A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Dimitrov, Kiril M.; Sharma, Poonam; Volkening, Jeremy D.; Goraichuk, Iryna V.; Wajid, Abdul; Rehmani, Shafqat Fatima; Basharat, Asma; Shittu, Ismaila; Joannis, Tony M.; Miller, Patti J.; Afonso, Claudio L.

doi:10.1186/s12985-017-0741-5

Virology Journal

Table 3 Summary of sequencing and assembly data of five samples that were identified to have mixed populations of Newcastle disease virus (NDV) and other avian viruses

From: A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Isolate number	% PF reads^a	Number of raw read pairs	Number of filtered read pairs^b	Forward read quality^c	Reverse read quality^c	Identified virus	Final coverage depth^c	Number of reads used for consensus^d	Consensus nucleotide length	Missing positions at 5' end^e	Length of internal gaps	Missing positions at 3' end^e	Percent coverage^f
1003	3.33	546797	540519	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	0\|4229\|6090\|8762\|18055	525597	15127		65		99.57
1003	3.33	546797	540519	2\|37\|38\|38\|38	2\|36\|37\|38\|38	IBV ^g	0\|2\|5\|8\|44	904	23711	269	3644	18	85.78
1005	3.44	564101	123024	2\|36\|37\|38\|38	2\|33\|36\|37\|38	NDV ^h	0\|7\|13\|19\|36	1161	14494	343	272	83	95.41
						AIV ⁱ - PB2	2\|685\|1003\|1446\|2774	16804	2283				100.00
						AIV - PB1	2\|1845\|2896\|3432\|4634	38261	2334				100.00
						AIV - PA	68\|1180\|1496\|1970\|4721	23466	2151				100.00
						AIV - HA	12\|595\|1057\|1598\|2604	14687	1683				100.00
						AIV - NP	25\|886\|1306\|1867\|2563	11252	1497				100.00
						AIV - NA	11\|416\|838\|1030\|1692	7707	1410				100.00
						AIV - M1, M2	11\|210\|811\|1357\|2195	5699	982				100.00
						AIV - NEP, NS1	15\|396\|787\|1222\|1707	3796	838				100.00
1009	3.21	526425	519854	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	0\|4216\|6887\|9403\|18079	485669	15127		65		99.57
						IBV	0\|15\|22\|35\|92	3743	27469	136	19	18	99.37
						AIV - PB2	0\|137\|175\|272\|545	2791	2283				100.00
						AIV - PB1	3\|370\|651\|835\|1177	7692	2324	20			98.99
						AIV - PA	0\|88\|117\|183\|446	1675	2151				100.00
						AIV - HA	0\|113\|256\|342\|578	2399	1683				100.00
						AIV - NP	0\|145\|277\|333\|523	2117	1485				100.00
						AIV - NA	4\|118\|225\|317\|637	2226	1410				100.00
						AIV - M1,M2	2\|46\|132\|183\|246	793	958	24			96.71
						AIV - NEP, NS1	0\|47\|83\|103\|139	368	838				100.00
1011	3.44	565083	538171	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	1\|3272\|5386\|7121\|16101	499378	15192				100.00
						AIV - PB2	0\|181\|290\|462\|1254	6242	2283				100.00
						AIV - PB1	2\|323\|482\|609\|1077	7728	2334				100.00
						AIV - PA	8\|127\|172\|220\|437	2743	2151				100.00
						AIV - HA	3\|217\|449\|685\|906	5306	1683				100.00
						AIV - NP	3\|180\|380\|605\|758	4314	1497				100.00
						AIV - NA	3\|74\|98\|153\|242	1383	1410				100.00
						AIV - M1,M2	4\|59\|255\|372\|579	2092	982				100.00
						AIV - NEP, NS1	3\|29\|70\|137\|216	516	808				100.00
998	1.80	295662	294217	2\|37\|38\|38\|38	2\|35\|37\|38\|38	NDV	0\|2248\|3275\|4719\|11528	280492	15103	20	69		99.41
						AIV - PB2	0\|22\|33\|48\|78	477	2246			34	98.51
						AIV - PB1	0\|34\|56\|85\|125	698	2217			60	97.36
						AIV - PA	2\|28\|55\|106\|178	767	2141	10			99.53
						AIV - HA	0\|9\|18\|29\|53	204	1643			40	97.65
						AIV - NP	0\|24\|43\|82\|126	430	1456	35		6	97.26
						AIV - NA	1\|21\|28\|41\|83	272	1304	31		75	92.23
						AIV - M1,M2	0\|8\|28\|65\|87	196	923	56			92.62
						AIV - NEP, NS1	0\|9\|17\|28\|40	94	810				100.00

^a the fraction of reads assigned to each sample out of all number of reads that passed filter (i.e. pass-filter reads)
^b the number of paired reads remaining after host and internal control filtering
^c numbers represent distribution (minimum | lower quartile | median | upper quartile | maximum)
^d numbers of paired reads used to re-call the final consensus for each sequence
^e for avian influenza viruses, the missing nucleotides refer to the beginning and the end of the coding sequences of the genes
^f the fraction of the expected full genome length covered by the consensus scaffold (i.e. not containing unknown nucleotides), for avian influenza genes, the coverage represents comparison to the coding sequences of the genes only
^g Infectious bronchitis virus
^h coverage depth and number of reads used to re-call the final consensus for this NDV isolate were impacted by the presence of influenza virus A in the sample (influenza reads were estimated to be approximately 98% of all reads, data not shown)
ⁱ Avian influenza virus; PB2 = segment 1 polymerase PB2; PB1 = segment 2 polymerase PB1; PA = segment 3 polymerase PA; HA = segment 4 hemagglutinin; NP = segment 5 nucleocapsid protein; NA = segment 6 neuraminidase; M1, M2 = segment 7 matrix protein 1 and matrix protein 2; NEP = segment 8 nuclear export protein and nonstructural protein 1

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ISSN: 1743-422X

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