Genome sequences of haemagglutinin cleavage site predict the pathogenicity phenotype of avian influenza virus: statistically validated data for facilitating rapid declarations and reducing reliance on in vivo testing

Figures & data

Table 1. Summary of molecular and in vivo pathotyping study data for H5 HPAIVs and LPAIVs.

Molecular determination		Cleavage site sequences	In vivo pathogenicity
			High	Low
HPAI	Gs/GD lineage H5Nx	PQRRRRKKR/G, PLREKRRKR/G, PLRERRRKR/G, PLRERRRRR/G, PLRGKRRKR/G, PPREKRRKR/G, PPRERRRKR/G, PQREKRKKR/G, PQRERRKKR/G, PQRERRRKR/G, LRRERRRKR/G, PLREKRRRKR/G, PQREKRRKKR/G, PQREGRRKKR/G, PQIEGRRRKR/G, PQGERRRKKR/G, PQIERRRRKR/G, PQRERRRKKR/G, PQSRRKKR/G	152 (98.06%, 95% CL: 94.45–99.60%)	3 (1.94%, 95% CL: 0.40–5.55%)
	Sporadic LPAI-to-HPAI mutation	PQKKKR/G, PQRKKR/G, PQKRKR/G, PQRRKKR/G, PQRKRKKR/G, PQRRRKKR/G, PQRKRKRKTR/G, PQRKRKTR/G, PQRETRRQKR/G, PERKRKTR/G	32 (84.21%, 95% CL: 68.75–93.98%)	6 (15.79%, 95% CL: 6.02–31.25%)
LPAI		PQRETR/G, PQKKTR/G, PQREIR/G, PQKETR/G, PQRKTR/G, PQTRTR/G	0 (0%, ^A97.5% CL: 0.0–1.45%)	253 (100%, ^A97.5% CL: 98.55–100.0%)

CL: confidence level.

^A One-sided 97.5% CL.

Table 2. Summary of molecular and in vivo pathotyping study data for H7 HPAIVs and LPAIVs.

Molecular determination	Cleavage site sequences	In vivo pathogenicity
		High	Low
HPAI	PETPKRRKR/G, PEIPKKRKR/G, PEIPKRKKR/G, PEIPKRRRR/G, PEIPRKRKR/G, PEIPKKKKR/G, PETPKRKRR/G, PETPKRRRR/G, PEIPKRRR/G, PEIPKKRKKR/G, PEIPKKREKR/G, PETPKRRERR/G, PETPKRKRKR/G, PEIPKKKKKKR/G, PENPKKRKTR/G	50 (93.10%, CL: 92.89–100%)	0 (0%, CL: 0.00–7.11%)
	PEIPKGRHRRPKR/G, PEIPKGSRVRR/G, PEKPKTCSPLSRCRETR/G, PEKPKTCSPLSRCRKTR/G, PELPKGTKPRPRR/G, PENPKDRKSRHRRTRTR/G, PENPKQACQKRMTR/G, PENPKQAHQKRMTR/G, PENPKQAYHKRMTR/G, PENPKQAYKKRMTR/G, PENPKQAYQKRMTR/G, PENPKQAYRKRMTR/G, PENPKTTKPRPRR/G, PENPRQAYRKRMTR/G
LPAI	PEIPKGR/G, PEKPKKR/G, PEIPKKR/G, PEKPKPR/G, PEKPKTR/G, PELPKRR/G, PENPKIR/G, PENPKNR/G, PENPKPR/G, PENPKTR/G, PENPNTR/G, PESPRPR/G, PQRETR/G, REPKPR/G	0 (0%, CL: 0.00–2.46%)	148 (100%, CL: 97.54–100.0%)

CL: one-sided 97.5% confidence level.

Table 3. H5 viruses characterized as HPAIV based upon molecular pathotyping that did not meet HPAIV criteria based upon experimental in vivo testing.

Virus	Cleavage site sequences	Pathogenicity in chickens	Molecular mechanism
A/chicken/Pennsylvania/1/83(H5N2)	PQKKKR/G	Low	Presence of glycosylation site at HA1 position 13 masks the cleavage site
A/turkey/England/87-92BFC/91(H5N1)	PQRKRKTR/G	Low	Unknown
A/chicken/Texas/298313/04(H5N2)	PQRKKR/G	Low	Unknown
A/ostrich/South Africa/AI1091/2006(H5N2)	PQRRKKR/G	Low	Unknown^a
A/ostrich/South Africa/AI2214/2011(H5N2)	PQRRRKKR/G	Low	Unknown^a

^a Presumed host attenuation for Galliformes.