Ambisense polarity of genome RNA of orthomyxoviruses and coronaviruses

Table 1 RNA segments of influenza A virus genome and encoded polypeptides

Viral RNA segments and their length (nt)1	Positive sense polypeptides (mol. wt., kDa)2	Negative stranded polypeptides, NSPs (mol. wt.; a.a.)3
PB1 (2341)	PB1 (86.6); PB1-N40 (89.4); PB1-F2 (10.5)	NSP1 (174, 239)
PB2 (2341)	PB2 (85.7); PB2-S1 (55)	NSP2 (116, 121, 130, 137)
PA (2223)	PA (84.2); PA-X (29); PA-N155 (62); PA-N182 (60)	NSP3 (95, 109)
HA (1778)	HA (61.5)	NSP4 (n.d.)
NP (1565)	NP (56.1); eNP (56.8)	NSP5 (117, 154)
NA (1413)	NA (50.1); NA43 (48.6)	NSP6 (91, 154)
M (1097)	M1 (27.8); M2 (11); M42 (13)	NSP7 (99, 102, 109)
NS (890)	NS1 (26.8); NEP (14.2); NS3 (21); tNS1 (17)	NSP8 (93, 167, 216)

¹RNA segments and nucleotide (nt) calculations were made for the A/PR8/34 (H1N1) virus.

²Canonical influenza A virus polypeptides synthesized through the negative genome strategy (Figure 1; for review see[1]).

³Negative stranded genomic open reading frames (ORFs) and predicted negative stranded proteins (NSPs) have been calculated for A/PR8/34 (H1N1) and A/Aichi/2/68 (H3N2) viruses[3-8]. Negative stranded ORFs were identified by in silico approach using the Open Reading Frame Finder program (https://www.ncbi.nlm.nih.gov/orffinder/). These ORFs can be realized through the positive genome strategy. The amino acid length (a.a.) of NSPs were based on the data presented mainly in ref.[8]. A.a. values reflect variations among human, avian and other mammalian virus strains. N.d. means the absence of ORFs longer than 90 a.a. NSP: Negative stranded protein.

Table 2 Negative sense genes in genomes of coronaviruses

Virus genera	Viral genomes	Number of NSGs in virus genome1,3	M.W. range of the NGPs2
Alpha-coronaviruses	HCov-229E: https://www.ncbi.nlm.nih.gov/nuccore/NC_002645.1	29/1/29/5	12.4-14.4
Beta-coronaviruses	SARS-CoV-1: https://www.ncbi.nlm.nih.gov/nuccore/NC_004718.3	34/0/35/2	11.5- 15.0
	SARS-CoV-2: https://www.ncbi.nlm.nih.gov/nuccore/MT635445.1	21/1/26/4	10.9- 17.2
	MERS: https://www.ncbi.nlm.nih.gov/nuccore/NC_019843.3	32/8/23/3	11.1- 18.6
	Pangolin-CoV: https://www.ncbi.nlm.nih.gov/nuccore/MT040335.1	29/3/17/4	10.8-19.9
	HCov-HKU1: https://www.ncbi.nlm.nih.gov/nuccore/NC_006577.2	15/1/13/2	11.5- 15.0
	Bat coronavirus RATG13: https://www.ncbi.nlm.nih.gov/nuccore/MN996532.1	17/2/29/1	10.9- 19.7
	Bovine coronavirus BCoV-ENT: https://www.ncbi.nlm.nih.gov/nuccore/NC_003045.1	25/1/26/0	20.8
	Murine hepatitis virus A59: https://www.ncbi.nlm.nih.gov/nuccore/FJ884687.1	29/5/42/7	11.2-36.8
Gamma-coronaviruses	Avian infectious bronchitis virus: https://www.ncbi.nlm.nih.gov/nuccore/NC_001451.1	20/6/8/3	12.7- 26.5
Delta-coronaviruses	Porcine coronavirus HKU15: https://www.ncbi.nlm.nih.gov/nuccore/NC_039208.1	26/5/29/3	11.2- 17.4

¹Negative sense genes (NSGs) were identified by in silico approach using the Open Reading Frame Finder program (https://www.ncbi.nlm.nih.gov/orffinder/). First and second digits show overall and numbers of the large gene open reading frames (ORFs) starting with classical AUG, respectively. Third and fourth numbers show overall and large gene numbers ORFs having noncanonical CUG, respectively. Large genes were assumed to have more than 300 nt long. GenBank ac.n. of the viral genomes are indicated.

²A range of mol. wt. (kDa) of negative gene proteins encoded by the large negative sense genes (≥ 300 nt) starting either with AUG or CUG codons are outlined.

³The data were partially presented in[15]. These partial elements were used here with the Publisher’s permission. NSGs: Negative sense genes; SARS-CoV: Severe acute respiratory syndrome coronavirus.