Incidence, diversity, and molecular epidemiology of sapoviruses in swine across Europe

Abstract

Porcine sapovirus is an enteric calicivirus in domestic pigs that belongs to the family Caliciviridae. Some porcine sapoviruses are genetically related to human caliciviruses, which has raised public health concerns over animal reservoirs and the potential cross-species transmission of sapoviruses. We report on the incidence, genetic diversity, and molecular epidemiology of sapoviruses detected in domestic pigs in a comprehensive study conducted in six European countries (Denmark, Finland, Hungary, Italy, Slovenia, and Spain) between 2004 and 2007. A total of 1,050 swine fecal samples from 88 pig farms were collected and tested by reverse transcription-PCR for sapoviruses, and positive findings were confirmed by sequencing. Sapoviruses were detected in 80 (7.6%) samples collected on 39 (44.3%) farms and in every country. The highest prevalence was seen among piglets aged 2 to 8 weeks, and there was no significant difference in the proportion of sapovirus-positive findings for healthy animals and animals with diarrhea in Spain and Denmark (the only countries where both healthy animals and animals with diarrhea were tested). On the basis of the sequence of the RNA polymerase region, highly heterogeneous populations of viruses representing six different genogroups (genogroups III, VI, VII, and VIII, including potential new genogroups IX and X) were identified, with a predominance of genogroup GIII (50.6%). Genogroup VIII, found in five of the six countries, had the highest degree of homology (up to 66% at the amino acid level) to human sapovirus strains. Sapoviruses are commonly circulating and endemic agents in swine herds throughout Europe. Highly heterogeneous and potential new genogroups of sapoviruses were found in pigs; however, no "human-like" sapoviruses were detected.

FIG. 1.

Phylogenetic analysis of sapoviruses, including porcine sapoviruses, detected in this study in Europe on the basis of the 286-nt RNA-dependent RNA polymerase region of caliciviruses. A dendrogram was constructed by the UPGMA method with the MEGA (version 3.1) program. The country origin of the strains is indicated by color coding (Denmark, red; Finland, light blue; Hungary, blue; Italy, purple; Slovenia, green; Spain, yellow). To maintain the continuity of the current nomenclature for sapovirus genogrouping, we used the previously proposed taxonomic names as a basis (14, 25). Sapoviruses in genogroups GI, GII, GIV, and GV are detected in humans. Sapoviruses of swine origin belong to genogroups GIII, GVI, GVII, GVIII, GIX, and GX. The following reference strains were obtained from the GenBank database (the GenBank accession numbers are provided in parentheses): PEC/Cowden/US (AF182760), PECLL14/US (AY425671), PECIVA36/NL (AY615805), Korean6802 (AY289186), London/92/UK (U95645), HUNs11/2000/HUN (AF488717), HUNs12/2000/HUN (AF488718), HUNs17/2000/HUN (AF488720), HUN3739/2008/HUN (FJ844411), Sapporo/82/JP (U77903), Houston/90/US (U95644), Po/SV/Yaracuy/1999/VE (AY633966), Po/SV/Miranda/2000/VE (AY633963), Po/SV/Miranda2/2001/VE (AY633965), PEC-Korean10802 (AY289188), OH-JJ259-00-US (AY826423), NC-QW270-03-US (AY826426), SWECI/VA10/NL (AY615807), OH-MM280-03-US (AY823308), MEX335/1991/MX (AY157869), PAN-1/78/US (AF091736), 43-06-18-p-3-6-ITA (AB221477), SWECIII/VA112/NL (AY615814), OH-LL26/2002/US (AY974195), OH-JJ681/2000/US (AY974192), Norwalk (M87661), Mex14917/00/MX (AF435810), Mex340/90/MX (AF435809), cruiseship/00/US (AY157863), Mc10/00/TH (AY237420), C12/00/JP (AY603425), Hou7-1181-90-US (AF435814), Arg39/Arg (AF405715), MEC/1/1999/US (AF338404), FCV (M86379), NB-like (AY082891), K7JP (AB221130), SWECII/VA103/NL (AY615811), and MI-QW19-02-US (AY826424).

FIG. 2.

Prevalence of sapovirus genogroups by age group on the basis of the findings for 78 sapovirus strains. The y axis represents the prevalence of genogroups (in percent). The count numbers in each bar slice represent the sample size for the genogroup. The total sample size for each age group is provided at the top of the bars.