GI-16 lineage (624/I or Q1), there and back again: The history of one of the major threats for poultry farming of our era

Franzo, Giovanni; Cecchinato, Mattia; Tosi, Giovanni; Fiorentini, Laura; Faccin, Francesca; Tucciarone, Claudia Maria; Trogu, Tiziana; Barbieri, Ilaria; Massi, Paola; Moreno, Ana

The present study, reporting the evolutionary history of GI-16 lineage, supports this hypothesis. In fact, this lineage includes two genotypes that have been considered independent for a long time: the 624/I and Q1. The first one was firstly recognized in 1993 in Italy, albeit retrospective studies demonstrated the local circulation since 1963 [12] , where it likely had a prominent role in IBV epidemiology. Nevertheless, its relevance appeared to gradually vanish during the 1990s. Almost simultaneously, a new genotype, often named Q1, emerged in China and was then reported in other Asian, Middle East, European and South American countries, being responsible of devastating economic losses [16, 21, 22, 39] . The present phylodynamic analysis demonstrates a common origin of 624/I and Q1, which has been estimated approximately at the beginning or middle of the XX century, depending on the considered genomic region. Nevertheless, the lower sequence number and shorter time window covered by HVR12 database pose in favor of the HVR3 based analysis reliability. Anyhow, these results testify the long lasting undetected circulation of this genotype in Italy. The absence of adequate monitoring and diagnostic tools at that time clearly justifies this evidence, which could be realistically extended to most of current IBV genotypes. Unfortunately, the lack of sequences relative to the period before 1963 prevents the precise reconstruction of viral population dynamics in this time frame. However, the skyline profile, especially from the 1960s onward, when actual data became available, shows that GI-16 was able to circulate and persist in Italy at low level until the 1980s, when a remarkable increase in relative genetic diversity was observed. The reason behind this variation in the epidemiological scenario are hard to explain. However, a progressive intensification of poultry production, leading to higher animal density, turnover and presence of several concomitant stressing factors and co-infections could have created favorable conditions for the rise of acute respiratory infections like IBV. Similarly obscure are the causes of the GI-16 decline in the late 1980s-early 1990s. An upgrade in the vaccination strategies was applied in the 1990s, through the introduction of 793B based vaccines [20] . A Mass plus 793B combined vaccination was proven effective in protecting against GI-16 induced disease [39] , and could therefore justify the observed scenario. However, the new protocol was effectively introduced only in the last part of the decade. Consequently, even if it could have actually contributed to this genotype control, other factors, like changes in farm management or progressive increase of population immunity, must have played a role. Interestingly, an autogenous inactivated 624/I based vaccine (strain 794/83FO), administered at 1d of age, was introduced in the routine vaccination protocols of several farms in the Emilia Romagna Region in the late 80's. Although inactivated vaccines are traditionally considered less effective, a contribution in decreasing animal susceptibility and thus viral circulation can be suggested.