T	C	C	A	C	T	T	C	C	G	A	C	A	G	C	T	A	G	G
	Ile			Pro			Leu			Pro			Thr			Ala			Arg
T5	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	⋅	⋅	⋅	A	⋅
T5	Val			*			Ile			+			*			*			Lys
T6	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	⋅	⋅	⋅	⋅	A	⋅
T6	Val			*			Ile			+			Ile			*			Lys
T77	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T77	*			Gin			*			+			Ile			Pro			Lys
T70	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T70	Val			*			Ile			+			Ile			Pro			Lys
T75	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T75	Val			*			Ile			+			Ile			Pro			Lys

B95-8	109531	109532	109533	109534	109535	109536	109546	109547	109548	109606	109607	109608	109702	109703	109704	109711	109712	109713	109729	109730	109731
	528			529			533			553			585			588			594
	A	T	T	C	C	A	C	T	T	C	C	G	A	C	A	G	C	T	A	G	G
	Ile			Pro			Leu			Pro			Thr			Ala			Arg
T5	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	⋅	⋅	⋅	A	⋅
T5	Val			*			Ile			+			*			*			Lys
T6	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	⋅	⋅	⋅	⋅	A	⋅
T6	Val			*			Ile			+			Ile			*			Lys
T77	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T77	*			Gin			*			+			Ile			Pro			Lys
T70	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T70	Val			*			Ile			+			Ile			Pro			Lys
T75	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T75	Val			*			Ile			+			Ile			Pro			Lys

B95-8	109531	109532	109533	109534	109535	109536	109546	109547	109548	109606	109607	109608	109702	109703	109704	109711	109712	109713	109729	109730	109731
	528			529			533			553			585			588			594
	A	T	T	C	C	A	C	T	T	C	C	G	A	C	A	G	C	T	A	G	G
	Ile			Pro			Leu			Pro			Thr			Ala			Arg
T5	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	⋅	⋅	⋅	A	⋅
T5	Val			*			Ile			+			*			*			Lys
T6	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	⋅	⋅	⋅	⋅	A	⋅
T6	Val			*			Ile			+			Ile			*			Lys
T77	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T77	*			Gin			*			+			Ile			Pro			Lys
T70	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T70	Val			*			Ile			+			Ile			Pro			Lys
T75	G	⋅	⋅	⋅	⋅	⋅	A	⋅	⋅	⋅	⋅	A	⋅	T	⋅	C	⋅	⋅	⋅	A	⋅
T75	Val			*			Ile			+			Ile			Pro			Lys