Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy

Abstract

noroviruses (noVs) are one of the major causative agents of non-bacterial gastroenteritis in humans worldwide. NoVs, belonging to Caliciviridae, are classified into ten genogroups (G) and eight P-groups based on major capsid protein (VP1) and of the RNA-dependent-RNA-polymerase (RdRp), respectively. In swine, the main genogroup and P-group identified are GII and GII.P; which can infect humans too. To date, only one case of GIIP.11 have been identified in swine in Italy while the circulation of other P-types is currently unknown. In the present study, 225 swine faecal samples were collected from 74 swine herds in Veneto region through on-farm monitoring. noV circulation was particularly high in older pigs. The phylogenetic analysis showed the co-circulation of NoVs belonging to two different P-types: GII.P11 and GII.P18, here described for the first time in Italy, presenting an extensive genetic diversity, never described before worldwide. Distinct noV genetic subgroups and unique amino acid mutations were identified for each P-type for the first time. This study demonstrated the co-circulation of diverse swine NoVs subgroups in Italy, raising questions on the origin of such diversity and suggesting that continuous monitoring of swine noVs is needed to track the emergence of potentially zoonotic viruses by recombination events. Food-and water-borne infections, which are mainly manifested with gastroenteritis in humans, represent a significant public health burden. Among food-borne viruses, Noroviruses (NoVs) are a leading pathogen, causing epidemic gastroenteritis cases worldwide 1. Low infectious dose, environmental resistance, strain diversity, and the shedding from asymptomatic persons, render human NoVs highly contagious pathogens. NoVs are transmitted through ingestion of contaminated food or water, either via the faecal-oral route or via airborne particles and contact with contaminated surfaces. NoV belongs to the Caliciviridae family, which includes small non-enveloped viruses of approximately 35 nm in diameter with single stranded positive RNA genome of 7.4-8.3 kb 2. Five genera: Vesivirus, Lagovirus, Sapovirus, Nebovirus and Norovirus as well as unassigned viruses are included in this family 3. Norovirus and Sapovirus genera contain human and animal enteric viruses. The NoV genome possesses 3 Open Reading frames (ORFs) encoding: a polyprotein (ORF1) that by protease processing produces six non-structural proteins, including a RNA-dependent-RNA-polymerase (RdRp), a major capsid protein, VP1 (ORF2), and a minor one, VP2 (ORF3). NoVs are classified into ten genogroups (G) based on the variation of the major capsid protein (VP1), and are further divided into 49 genotypes 3. Due to the recombination events that occur between ORF1 and ORF2, a dual nomenclature based on VP1 and RdRp was recently proposed 3. Based on the RdRp sequence, NoVs are classified into eight P (polymerase)-groups and further divided into 60 P-types. Human NoV infections are caused by GI, GII, and GIV genotypes, with a higher frequency of ...

Epidemiology of Astrovirus, Norovirus and Sapovirus in Greek pig farms indicates high prevalence of Mamastrovirus suggesting the potential need for systematic surveillance

“…Porcine Noroviruses (PoNoVs) have been detected mainly in asymptomatic adult pigs [ 25 , 39 ]). GII PoNoVs have been detected in pigs in the USA, in Latin America, and in several European countries, in both symptomatic and asymptomatic animals [ 11 , 17 , 18 , 20 , 21 , 40 ].…”

“…This fact has raised public health concerns regarding the zoonotic potential of porcine NoVs and the role of swine in the epidemiology of this infection, owing to the possibility of emergence of new viral recombinant strains that can be transmitted directly to humans [ 40 , 41 , 43 , 44 ]. So far, the association of swine NoVs with human infections remains unclear and further research is needed in order for this virus infection to be elucidated or controlled [ 39 ].…”

Swine Norovirus: Past, Present, and Future

“…Since then and until 2022, 47 studies investigating the presence of swine norovirus around the world have been published, including studies that did not detect swine norovirus. The investigations of swine noroviruses were either the result of retrospective studies on archived swine faecal samples [ 20 , 21 , 22 , 23 , 24 , 25 , 26 ] or studies with ad hoc sampling strategies to investigate the presence of swine noroviruses in a target geographic area [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 ]. Both types of studies present different sampling approaches, hampering a straightforward data comparison.…”

“…Indeed, the information available, although increased over the years, is fragmented, and, most importantly, some studies represent single reports without any follow-up investigations (i.e., studies conducted in Belgium [ 44 ], Slovenia [ 34 ], Spain [ 31 ], Hungary [ 37 ] and Greece [ 45 ], Ethiopia [ 41 ], Taiwan [ 46 ], South Korea [ 32 ], Venezuela [ 47 ]). Only a few countries made more effort in detecting and characterising swine noroviruses, and two or more studies are available for each of these countries (i.e., Italy [ 21 , 22 , 28 , 48 ], USA [ 13 , 20 , 40 , 49 , 50 ], Canada [ 26 , 48 ], China [ 39 , 49 , 50 , 51 ], Japan [ 19 , 20 , 35 , 36 , 52 , 53 , 54 ], Germany [ 33 , 55 ], The Netherlands [ 55 , 56 ], Brazil [ 25 , 29 , 30 , 57 ]). It appears that efforts to investigate the circulation of swine norovirus should be implemented in all continents.…”

“…Swine norovirus was also reported in Oceania (New Zealand) more than ten years ago [ 60 ]. Thus far, eight European countries have detected the presence of swine noroviruses in their swine populations over a 21-year period between 1998 and 2019 [ 21 , 22 , 24 , 28 , 31 , 33 , 34 , 44 , 45 , 48 , 59 , 60 , 70 ]. Italy has generated six studies on swine noroviruses between 2008 and 2019, reporting the first detection in 2014 while investigating samples collected between 2006 and 2007 [ 24 ].…”