Comparative genomic analysis of two emergent human adenovirus type 14 respiratory pathogen isolates in China reveals similar yet divergent genomes

Figures & data

Table 1 The genome, fiber, hexon, and E1A sequences of adenovirus species A–G used in this study

Type	Strain	Year isolated	Country	Sequence	GenBank accession no.
HAdV-A12	Huie	1954	USA	Genome	AC_000005
HAdV-B3	GB	1953	USA	Genome	AY599834
HAdV-B7	Gomen	1952	USA	Genome	AY594255
HAdV-B11p	Slobitski	1956	USA	Genome	NC_011202
HAdV-B11a	273	1969	Spain	E1A Fiber Hexon	FJ841916 FJ841908 FJ841900
HAdV-B11a	6380	1997	USA	E1A Fiber Hexon	FJ841919 FJ841907 FJ841899
HAdV-B11a	2474	2001	Taiwan	E1A Fiber Hexon	FJ841922 FJ841914 FJ841906
HAdV-B11a	760	2002	Taiwan	E1A Fiber Hexon	FJ841921 FJ841913 FJ841905
HAdV-B11a	RKI-2797-04	2004	Turkey	Fiber Hexon	AY972816 AY972815
HAdV-B11a	SNG1222	2005	Singapore	E1A Fiber Hexon	FJ841920 FJ841912 FJ841904
HAdV-B14p	de Wit	1955	Netherlands	Genome	AY803294
HAdV-B14p	16845	1974	Netherlands	E1A Fiber Hexon	FJ841917 FJ841910 FJ841902
HAdV-B14p1	2971	2007	USA	E1A Fiber Hexon	FJ841915 FJ841909 FJ841901
HAdV-B14p1	Dublin	2009	Ireland	Fiber Hexon	HQ163916 HQ265808
HAdV-B14p1	303600	2007	USA	Genome	FJ822614
HAdV-B14p1	BJ430	2010	China	Genome	JN032132
HAdV-B14p1	GZ01	2010	China	Genome	JQ824845
HAdV-B14p1	CHN2012	2012	China	Genome	JX892927
HAdV-B14	Gansu2011-01	2011	China	Hexon	JX310315
HAdV-B16	ch.79	1955	USA	Genome	AY601636
HAdV-B21	AV-1645	1956	Saudi Arabia	Genome	AY601633
SAdV-21	Bertha	1954	USA	Genome	AC_000010
HAdV-B34p	Compton	1972	USA	Genome	AY737797
HAdV-B35p	Holden	1973	USA	Genome	AY128640
HAdV-B50	Wan	1988	USA	Genome	AY737798
HAdV-B55	QS-DLL	2006	China	Genome	FJ643676
HAdV-C1	Adenoid 71	1953	USA	Genome	AF534906
HAdV-D9	Hicks	1954	USA	Genome	AJ854486
HAdV-E4	RI-67	1952	USA	Genome	AY594253
HAdV-F40	Dugan	1979	Netherlands	Genome	NC_001454
HAdV-G52	T03-2244	2003	USA	Genome	DQ923122

The genome of HAdV-B14p1 GZ01 is shown in boldface.

Figure 1 Genomic organization and transcription map of HAdV-B14p1 strain GZ01. The grey arrows indicate the early, intermediate, and late transcription units; the red arrows indicate coding regions. Arrows reflect the direction of the coding transcripts.

Figure 2 Identification of the genome types of HAdV-B14 strains GZ01 (Guangzhou), BJ430 (Beijing), and CHN2012 (Beijing). The in silico restriction enzyme analysis (REA) digestion patterns of HAdV-14 genomes were generated using the Vector NTI 10.3.0 software (Invitrogen Corp., San Diego, CA, USA). Genome digestion patterns of the strains are as follows: (A) de Wit or prototype (AY803294); (B) GZ01 (JQ824845); (C) 303600, reported as HAdV-B14p1 (FJ822614); (D) BJ430 (JN032132); and (E) CHN2012 (JX892927). These were analyzed with BamHI, BclI, Bgll, BglII, BstEII, EcoRI, HindIII, HpaI, SalI, SmaI, XbaI, and XhoI, as described by Li et al.⁵⁹ All the three recent China outbreak genomes correspond to the genome type of HAdV-14p1 and have identical REA profiles to each other. They are divergent from the HAdV-B14 prototype (1955). M: 1 kb DNA Sizing Ladder.

Figure 3 HAdV-B Inverted terminal repeats (ITR) analysis. An alignment of the left ITRs of select HAdV-B prototypes is presented, with two sets of critical sequence motifs (boxed): (1) Replication- Core origin, NF I and NF III binding sites, and (2) Sp1 and ATF binding sites. Nota bene, ‘.’ represent identical bases and ‘-’ represent deletions or gapping for sequence alignment. HAdV-B1: HAdV-B3, -B7, -B16, -B21, and -B50; HAdV-B2: HAdV-B11, -B14, -B34, -B35, and -B55.

Figure 4 Phylogenetic analysis of the E1A, fiber, and hexon genes, as well as the whole genome sequences, from all HAdV-B14 strains and representatives of other HAdV species. Nucleotide sequences of the E1A, fiber, and hexon genes, as well as limited whole genomes, are available from GenBank. Taxon names include GenBank acc. no., isolation country, strain name, and year of isolation. Phylogenetic trees were generated by using the neighbor-joining method with 1000 replicates and constructed by the MEGA 5.1.0 software (http://www.ebi.ac.uk/tools/mafft). In these analyses, default parameters were applied, with a maximum-composite-likelihood model. Bootstrap numbers shown at the nodes indicate the percentages of 1000 replications producing the clade, with values above 80 considered robust. The scale bar is in units of nucleotide substitutions per site. The China HAdV-B14 strains were indicated with filled triangles.

Figure 5 Global genome mutation map visualization of the alignment of genomes from HAdV-14 strains de Wit, 303600, BJ430, GZ01, and CHN2012. To assess the lineages and molecular evolution relationships of these pathogens, Genome Mutation Mapper (GMM; unpublished beta version) is used to provide a global visualization of the nucleotide differences, including insertions and deletions (indels). The contemporaneously circulating and independently isolated HAdV-B14p1 strains have divergent, yet similar mutation profiles, with the indels defining their lineages. For this analysis, the genome of HAdV-14p1_303600/USA/2007 is set as the reference to which the other genomes are compared. Query 1: HAdV-B14p_deWit/The Netherlands/1955 (prototype); Query 2: HAdV-B14p1_BJ430/China//2010; Query 3: HAdV-14p1_GZ01/China/2010; and Query 4: HAdV-B14p1_CHN2012/China/2012. The triangles and inverted triangles indicate deletions and insertions, respectively; blue hash lines indicate base substitutions. Select gene markers are displayed for reference (locations are approximate), as are the genome size markers noted along the bottom.

Table 2 Comparison of Mutations Across the Genomes of four HAdV-B14 Strains

Position	Region	Product	14p deWit	14p1 BJ430	14p1 GZ01	CHN 2012	Non-synonymous Substitution				Synonymous Substitution
							14p deWit	14p1 BJ430	14p1 GZ01	CHN 2012	14p deWit	14p1 BJ430	14p1 GZ01	CHN 2012
68	ITR	—	C -> T	—	—	—	—	—	—	—	—	—	—	—
134	ITR	—	—	—	—	C -> G	—	—	—	—	—	—	—	—
141	NCR	poly(T)	▾ T	—	—	▾ T	—	—	—	—	—	—	—	—
200	NCR	—	C -> T	—	—	—	—	—	—	—	—	—	—	—
202	NCR	—	C -> T	—	—	—	—	—	—		—	—	—	—
209	NCR	—	G -> C	—	—	—	—	—	—		—	—	—	—
222	NCR	—	T -> C	—	—	—	—	—	—		—	—	—	—
225	NCR	—	—	—	C -> T	—	—	—	—	—	—	—	—	—
403	NCR	—	—	—	—	G -> A	—	—	—	—	—	—	—	—
491	NCR	—	—	—	—	G -> A	—	—	—	—	—	—	—	—
604	E1A	29.1K 25.7K 6.5K	C -> A	—	—	—	L -> M	—	—	—	—	—	—	—
729	E1A	29.1K 25.7K	—	—	G -> A		—	—	—	—			L -> L
879	E1A	29.1K 25.7K	T -> C	—	—	—	—	—	—	—		—	—	—
887	E1A	29.1K 25.7K	G -> C	—	—	—	G -> A	—	—	—	—	—	—	—
989	E1A	29.1K 25.7K	T -> C	—	—	—	F -> S	—	—	—	—	—	—	—
1028	E1A	29.1K 25.7K	▴GTG	—	—	—	SV -> I	—	—	—	—	—	—	—
1229	E1A	Intron	G -> A	—	—	—	—	—	—	—	—	—	—	—
1299	E1A	29.1K 25.7K	—	A -> G	A -> G	—	—	—	—	—	S -> S	—	S -> S
1299	E1A	6.5K	—	A -> G	A -> G			H -> R	H -> R		—	—	—	—
1392	E1A	29.1K 25.7K	T -> C	—	—	—	—	—	—	—	L -> L	—	—	—
1537	NCR	—	T -> G	—	—	—	—	—	—	—	—	—	—	—
1538	NCR	—	C -> T	—	—	—	—	—	—	—	—	—	—	—
1553	NCR	—	A -> C	—	—	—	—	—	—	—	—	—	—	—
1801	E1B	20K	C -> T	—	—	—	—	—	—	—	C -> C	—	—	—
1903	E1B	20K	—	T -> C	T -> C	—	—	—	—	—		A -> A	A -> A
2852	E1B	54.9K	A -> G	A -> G	A -> G	A -> G	K -> R	K -> R	K -> R	K -> R	—	—	—	—
3015	E1B	54.9K	T -> A	—	—	—	—	—	—	—	G -> G	—	—	—
3265	E1B	54.9K	G -> A	—	—	—	A -> T	—	—	—	—	—	—	—
3927	IX	poly(A)	▾AA	▴A	▴A	▴A	—	—	—	—	—	—	—	—
4273	IV2a	IVa2	A -> G	—	—	—	—	—	—	—	L -> L	—	—	—
4515	IV2a	IVa2	A -> G	—	—	—	—	—	—	—	H -> H	—	—	—
4848	IV2a	IVa2	A -> T	—	—	—	H -> Q	—	—	—	—	—	—	—
6248	E2B	Polymerase	C -> T	—	—	—	—	—	—	—	E -> E	—	—	—
6913	E2B	Polymerase	C -> G	—	—	—	E -> Q	—	—	—	—	—	—	—
7207	E2B	Polymerase	G -> C	—	—	—	L -> V	—	—	—	—	—	—	—
7757	E2B	Polymerase	C -> T	—	—	—	—	—	—	—	G -> G	—	—	—
7772	E2B	Polymerase	A -> G	—	—	—	—	—	—	—	V -> V	—	—	—
7877	E2B	Polymerase	C -> T	—	—	—	—	—	—	—	P -> P	—	—	—
7911	E2B	Polymerase		G -> C	G -> C		—	—	—	—	—	S -> S	S -> S	—
8300	E2B	Polymerase	—	C -> G	—	—	—	K -> N	—	—	—	—	—	—
8701	E2B	pTP	A -> G	—	—	—	—	—	—	—	A -> A	—	—	—
9532	E2B	pTP	G -> A	—	—	—	—	—	—	—	I -> I	—	—	—
9943	E2B	pTP	G -> A	—	—	—	—	—	—	—	V -> V	—	—	—
10085	E2B	pTP	G -> T	—	—	—	P -> H	—	—	—	—	—	—	—
10135	E2B	pTP	G -> A	—	—	—	—	—	—	—	I -> I	—	—	—
10303	E2B	pTP	A -> G	—	—	—	—	—	—	—	A -> A	—	—	—
10658	NCR	poly(T)	▾T	▾TT	▾TTTTT	▾T	—	—	—	—	—	—	—	—
10685	E2B/L1	43K	T -> A	T -> A	T -> A	T -> A	—	—	—	—	R -> R	R -> R	R -> R	R -> R
11187	E2B/L1	43K	C -> T	—	—	—	—	—	—	—	T -> T	—	—	—
11304	E2B/L1	43K	T -> C	—	—	—	—	—	—	—	F -> F	—	—	—
11420	E2B/L1	43K	—	—	—	C -> T	—	—	—	—	—	—	—	A -> A
11532	E2B/L1	43K	C -> T	—	—	—	—	—	—	—	R -> R	—	—	—
11805	E2B/L1	43K	A -> G	—	—	—	—	—	—	—	E -> E	—	—	—
12088	E2B/L1	pIII	G -> A	—	—	—	—	—	—	—	V -> V	—	—	—
12268	E2B/L1	pIII	G -> T	—	—	—	—	—	—	—	L -> L	—	—	—
13013	E2B/L1	pIII	T -> C	—	—	—	—	—	—	—	L -> L	—	—	—
13266	E2B/L1	poly(A)	—	▾A	▾AA	—	—	—	—	—	—	—	—	—
13691	NCR	—	C -> T	—	—	—	—	—	—	—	—	—	—	—
14687	L2	PENTON	C -> T	—	—	—	S -> F	—	—	—	—	—	—	—
14788	L2	Penton	A -> G	—	—	—	N -> D	—	—	—	—	—	—	—
15568	L2	VII	T -> C	—	—	—	—	—	—	—	I -> I	—	—	—
15739	L2	VII	—	G -> A	G -> A	—	—	—	—	—	—	L -> L	L -> L	—
16867	L2	pV	T -> C	—	—	—	—	—	—	—	Y -> Y	—	—	—
17348	NCR	poly(A)	—	▴A	▴A	▴A	—	—	—	—	—	—	—	—
17408	L3	VI	G -> A	—	—	—	D -> N	—	—	—	—	—	—	—
17594	L3	VI	—		G -> A		—	—	R -> K	—	—	—	—	—
17618	L3	VI	—	—	G -> A	—	—	—	—	—	—	—	Q -> Q	—
18944	L3	Hexon	G -> A	—	—	—	—	—	—	—	K -> K	—	—	—
19593	L3	Hexon	A -> G	A -> G	A -> G	A -> G	—	—	—	—	K -> K	K -> K	K -> K	K -> K
19748	L3	Hexon	A -> G	—	—	—	I -> M	—	—	—	—	—	—	—
20309	L3	HEXON	A -> G	—	—	—	—	—	—	—	L -> L	—	—	—
21810	NCR	—	T -> C	—	—	—	—	—	—	—	—	—	—	—
22886	E2A	DBP	A -> G	—	—	—	—	—	—	—	G -> G	—	—	—
22923	E2A	DBP	—	—	C -> T	—	—	—	—	—	—	—	K -> K	—
23153	E2A	DBP	G -> A	—	—	—	—	—	—	—	P -> P	—	—	—
24008	L4	100K	T -> C	T -> C	T -> C	T -> C	—	—	—	—	I -> I	I -> I	I -> I	I -> I
24325	L4	100K	C -> T	—	—	—	—	—	—	—	V -> V	—	—	—
24453	L4	100K	G -> A	—	—	—	G -> D	—	—	—	—	—	—	—
25117	L4	100K	A -> G	—	—	—	—	—	—	—	L -> L	—	—	—
25481	L4	100K	T -> C	—	—	—	—	—	—	—	L -> L	—	—	—
26048	L4	22K 33K	G -> A	—	—	—	—	—	—	—	P -> P	—	—	—
26112	L4	22K 33K	G -> A	—	—	—	V -> I	—	—	—	—	—	—	—
26923	L4	VIII	A -> G	—	—	—	—	—	—	—	P -> P	—	—	—
27569	E3	14.6K	G -> A	—	—	—	V -> I	—	—	—	—	—	—	—
27698	E3	14.6K	A -> G	—	—	—	T -> A	—	—	—	—	—	—	—
28128	E3	18.4K	C -> T	—	—	—	—	—	—	—	F -> F	—	—	—
28139	E3	18.4K	A -> C	—	—	—	K -> T	—	—	—	—	—	—	—
28568	E3	20.1K	G -> A	—	—	—	V -> I	—	—	—	—	—	—	—
28952	E3	20.8K	T -> C	—	—	—	V -> A	—	—	—	—	—	—	—
29022	E3	20.8K	G -> A	—	—	—	—	—	—	—	Q -> Q	—	—	—
29223	E3	20.8K	A -> G	—	—	—	—	—	—	—	A -> A	—	—	—
29277	E3	20.8K	A -> T	—	—	—	K -> N	—	—	—	—	—	—	—
29312	E3	20.8K	—	—	—	T -> C	—	—	—	S -> P	—	—	—	—
29335	E3	20.8K	C -> T	—	—	—	P -> S	—	—	—	—	—	—	—
29481	NCR	poly(T)	—	▴T	—	—	—	—	—	—	—	—	—	—
29758	E3	10.1K	T -> C	—	—	—	—	—	—	—	I -> I	—	—	—
30054	E3	15.2K	C -> T	—	—	—	H -> Y	—	—	—	—	—	—	—
30057	E3	15.2K	C -> T	—	—	—	P -> S	—	—	—	—	—	—	—
30621	U	U	G -> A	—	—	—	—	—	—	—	F -> F	—	—	—
30733	U	U	—	G -> A	G -> A	—	—	—	—	—	—	I -> I	I -> I	—
31546	L5	FIBER	▾AGAAAA	—	—	—	▾KE	—	—	—	—	—	—	—
31561	L5	FIBER	C -> T	—	—	—	—	—	—	—	T -> T	—	—	—
31786	NCR	—	—	G-> C	G-> C	—	—	—	—	—	—	—	—	—
31791	NCR	Poly(A)	▴A	▴A	▴A	▴A	—	—	—	—	—	—	—	—
31797	NCR	—	T -> C	—	—	—	—	—	—	—	—	—	—	—
31940	E4	ORF6/7	T -> G	—	—	—	Y -> S	—	—	—	—	—	—	—
31979	E4	ORF6/7	G -> T	—	—	—	A -> D	—	—	—	—	—	—	—
32017	E4	ORF6/7	C -> A	—	—	—	Q -> H	—	—	—	—	—	—	—
32028	E4	—	—	—	—	C -> T	—	—	—	—	—	—	—	—
33005	E4	ORF4	C -> T	—	—	—	R -> K	—	—	—	—	—	—	—
33492	E4	ORF3	G -> T	—	—	—	—	—	—	—	R -> R	—	—	—
33614	E4	ORF2	C -> T	—	—	—	—	—	—	—	L -> L	—	—	—
33874	E4	ORF2	C -> G	—	—	—	E -> Q	—	—	—	—	—	—	—
34016	E4	ORF1	T -> C	—	—	—	—	—	—	—	L -> L	—	—	—
34205	E4	ORF1	G -> C	—	—	—	F -> L	—	—	—	—	—	—	—
34254	E4	ORF1	G -> T	—	—	—	S -> Y	—	—	—	—	—	—	—
34471	NCR	—	G -> A	—	—	—	—	—	—	—	—	—	—	—
34498	NCR	poly(A)	▴A	—	—	▴A	—	—	—	—	—	—	—	—
34534	NCR	—	—	—	—	C -> G	—	—	—	—	—	—	—	—
34549	NCR	—	A -> C	—	—	—	—	—	—	—	—	—	—	—
34553	NCR	poly(A)	▴AA	—	—	—	—	—	—	—	—	—	—	—
34700	ITR	—	G -> A	—	—	—	—	—	—	—	—	—	—	—

HAdV-B14 prototype (de Wit; 1955), GZ01 (2010), BJ430 (2010), and CHN2012 genomes are analyzed with respect to base substitutions (SNPs) and insertions and deletions (indels), using the 2007 U.S. strain 303600 as reference. Nucleotide and amino acid sequence changes are noted, along with their genome locations and coding consequences. Abbreviations and symbols are as follows: inverted terminal repeat, ITR; non-coding region, NCR; insertion, ▾; deletion, ▴; no change or not applicable, -.

Li QG, Zheng QJ, Liu YHet al.Molecular epidemiology of adenovirus types 3 and 7 isolated from children with pneumonia in Beijing. J Med Virol 1996;49: 170–177.

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