First Identification and Characterization of Porcine Enterovirus G in the United States

Porcine enterovirus G (EV-G) is a member of the family Picornavirdae, genus Enterovirus. To date, eleven EV-G types (EV-G1 through EV-G11) have been identified in pigs from Asia and Europe however they have never been reported in North America. In this study, we isolated and characterized the complete genome of NP/2013/USA, an EV-G from a porcine diarrhea sample from the United States. The complete genome consists of 7,390 nucleotides excluding the 3′ poly(A) tail, and has an open reading frame that encodes a 2,169 amino acid polyprotein. NP/2013/USA was most similar at the nucleotide (84%) and amino acid (95%) level to the HM131607, an EV-G1 type isolated from China in 2012.

PEV infections are generally asymptomatic. However, occasionally PTV and PSV have been associated with a wide variety of clinical conditions such as polioencephalomyelitis, enteric disease, and pneumonia [2,7,8]. EV-G has been isolated from healthy swine fecal samples in Asia and Europe, as well as from wild boars in Hungary [6][7][8][9][10]. Recently, EV-G was isolated from pigs with diarrhea, however no association was identified between EV-G detection and the disease [6].
To date there are only seven whole genomes sequences of EV-G from samples collected from Asia and Europe. EV-G has never been reported in the United States [15]. Here we report the complete genome of an EV-G virus isolated from a clinical sample submitted to Newport Laboratories, Worthington, MN.

Ethics Statement
EV-G used in this study was isolated from a sample submitted to Newport Laboratories for routine diagnostic testing. The sample was obtained from a naturally infected animal in the field, by qualified veterinarians, as a part of normal veterinary care and diagnostic testing procedures.

Virus Growth
EV-G was isolated from intestinal homogenate submitted to Newport Laboratories in August, 2013, from commercial 4-week old pig with diarrhea for diagnostic testing.

PTV, PSV and EV-G Detection
RNA was extracted from Marc-145 cells with 100% CPE. 1 ml of cell culture supernatant was centrifuged at 15006g for 10 minutes. RNA was extracted from 140 ml of the supernatant using a QIAamp Viral RNA kit (Qiagen, Valencia, CA) according to manufacturer's instructions. RNA was eluted in 35 ml of the supplied elution buffer.

RNA Isolation for Next Generation Sequencing
Marc-145 cells that showed 100% CPE following virus infection were used for RNA extraction. 20 ml of cell culture supernatant was filtered using the 0.2 mm bottle top filters (Thermo Scientific, Lenexa, Kansas). The filtrate was centrifuged at 50,0006g for 2 hrs. Supernatant was discarded and the pellet was suspended in 1000 ml of water. Samples were concentrated to a final 100 ml volume using Amicon ultra centrifugal filters (0.5 ml; 50 KDa) (Millipore, Tullagreen, Ireland). Cellular DNA and RNA were removed by incubation with DNase I (25 units Sequencing and Data Analysis 10 mg of total RNA was depleted of ribosomal RNA using GeneRead rRNA depletion kit (Qiagen) and RNA sequencing libraries were generated using the Ion Total RNA-seq kit v2 (Ion Torrent, Life Technologies) according to manufacturer's instructions. Sequencing was carried out using Ion Personal Genome Machine (PGM) sequencing platform (Life Technologies, Grand Island, NY) as previously described [17]. Sequence reads were assembled into contigs using the SeqMan NGen program (DNAstar, Madison, WI). Sequence alignments and phylogenetic analyses were performed using MEGA 5.05 [18]. Phylogenetic comparisons were conducted using maximum likelihood analysis. Bootstrap confidence values were determined using 1000 replicates. Amino acid and nucleotide similarities were determined by using Jotun-Hein method in MegAlign program (DNAstar, Madison, WI). The EV-G was designated NP/2013/USA and submitted to GenBank (KF985175). The deep sequencing dataset

Viral Isolation
Newport Laboratories received an intestinal homogenate sample from a pig with diarrhea for diagnostic testing. Samples were positive for group A rotavirus (Ct = 33) and negative for groups B and C rotavirus by one step RT-PCR (data not shown). Subsequently, isolation of group A rotavirus was attempted on MARC-145, however, was unsuccessful as determined by one step RT-PCR despite CPE suggestive of virus propagation. Samples were next tested for PTV, Sapelovirus (PEV-8), and EV-G by one step RT-PCR (data not shown). The samples were positive only for EV-G. Further deep sequencing identified viral reads mapping soley to EV-G.

Sequence Analysis
The NP/2013/USA genome was sequenced with an Ion Torrent Personal Genome Machine. The complete genome contained 7,390 nucleotides (nt) excluding the 39 poly(A) tail. The 59-UTR consisted of 811 nucleotides and the 39-UTR was comprised of 72 nucleotides. A single large open reading frame was identified from nucleotides 812 to 7318 and encoded a hypothetical 2,169 amino acid polyprotein. The genome had 28.3% A, 24.9% T, 24% G, and 22.9% C which is similar to the other EV-G isolates. The genome organization of NP/2013/USA was identical to the CPE group III strains, now classified as EV-G [4,8,9,19].
To elucidate the genetic relatedness of NP/2013/USA with PTV, PSV, and EV-G types, a phylogenetic tree was constructed using the maximum likelihood algorithm and bootstrapped using 1000 replicates using the complete genome sequence. NP/2013/ USA segregated into the same clade as other EV-G and was clearly distinct from PTV and PSV (Fig. 1). NP/2013/USA was most closely related to EV-G.
Enteroviruses utilize recombination as a mechanism for evolution, with genetic diversification principally in genes encoding structural proteins [20]. Genetic analysis of NP/2013/USA suggests a similar pattern of recombination. The 59-UTR, 39-UTR, and non-structural genes had 89%, 99% and 85% nucleotide identity to a 2012 Chinese EV-G1 isolate (HM131607). In contrast, the region encoding the structural proteins had only 79% identity to the same virus. Previously, recombination was described to occur in the region involving the 59-UTR [7]. However, recent studies suggested that sequence differences in the 59-UTR are the result of the accumulation of mutations but not a recombination event [6]. Furthers studies by Nguyen et al. indicate that EV-G types circulating in Europe and Asia share a common 59-UTR sequence with the prototype EV-G1 (AF363453) and -G2 (AF363455) isolated in 1973 and 1975 respectively [6]. With only 89% nucleotide identity to previously sequenced EV-G, it is unclear whether the 59UTR of NP/2013/ USA is derived via recombination.
EV-G infection was detected at higher frequencies in younger pigs than in adults from Vietnam, Czech Republic, China, Hungary, Italy, and Spain [6,12,[21][22][23]. EV-G1, 6, and 8-11 types were found in pigs of ages 3-9 weeks, 7-9 months, and 52-165 months respectively [6]. Similar age associated differences in infection frequencies of enterovirus serotypes were identified in young children [24]. NP/2013/USA, an EV-G1 type, was isolated from nursery pigs (3-10 weeks of age) similar to other EV-G1 [6]. While NP/2013/USA was isolated from pigs with diarrhea, group A rotavirus was also present in the fecal samples. The contribution of each virus to clinical disease is unclear however group A rotaviruses have been well established as pathogens of pigs with diarrhea the most common clinical presentation. A controlled pig inoculation experiment is needed to ascertain the pathogenic potential of NP/2013/USA.
In conclusion, the present study was the first to identify EV-G in pigs in the United States. NP/2013/USA's nucleotide and protein sequence was most homologous to HM131607, an EV-G1 isolate from China in 2012. It is unclear whether our finding of EV-G in U.S. pigs represents a recent introduction of this virus to the U.S. or whether EV-G has circulated in U.S. herds undetected for some time. Previous work has failed to find EV-G in U.S. pigs [15]. Also of interest is the recent introduction of porcine epidemic diarrhea virus (PEDV) into the U.S. swine herd [25]. Massive outbreaks of PED occurred throughout the U.S. in 2013 following the introduction of this foreign virus. Interestingly, the PEDV epidemic in the U.S. is genetically nearly identical to a Chinese PEDV isolated in 2012 [26,27]. It is unclear whether the isolation of a second virus not previously seen in the U.S. with high genetic similarity to contemporary Chinese viruses is coincidental or due to a similar recent introduction. Serological testing of contemporary and historic samples is needed to clarify the epidemiology of EV-G in the U.S.
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