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

Abstract

The genetic variability of Infectious bronchitis virus (IBV) is one of the main challenges for its control, hindering not only the development of effective vaccination strategies but also its classification and, consequently, epidemiology understanding. The 624/I and Q1 genotypes, now recognized to be part of the GI-16 lineage, represent an excellent example of the practical consequences of IBV molecular epidemiology limited knowledge. In fact, being their common origin unrecognized for a long time, independent epidemiological pictures were drawn for the two genotypes. To fix this misinterpretation, the present study reconstructs the history, population dynamics and spreading patterns of GI-16 lineage as a whole using a phylodynamic approach. A collection of worldwide available hypervariable region 1 and 2 (HVR12) and 3 (HVR3) sequences of the S1 protein was analysed together with 258 HVR3 sequences obtained from samples collected in Italy (the country where this genotype was initially identified) since 1963. The results demonstrate that after its emergence at the beginning of the XX century, GI-16 was able to persist until present days in Italy. Approximately in the late 1980s, it migrated to Asia, which became the main nucleus for further spreading to Middle East, Europe and especially South America, likely through multiple introduction events. A remarkable among-country diffusion was also demonstrated in Asia and South America. Interestingly, although most of the recent Italian GI-16 strains originated from ancestral viruses detected in the same country, a couple were closely related to Chinese ones, supporting a backward viral flow from China to Italy. Besides to the specific case-study results, this work highlights the misconceptions that originate from the lack of a unified nomenclature and poor molecular epidemiology data generation and sharing. This shortcoming appears particularly relevant since the described scenario could likely be shared by many other IBV genotypes and pathogens in general.

Molecular and biological characteristics of the infectious bronchitis virus TC07-2/GVI-1 lineage isolated in China

“…This is likely also the case of the GVI-1 lineage. Thus, we speculate that some of the so called "emerging" genotypes may actually be ancient genetic groups that have not been correctly identified or classified (Franzo et al, 2018). Based on the VN results, strains LHB/110615 and I0221/17 were found to be of the same serotype and shared 94.9% antigenic relatedness; however, despite the comparative sequence conservation of the S1 subunit for the GVI-1 viruses in this study, obvious antigenic diversity was also found.…”

“…This hypothesis can be confirmed by the availability and analysis of the complete genomic sequences of the CO8089L/CO8091Llike strains in Colombia and GVI-1 viruses in Asian countries. Increasing evidence shows that the circulation of many "novel" genotypes and lineages often predate their first identification (Franzo et al, 2017(Franzo et al, , 2018. This is likely also the case of the GVI-1 lineage.…”

“…However, recent studies have revealed a close relationship between the sequences of the GI-16 lineage and IBV strain 624I that had circulated in Italy in the early 1990s (Laconi et al, 2019). Further studies have demonstrated that after its emergence at the beginning of the XX century, GI-16 was able to persist until today in Italy (Franzo et al, 2018). In the late 1980s, GI-16 migrated to Asia, which became the primary nucleus for further spread to the Middle East, Europe, African countries, and especially South America, likely through multiple introduction events (Franzo et al, 2018).…”

“…Further studies have demonstrated that after its emergence at the beginning of the XX century, GI-16 was able to persist until today in Italy (Franzo et al, 2018). In the late 1980s, GI-16 migrated to Asia, which became the primary nucleus for further spread to the Middle East, Europe, African countries, and especially South America, likely through multiple introduction events (Franzo et al, 2018). For the GVI-1 lineage, further studies that monitor, isolate, and sequence more complete genomes of the GVI-1 strains from different countries may provide insight into the origin and evolution of the GVI-1 viruses.…”

Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017

“…The comprehensive studies of Polish IBV isolates from 1998 to 1999 using serological and molecular tests conducted in cooperation with Italian researchers showed that the 793B type was a major component of the IBV population in Poland during this period, but serologically the presence of 624/I isolates was also identified and one isolate even showed no serological cross-reaction in an HI test nor amplification in RT-PCR (Capua et al, 1999). Recently, the 624/I and Q1 types were determined to affiliate to the GI-16 lineage, which has been present in Europe (Italy) since 1963 and persists until now (Franzo et al, 2018). In the period 2011-2013 numerous cases of D1466 IBV (GII-1 lineage) were detected, however, in subsequent years (2014)(2015), the number of D1466-positive samples dropped to 3.1%, and currently we do not detect these viruses at all (Domanska-Blicharz et al, 2012;Domanska-Blicharz et al, 2017).…”