TABLE 1.

Highly translated viral mRNAs and their encoded protein function categories at 2, 4, and 8 h post-VACV infection

Time of expression and VACV WR ORFa	VACV Copenhagen ORF	Temporal expressionb	Functional category	No. of readsc
2 h
009/210	C11R	E	Host interaction	21,247,140
103	H5R	E/Ld	Transcription	19,521,388
18		E	Unknown	18,505,965
59	E3L	E	Host interaction	16,992,412
72	I3L	E	DNA replication	12,105,947
89	L2R	E	Virion association	8,753,364
29	N2L	E	Host interaction	6,987,681
200	B19R	E	Host interaction	6,446,599
172	A46R	E	Host interaction	5,931,269
41	F2L	E	DNA replication	5,731,347
4 h
70	I1L	I	Virion association	31,221,695
133	A14L	L	Virion association	27,674,145
56	F17R	L	Virion association	18,595,167
131	A12L	I	Virion association	17,138,138
103	H5R	E/L	Transcription	15,370,215
132	A13L	L	Virion association	12,605,197
139	A19L	I	Virion association	11,987,935
137	A17L	L	Virion association	11,388,463
28	N1L	E/Ld	Host interaction	11,342,780
157	A34R	I	Virion association	9,677,241
8 h
133	A14L	L	Virion association	32,690,917
70	I1L	I	Virion association	24,134,410
167	A42R	I	Virion association	18,693,389
56	F17R	L	Virion association	17,013,444
131	A12L	I	Virion association	16,613,835
28	N1L	E/L	Host interaction	14,260,755
103	H5R	E/L	Transcription	13,848,524
132	A13L	L	Virion association	12,915,930
139	A19L	I	Virion association	12,450,056
137	A17L	L	Virion association	10,427,057

^aFor each time period post-VACV infection, the top 10 most highly translated mRNAs are listed.

^bThe classification is according to Yang et al. (22, 48). E, early; I, intermediate; L, late.

^cThe mRNAs are listed in rank order in terms of the normalized number of reads mapped to the ORF.

^dThe L-stage promoter was not distinguished from the intermediate one.