GI-16 lineage (624/I or Q1), there and Back Again: the history of one of the major threat for poultry farming of our era

Abstract

26 The genetic variability of Infectious bronchitis virus (IBV) is one of the main challenges for its 27 control, hindering not only the development of effective vaccination strategies but also its 28 classification and, consequently, epidemiology understanding. The 624/I and Q1 genotypes, now 29 recognized to be part of the GI-16 lineage, represent an excellent example of the practical 30 consequences of IBV molecular epidemiology limited knowledge. In fact, being their common 31 origin unrecognized for a long time, independent epidemiological pictures were drawn for the two 32 genotypes. To fix this misinterpretation, the present study reconstructs the history, population 33 dynamics and spreading patterns of GI-16 lineage as a whole using a phylodynamic approach. A 34 collection of worldwide available hypervariable region 1 and 2 (HVR12) and 3 (HVR3) sequences 35 of the S1 protein was analysed together with 258 HVR3 sequences obtained from samples collected 36 in Italy (the country where this genotype was initially identified) since 1963. The results 37 demonstrate that after its emergence at the beginning of the XX century, GI-16 was able to persist 38 until present days in Italy. Approximately in the late 1980s, it migrated to Asia, which became the 39 main nucleus for further spreading to Middle East, Europe and especially South America, likely 40 through multiple introduction events. A remarkable among-country diffusion was also demonstrated 41 in Asia and South America. Interestingly, although most of the recent Italian GI-16 strains 42 originated from ancestral viruses detected in the same country, a couple were closely related to 43 Chinese ones, supporting a backward viral flow from China to Italy.44 Besides to the specific case-study results, this work highlights the misconceptions that originate 45 from the lack of a unified nomenclature and poor molecular epidemiology data generation and 46 sharing. This shortcoming appears particularly relevant since the described scenario could likely be 47 shared by many other IBV genotypes and pathogens in general. Introduction 52 Infectious bronchitis virus (IBV) is currently classified in the species Avian coronavirus, genus 53 Gammacoronavirus, family Coronaviridae. The viral genome is about 27 Kb 54 long and encodes for different proteins, such as the RNA-dependent RNA polymerase (RdRp), 55 numerous accessory and regulatory proteins and the Spike, Envelope, Membrane, and Nucleocapsid 56 structural proteins [1]. IBV currently represents one of the most relevant diseases of poultry 57 farming, being responsible for respiratory signs, reproductive disorders and relevant mortality, 58 particularly in presence of nephropathogenic strains or secondary infections [2]. Similarly to other 59 RNA viruses, it is characterized by high evolutionary and recombination rates, which drive the 60 rapid evolution of this pathogen and lead to a remarkable genetic and phenotypic heterogeneity [3]. 61 The Spike protein, further processed in the S1 and S2 sub-units, is by far the ...

The Effect of Global Spread, Epidemiology, and Control Strategies on the Evolution of the GI-19 Lineage of Infectious Bronchitis Virus

“…However, a small Asian clade stemming from the European one was present (Supplementary Figure S1). While not directly relevant to the purpose of this study, this finding may reflect a previously observed pattern for IBV lineage GI-16 (Q1) [39], and its epidemiological implications and potential developments should be considered and monitored.…”

Reconstruction of Avian Reovirus History and Dispersal Patterns: A Phylodynamic Study

“…While North America was the main nucleus of viral dispersal, other significant contacts among areas were reported and these reflected previously described patterns for other avian infectious diseases and/or mirrored well-established economic and commercial relationships among areas. The bidirectional flow of viral strains involving Asia and Europe was already reported for IBV [53,54], as well as the "mediator role" played by the Middle East in this migratory path [55]. Similarly, different areas were involved in ARVs' introduction to Africa, reflecting the changing economic relationships and interests of different areas of the world with different countries of this continent.…”

Conflicting Evidence between Clinical Perception and Molecular Epidemiology: The Case of Fowl Adenovirus D

“…Although these intrinsic methodological and data limitations can prevent the accurate reconstruction of the ancient virus origin, a reliable depiction of recent patterns could be reached. The viral population was featured by a progressive rise and high-level circulation until about the 2000s, a pattern shared by many other livestock pathogens [50][51][52][53]. This mirrors the progressive intensification of farming that, in turn, led to an increase in animal densities, movements and trades, creating favorable conditions for viral population expansion [51,53,54].…”