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Porcine epidemic diarrhea virus (PEDV) emerged in the United States (U.S.) swine population in 2013, initiating an initial significant epidemic followed by a state of endemicity in the U.S. Despite continued monitoring, the epidemiology of PEDV during its endemic phase remains inadequately researched. Our study aimed to characterize the spatial–temporal distribution of postepidemic PEDV cases in the U.S. breeding herd and identify associated risk factors. Data from 1089 breeding farms in 27 states, reported to the Morrison Swine Health Monitoring Project from July 2014 to June 2021, were analyzed. We stratified the data into six U.S. regions and employed SaTScan for spatiotemporal permutation and cluster analysis. Survival analysis was used to assess risk factors. A notable seasonal clustering of PEDV cases was observed in winter (January–March; p = 0.001, relative risk = 2.2) with regional variation. Ten high‐rate spatial–temporal clusters (p < 0.05) were identified ranging from 2.5 to 833.7 km2 and lasting 1–5 months, occurring in four regions between 2015 and 2021. For the study period, a total of 625 cases of PEDV were recorded on 372 farms. The total number of PEDV cases decreased from 95 breeding farms in 32 counties (2014–2015) to 53 farms in 28 counties (2020–2021), indicating an overall reduction in occurrence and spatial extent. Feed mitigants demonstrated a protective effect, significantly reducing the risk of PEDV occurrence (hazard ratio = 0.3, p = 0.003), while air filtration systems exhibited marginal benefits (hazard ratio = 0.3, p = 0.06). Other important risk factors included county farm density with farms in high‐density regions (>31 farms/100 km2) being 1.3 times more likely to experience outbreaks than in medium‐density regions (13–31 farms/1000 km2; p < 0.001). Additionally, farms in region E had higher odds of outbreaks compared to region B. The overall decline in PEDV cases and reduced spatial extent reflect industry efforts in postepidemic control and elimination. The protective effects of feed mitigants warrant further investigation. Our findings underscore the opportunity for coordinated efforts to eliminate PEDV in the U.S. and emphasize the need for comprehensive risk profiling associated with industry practices. [ABSTRACT FROM AUTHOR]

Movement restrictions are a critical component of response plans for an African swine fever (ASF) outbreak in the United States. These restrictions are likely to include requiring permits to move animals and products within, into, and out of 5‐km control areas (CAs) established around confirmed positive farms. For quarantined finishing farms located within a CA, diagnostic testing is an expected criterion for receival of a permit to move pigs to a harvest facility or removal of quarantine. A stochastic disease transmission and active surveillance model were used to evaluate premovement active surveillance protocols varying by the number of samples and timing of sample collection before movement. Surveillance protocol scenarios were evaluated for several different sampling prioritization schemes; virus strains of medium or high virulence; barn sizes of 1,200, 2,400, and 4,800 pigs; and farms with average to high mortality and morbidity during routine production. Surveillance protocols that included prioritization schemes targeting dead pigs and pigs with clinical signs resulted in the highest probabilities of detection and the lowest numbers of infectious pigs at the time of movement in barns that went undetected. There was some evidence that targeting sick pigs prior to dead pigs may be more effective for moderately virulent strains. However, in most scenarios, including all highly virulent strain scenarios and moderately virulent strain scenarios in barn sizes of 1,200 with average farm performance, prioritization of dead versus sick pigs first did not have a large impact on the predicted outcomes. Increasing sample sizes improved outcomes, though only marginal gains were achieved once the available dead and sick were sampled. Predicted outcomes may be further improved by sampling the available dead and sick pigs in a barn across multiple days, though the associated increase in the probability of detection was minor. [ABSTRACT FROM AUTHOR]

Simple Summary: Rotavirus is an increasingly widespread zoonotic agent, the segmented feature of rotavirus genome is responsible for the emergence of new diverse viruses and inter-species transmission. Therefore, monitoring the genetic diversity of rotavirus is helpful to understand its evolution. In this study, a novel potential zoonotic G4P[6] rotavirus with a 344-nt duplication sequence in the non-encoding gene of NSP5 was for the first time detected in a diarrhoea pig sample collected from Guangdong Province, China. Further genome analyses revealed genome reassortment between human-origin and porcine-origin rotavirus. Rotavirus is a major causative agent of diarrhoea in children, infants, and young animals around the world. The associated zoonotic risk necessitates the serious consideration of the complete genetic information of rotavirus. A segmented genome makes rotavirus prone to rearrangement and the formation of a new viral strain. Monitoring the molecular epidemiology of rotavirus is essential for its prevention and control. The quantitative RT-PCR targeting the NSP5 gene was used to detect rotavirus group A (RVA) in pig faecal samples, and two pairs of universal primers and protocols were used for amplifying the G and P genotype. The genotyping and phylogenetic analysis of 11 genes were performed by RT-PCR and a basic bioinformatics method. A unique G4P[6] rotavirus strain, designated S2CF (RVA/Pig-tc/CHN/S2CF/2023/G4P[6]), was identified in one faecal sample from a piglet with severe diarrhoea in Guangdong, China. Whole genome sequencing and analysis suggested that the 11 segments of the S2CF strain showed a unique Wa-like genotype constellation and a typical porcine RVA genomic configuration of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Notably, 4 of the 11 gene segments (VP4, VP6, VP2, and NSP5) clustered consistently with human-like RVAs, suggesting independent human-to-porcine interspecies transmission. Moreover, a unique 344-nt duplicated sequence was identified for the first time in the untranslated region of NSP5. This study further reveals the genetic diversity and potential inter-species transmission of porcine rotavirus. [ABSTRACT FROM AUTHOR]

Herpesviruses are ubiquitous viruses which infect a wide range of hosts. Novel herpesviruses are being increasingly detected in free‐ranging bird populations and there are growing concerns for cross‐species infection and spillover events. Herein, multiple sporadic outbreaks of mortality caused by a herpesvirus are described in domestic geese in Queensland, Australia. Goose herpesvirus was initially detected in 1989 in south‐east Queensland, and this article details four further recent outbreaks and reports novel genome sequencing and phylogeny of the preliminarily designated anatid alphaherpesvirus 2 (AnHV‐2). Affected flocks were housed outdoors and comingled with other domesticated and wild anseriforms and other birds which were unaffected by disease. Affected geese displayed anorexia, lethargy, weakness, vomiting, and diarrhoea prior to death within 12–24 hr of the onset of clinical signs. Post‐mortem examinations showed variable hepatic necrosis, splenic necrosis, fibrinonecrotising enteritis, lymphoid necrosis, necrotising thymitis, necrotising adrenalitis, and vasculitis. Intranuclear inclusion bodies were observed in hepatocytes, biliary epithelium, small intestinal mucosal epithelium, thymus, endothelial cells, ovarian stromal cells, adrenal cortical cells, and neuronal cell bodies in peripheral nerve ganglia. Transmission electron microscopy visualised herpesviral particles in virus culture supernatant, and within the nuclei of hepatocytes, biliary epithelium, and endothelial cells in case tissues. The genome sequence of this herpesvirus, designated anatid alphaherpesvirus 2 (AnHV‐2), is described. While investigating goose mortalities, archived isolate from a swan with suspected herpesvirus infection was tested and genome sequencing identified a further novel herpesvirus, proposed anatid alphaherpesvirus 3 (AnHV‐3). The AnHV‐2 and AnHV‐3 genomes were more similar to each other, with a nucleotide identity of 76.1%, than to reference genome sequences. Phylogenetically, the new genomes formed a distinct clade within the alphaherpesvirus genus Mardivirus. We sequenced four AnHV‐2 genomes from different cases and these did not display consistent divergence over time or distance. Expanded surveillance and outbreak testing are recommended, facilitated by the development of a specific real‐time PCR for the rapid detection of AnHV‐2. [ABSTRACT FROM AUTHOR]

Four types of influenza viruses (A-D) have been confirmed (https://www.cdc.gov/flu/about/viruses/types. htm). The recently discovered influenza D virus is thought to cause respiratory diseases primarily in cattle and to a lesser [...]

Abstract Pigs are often co-infected by different viral strains from the same virus. Up to now, there are few reports about co-existence of different porcine circovirus type 2 (PCV2) strains in China. The aim of this study was to evaluate it in Chinese swine herds. 118 PCV2 positive DNAs isolated from diseased pigs identified by classic PCR were re-detected using a modified differential PCR assay. The results indicated that co-existence rates of PCV2 were 32.2% (38/118) in diseased pigs and 0% (0/41) in asymptomatic pigs. Four PCV2 complete genomes were cloned from two co-infected samples and their nucleotide (nt) identities were 95%-97.3%. The phylogenetic analysis showed that four PCV2 strains were divided into different genotypes, PCV2a, PCV2b, PCV2d and PCV2e, respectively. In addition, co-existence were not detected in 41 serum samples from healthy pigs but PCV2 single infection (31.7%, 13/41) existed. These data revealed that the co-existence of different strains of PCV2 might contribute to the development of more severe clinical symptoms for pigs. This is the first report confirming the co-existence of different PCV2 strains in Chinese swine herds. Meanwhile, this study could help us to understand new infection and prevalence forms of PCV2 clinically.

Abstract To determine whether the novel porcine parvovirus type 4 (PPV4) recently reported in America is prevalent in China, a set of specific primers was designed and used for molecular survey of PPV4 among the clinical samples collected from various provinces of China between 2006 and 2010. The results showed that PPV4 is present in Chinese swine herds at a rate of 2.09% (12/573) among the clinical samples examined and 0.76% (1/132) among the samples taken from healthy animals. We also noted that PPV4 was not detected in samples taken prior to 2009. Analysis of the coding sequences showed that the Chinese and American PPV4 genome sequences are closely related with greater than 99% nucleotide sequence identity. Similar to a previous study, viral genomes in head-to-tail configuration of various lengths of the non-coding region were detected. Our findings confirmed that PPV4 is a unique recently discovered virus in pigs. Phylogenetically, PPV4 is most closely related to bovine parvovirus 2 (BPV2, which is not a Bocavirus and is not assigned to any Parvovirinae genus) and shares limited ORF1 (33.6%) and ORF2 (24.5%) amino acid identity. With respect to genome structure and organization, PPV4 encodes an ORF3 in the middle of the viral genome that resembles the Bocavirus genus. However, the PPV4 ORF3 encoded protein shares minimal amino acid identity with the ORF3 encoded proteins of the Bocavirus genus.