Wild bird trade at live poultry markets potentiates risks of avian influenza virus introduction in Iran

Figures & data

Table 1. Iranian wild bird samples obtained in October 2019 from several live bird markets in northern Iran and testing positive for avian influenza virus

Bird species	Swab sample	Subtype	Cq	Accession number
Eurasian teal	Cloacal-137	H9N2	22.78	MZ277345 (HA)- MZ277346 (MP) – MZ277347 (NA) – MZ277348 (NP) – MZ277349 (NS) – MZ277350 (PA) – MZ277351 (PB1)- MZ277352 (PB2)
Eurasian teal	Cloacal-140	H9N2	24.05	MZ277330 (HA)
Eurasian teal	Cloacal-148	H9N2	26.00	MZ277331 (HA)
Eurasian teal	Cloacal-158	H9N2	21.71	MZ277332 (HA)
Eurasian teal	Cloacal-163	H9N2	23.76	MZ277353 (HA)- MZ277354 (MP)- MZ277355 (NA) – MZ277356 (NP) – MZ277357 (NS) – MZ277358 (PA) – MZ277359 (PB1) -MZ277360 (PB2)
Eurasian teal	Cloacal-166	H9N2	24.31	MZ277333 (HA)
Eurasian teal	Cloacal-167	H9N2	27.62	MZ277334 (HA)
White-fronted goose	Cloacal-238	H9N2	29.36	MZ277337 (HA)- MZ277338 (MP) – MZ277339 (NA)- MZ277340 (NP)- MZ277341 (NS)- MZ277342 (PA) – MZ277343 (PB1) -MZ277344 (PB2)
White-fronted goose	Cloacal-239	H9N2	26.66	MZ277361 (HA) – MZ277368 (MP)- MZ277361 (NA) – MZ277362 (NP)- MZ277363 (NS) – MZ277364 (PA)- MZ277365 (PB1) -MZ277366 (PB2)
White-fronted goose	Cloacal-268	H9N2	21.57	MZ277369 (HA)- MZ277370 (MP)- MZ277371 (NA) – MZ277372 (NP) – MZ277373 (NS) – MZ277374 (PA) – MZ277375 (PB1) -MZ277376 (PB2)
White-fronted goose	Cloacal-298	H10N3	30.82	MZ277336(HA), MZ562475 (NA)

Cq – RT-qPCR on generic M-gene target; indirect measure of viral RNA load.

Figure 1. Phylogenetic analysis of the hemagglutinin open reading frame of H9N2 viruses from Iran. Trees were generated by maximum likelihood calculations using the IQ Tree software version 2.1.1 applying the best fit codon-based model according to the Bayesian informative criterion MG+F1X4+G4. Numbers at nodes signal robustness according to ultrafast bootstrap support. Red colored sequences have been established in this study. Other sequences from Iran have been labelled green. Clades within the H9 HA subtype are indicated to the right of the tree. Asterisks denote switches of Y439- and G1-like viruses between wild bird and poultry populations as explained in the discussion

Data availability statement and data deposition

All data established are either shown in the manuscript or are available at public databases (NCBI GenBank). https://www.ncbi.nlm.nih.gov/nucleotide/.