Molecular analysis of Porcine Circovirus Type 2 strains from Uruguay: Evidence for natural occurring recombination

Genomic Characterization and Pathogenicity of BJEU06-1-Like PRRSV-1 ZD-1 Isolated in China

Porcine reproductive and respiratory syndrome virus (PRRSV)-1 and PRRSV-2 have long been cocirculating in China. To date, all PRRSV-1 strains in China have been classified as subtype 1. We investigated the prevalence of PRRSV-1 in several areas of China from 2016 to 2022 and found that BJEU06-1-like strains comprised the main epidemic branch of PRRSV-1. Pathogenicity data for this subgroup are currently lacking. In this study, the Chinese BJEU06-1-like PRRSV-1 strain ZD-1 was isolated from primary alveolar macrophages (PAMs). ZD-1 has undergone no recombination and has a 5-aa discontinuous deletion in the Nsp2 protein, similar to other BJEU06-1-like strains; additionally, ZD-1 has a 26 aa C-terminal truncation in the GP3 gene. Pathogenicity studies revealed that ZD-1 causes obvious clinical symptoms: prolonged fever; reduced body weight; alveolar epithelial proliferation and moderate alveolar diaphragm widening in the lungs; diffuse lymphocytic hyperplasia in the lymph nodes; high levels of viremia in the serum; and elevated viral loads in the lungs, lymph nodes, and tonsils. These results suggested that the BJEU06-1-like PRRSV-1 strain ZD-1 is moderately pathogenic to piglets. This is the first study to evaluate the pathogenicity of the BJEU06-1-like branch in China, enriching the understanding of PRRSV-1 in China.

Exploring the Cause of Diarrhoea and Poor Growth in 8-11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing

Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.

Genetic and phylogenetic analysis of porcine circovirus type 2 on Jeju Island, South Korea, 2019-2020: evidence of a novel intergenotypic recombinant

Porcine circovirus type 2 (PCV2) is the most ubiquitous viral pathogen of pigs and has persistently affected the global swine industry. Since first being identified in South Korea in 1999, the virus has undergone considerable genetic change and genotype shifts during the past two decades. These events have contributed to the coexistence of genotypes PCV2a, PCV2b, and PCV2d in Korean pig populations, which may promote viral recombination. The genotypic and phylogenetic characteristics of PCV2 strains circulating in pig herds on Jeju Island from 2019 to 2020 were the focus of this study. Genotype-specific PCR indicated that PCV2d is the dominant viral genotype and that coinfections with PCV2d and PCV2a (75%) or PCV2a and PCV2b (25%) are common in provincial pig herds. The complete genome sequences of 11 PCV2 strains, including three PCV2a, two PCV2b, and six PCV2d strains, were determined. A genomic comparison showed that all of the viruses had the highest nucleotide sequence identity to their corresponding genotypic reference strain. Notably, genetic and phylogenetic analysis revealed that one PCV2d strain, KNU-1931, exhibited nucleotide sequence variation in the ORF1 gene when compared to other PCV2d strains but showed a high degree of similarity to the PCV2b strains. Comprehensive recombination analysis suggested that KNU-1931 originated from natural recombination within ORF1 between PCV2b (the minor parent) and PCV2d (the major parent) strains. Our findings provide information about the frequency of genetic recombination between two different PCV2 genotypes circulating in the field domestically, illustrating the importance of continual intergenotypic recombination for viral fitness when multiple genotypes are present.

Genetic diversity of Indian porcine circovirus type 2 (PCV2) isolates (2006-2018)

Porcine circovirus type 2 (PCV2) is an emerging viral infection in swine population and results in severe economic loss to piggeries worldwide. The present study was conducted to explore the genetic diversity of PCV2 circulating in swine population of India from 2006–2018. A total of 74 heart, lungs, spleen and lymph nodes collected from different regions in Uttar Pradesh, India were subjected to molecular analysis. For studying genetic diversity, the complete nucleotide and ORF2 sequences of 95 PCV2 including 43 nucleotide sequences from India were used. DNA was extracted from samples and positive samples were subjected to full genome sequencing and phylogenetic analysis was done by maximum likelihood method. Phylogenetic analysis of 40 Indian PCV2 genomes downloaded from GenBank along with three new isolates from the current study based on the complete genome and cap gene together with nucleotide sequences of PCV2 isolates from different countries results in a tree in which Indian isolates clustered in 4 different branches includes PCV2b-1C, PCV2a-2D, PCV 2b-1A/B, PCV 2d-2 recombinant group and two new cluster in which one clustered along with unclassified PCV2 viruses from Indonesia and Croatia. The comparison of ORF2 gene among Indian isolates revealed nucleotide identity ranging from 88.6% to 99.6%, indicating the genetic diversity of PCV2 strains circulating in Indian pig. The present work reports for the first time in India the PCV2-1A/B cluster of 2b genotype and all the Indian isolates available in India from 2006–2018 were used in this analysis.

Viral metagenomics in Brazilian Pekin ducks identifies two gyrovirus, including a new species, and the potentially pathogenic duck circovirus

Viral metagenomics coupled to high-throughput sequencing has provided a powerful tool for large-scale detection of known and unknown viruses associated to distinct hosts and environments. Using this approach, known and novel viruses have been characterized from sylvatic and commercial avian hosts, increasing our understanding of the viral diversity in these species. In the present work we applied an exploratory viral metagenomics on organs (spleen, liver and bursa of Fabricious) of Pekin ducks from Southern Brazil. The virome contained sequences related to a known duck pathogen (duck circovirus) and a number of other circular ssDNA viruses. Additionally, we detected avian gyrovirus 9 (to date detected only in human feces) and one new avian gyrovirus species, to which is proposed the name avian gyrovirus 13 (GyV13). This study is expected to contribute to the knowledge of the viral diversity in Pekin ducks.

Genetic analysis of porcine circovirus type 2 (PCV2) in Queensland, Australia

OBJECTIVE

To determine the current porcine circovirus type 2 (PCV2) genotypes circulating in pigs in Queensland (QLD).

METHODS

The PCV2 infection status of pigs was determined by real-time PCR testing of 210 lymph nodes and 30 serum samples derived from 45 QLD farms. PCV2-positive samples from 22 pigs from 15 farms were subjected to conventional polymerase chain reaction (PCR) and sequencing of the full PCV2 genome. Phylogenetic analysis of 17 of these sequences in relation to published PCV2 sequences was then performed, and the genotypes were compared.

RESULTS

PCV2 DNA was detected in 95 lymph nodes and 15 serum samples. Phylogenetic analysis of 17 PCV2 sequences demonstrated that seven belonged to genotype PCV2b, two to PCV2d, one to PCV2f and seven to an "intermediate group" that clustered with PCV2d on the full genome analysis.

CONCLUSION

This work confirms earlier studies reporting the presence of PCV2b in Australia. It is the first study to report that PCV2d and PCV2f are also present in this country. PCV2d is currently a fast-spreading genotype globally, with reported high virulence. The potential implications of these findings with respect to pathogenicity and vaccine efficacy require further investigation.

High-frequency mutation and recombination are responsible for the emergence of novel porcine reproductive and respiratory syndrome virus in northwest China

Porcine reproductive and respiratory syndrome (PRRS) is one of the most highly infectious diseases in the pig industry, resulting in enormous economic losses worldwide. In this study, a PRRS virus (PRRSV) strain was isolated from primary porcine alveolar macrophage cells in Xinjiang in northwest China. This new strain was sequenced and designated as XJzx1-2015, and its sequence was then compared to those of other representative PRRSV strains from around the world. Complete genomic characterisation showed that the full-length nucleotide sequence of XJzx1-2015 exhibited low-level similarity to NB/04 (91.6%), JXA1 (90.5%), CH-1a (90.2%), VR-2332 (86.9%), QYYZ (85.7%), and JL580 (82.2%), with the highest similarity to HK13 (91.7%) sequence identity. Nonstructural protein 2 (NSP2) and glycosylated protein (GP) 2 of XJzx1-2015 had deletions of five and two amino acids, respectively, corresponding to strain VR-2332 positions 475-479 and 173-174. Phylogenetic analysis based on complete genome sequences showed that XJzx1-2015 and four other strains from China formed a new subgenotype closely related to other sublineage 8.7 (JXA1-like) strains belonging to the North American genotype. However, phylogenetic analysis based on NSP2 and GP5 showed that XJzx1-2015 clustered with sublineage 8.7 (JXA1-like, CH-1a-like) and lineage 3 (QYYZ-like) strains, respectively. Recombination analysis indicated that XJzx1-2015 is an intersubgenotype recombinant of CH-1a-like and QYYZ-like strains. Overall, our findings demonstrate that XJzx1-2015 is a novel PRRSV strain with a significantly high frequency of mutation and a recombinant between lineage 3 and sublineage 8.7 identified in northwest China. These results provide important insights into PRRSV evolution.

Emergence of a novel recombinant porcine circovirus type 2 in China: PCV2c and PCV2d recombinant

Porcine circovirus type 2 (PCV2) has been causing huge economic losses in Chinese swine herds since it was first identified in China in 1999. Genotypes of PCV2 except for PCV2c coexist in swine herds in China, which may facilitate virus recombination. In the current study, six novel PCV2 strains were detected in China, and these strains shared high nucleotide similarity of the Rep gene with the PCV2c strain DK1987PMWSfree and high homology of the Cap gene with PCV2d. Genome sequence analysis revealed that the complete genomes of these strains were 1767 nucleotides (nt) in length and shared 99.8%-99.9% nucleotide identity with each other and 91.7%-98.7% with representative strains. Phylogenetic analysis, sequencing analysis, base-by-base comparisons and comprehensive recombination analysis demonstrated that these six strains originated from recombination within the Rep gene between PCV2c and PCV2d strains. Surprisingly, further investigation through theoretical recombination analysis of Chinese PCV2 GenBank sequences showed that these novel patterns of recombinant PCV2 strains have been generated since 2010. Collectively, our findings provide additional evidence of inter-genotypic recombination of PCV2.

Efficacy of Type 2 PRRSV vaccine against challenge with the Chinese lineage 1 (NADC30-like) PRRSVs in pigs

The objective of the present study was to determine the cross-protection of Ingelvac PRRS MLV against challenge with the new lineage 1 PRRSV emerged in China in pigs. Two lineage 1 PRRSV strains (FJZ03 and FJWQ16 originated from recombination event between NADC30 and JXA1-like strain). We found that pigs vaccinated with the vaccine were protected against challenge with the FJZ03 as shown by fewer days of clinical fever, reduced lung pathology scores, lower PRRS virus load in the blood and developed broadly neutralizing antibodies with high titers to FJZ03. In contrast, vaccine provided limited protection against challenge with FJWQ16 with higher fever, lower antibody titers, lower neutralizing antibodies and higher viral loads in blood. These results demonstrate PRRSV-MLV provides incomplete protection against new lineage 1 PRRSVs.

Recombination in lineage 1, 3, 5 and 8 of porcine reproductive and respiratory syndrome viruses in China

Porcine reproductive and respiratory syndrome (PRRS) is one of the most important viral swine diseases, resulting in immense economic losses in Chinese pig industry. Currently, four major lineages: lineage 1 (NADC30-like), 3 (QYYZ-like), 5.1 (VR2332-like) and 8.7 (JXA1-like) of type 2 PRRSV (North American type) have been circulating in China based on classification system, which have caused concern about the potential of virus recombination. In the present study, a novel variant of PRRSV strain named FJLIUY-2017 was isolated from abortion rate (25%) in pregnant gilts in Fujian Province in China in 2017. To further our knowledge about the novel virus strain, we characterized the complete genome of FJLIUY-2017. Comparison to PRRS sequences in GenBank confirmed the absence of close relatives (<92%), but indicated FJLIUY-2017 belonged to NADC30-like PRRSV. The full length of FJLIUY-2017 was determined to be 15017 nucleotides (nt), excluding the poly(A) tail, shared 86.2-86.6% identity with JXA1-like strains (JXA1, TJ and FJYR), 88.9-90.6% with NADC30-like PRRSVs (NADC30, FJZ03 and CHsx1401), 86.4-86.5% with VR2332-like (VR2332, RespPRRS MLV and BJ-4) and only 60.8% with LV (European type). Recombination analyses revealed genomic breakpoints in structural (ORF3, ORF4 and ORF7) and nonstructural (Nsp1, Nsp2, Nsp6, Nsp9, Nsp11 and Nsp12) regions of the genomes with evidence for recombination events between lineages 1, 3, 5.1 and 8.7. Taken altogether, the results of our study provide further confirmation that PRRSV is prone to undergo recombination events. Thus, it is critical to monitor PRRSV evolution in China and establish an effective strategy for the control of PRRS.

Porcine circovirus 2 in the North Eastern region of India: Disease prevalence and genetic variation among the isolates from areas of intensive pig rearing

Porcine Circovirus type-2 (PCV-2) is considered as a major threat to the piggery sector in India. To ascertain the epidemiological status and infection level of PCV2, a pilot study was undertaken to find out the prevalence of PCV2 in swine population by ELISA and PCR in the interior and border areas of Meghalaya which includes the area where accessibility and medical aid is a rare phenomenon. A total of 249 serum samples were collected from October 2014 to February 2016 from three divisions of Meghalaya: Khasi, Jaintia and Garo Hills Divisions. The mean positivity of PCV-2 antibodies in suspected sera was 83.93% whereas 62.25% of the suspected samples respectively were found to contain PCV2 as detected by PCR. Additional 190 tissue samples were collected during necropsy from both symptomatic and asymptomatic animals following reported outbreak in this region, which indicated a mean positivity of 18.94% (36/190); out of which 13 samples were subjected to sequencing to find out the genetic diversity of PCV2 amongst the field isolates. Molecular characterization and phylogenetic analysis of PCV2 isolates based on cap gene depicted genetic diversity among the strains in pig population of Meghalaya as the isolates belonged to PCV2a, PCV2b-1c and PCV2d genotypes; identification of the PCV2d genotype is probably the first report from Meghalaya. Four isolates forming an outlier group in the phylogenetic tree were arising out of natural inter-genotypic recombination between PCV2a and PCV2b. PCV2 being immunosuppressive in nature impairs the host immune response increasing the susceptibility to other co-infections leading to disease severity and high mortality in pig population. This baseline data gives a brief epidemiological status of PCV2 infection and circulating PCV2 genotype in this region which will be useful in the formulation of control and eradication programs in remotes areas of Meghalaya where accessibility is less and vaccination is a rare practice.

Novel canine circovirus strains from Thailand: Evidence for genetic recombination

Canine circoviruses (CanineCV's), belonging to the genus Circovirus of the Circoviridae family, were detected by next generation sequencing in samples from Thai dogs with respiratory symptoms. Genetic characterization and phylogenetic analysis of nearly complete CanineCV genomes suggested that natural recombination had occurred among different lineages of CanineCV's. Similarity plot and bootscaning analyses indicated that American and Chinese viruses had served as major and minor parental viruses, respectively. Positions of recombination breakpoints were estimated using maximum-likelihood frameworks with statistical significant testing. The putative recombination event was located in the Replicase gene, intersecting with open reading frame-3. Analysis of nucleotide changes confirmed the origin of the recombination event. This is the first description of naturally occurring recombinant CanineCV's that have resulted in the circulation of newly emerging CanineCV lineages.

Detection and phylogenetic characterization of porcine circovirus 2 from pigs in Mozambique

Porcine circovirus-associated diseases (PCVADs), caused by porcine circovirus 2 (PCV-2), have a significant economic impact on the swine industry worldwide. In Africa, there is little information, to date, regarding the occurrence of PCV-2, and it has not been reported in Mozambique's swine population. We randomly collected mesenteric lymph nodes ( n = 111) from slaughtered pigs from 9 districts in southern Mozambique. PCV-2 DNA was detected in 54% (62 of 111) of the samples and 78% (23 of 31) of the farms. PCV-2 antigen was detected by immunohistochemistry in lymph nodes (6 of 62; 10%) that were positive for PCV-2 by PCR. Histopathologic changes observed in these lymph nodes were lymphoid depletion, multifocal nodal necrosis, and infiltrates of histiocytes and multinucleate giant cells. One positive sample from each district was selected in order to obtain sequences covering the ORF2 region. Five sequences clustered with PCV-2d, of which 3 sequences from Maputo, Namaacha, and Moamba were grouped with PCV-2d-2; 2 sequences from Manhiça and Matola were grouped as PCV-2d-1; and 4 sequences from Boane, Matutuíne, Chibuto, and Xai-Xai were closely related to PCV-2b-1A/B genotypes. Our study indicates that a diversity of PCV-2 viruses is circulating in the Mozambican swine population.

High prevalence of PCV2d in Hunan province, China: a retrospective analysis of samples collected from 2006 to 2016

Porcine circovirus 2 (PCV2) has been widely prevailing in China since the first report in 2001, causing huge economic losses to the pig industry. In the present study, 674 samples were collected from 2006 to 2016 in Hunan province, and 62% were positive for PCV2. An increase was observed from 2006 to 2011 (72.1%-89.1%), and a decrease was observed from 2012 to 2016 (78.9%-36.8%). The prevalence of genotype PCV2a, PCV2b, and PCV2d was 0, 44.7% and 67%, respectively. During 2006-2007, PCV2b was the main genotype circulating in Hunan, while, in 2008, PCV2d became the predominant one. Coinfection with PCV2b and PCV2d was observed frequently, and the positive rates of coinfection ranged from 6.3% to 18.9% during 2006-2016. The complete genome was sequenced for 54 positive samples, and four were identified as PCV2b-1, 22 as PCV2b-2, four as PCV2d-1 and 24 as PCV2d-2, based on phylogenetic analysis of the complete genome and ORF2 region. Recombination analysis using the complete genome sequences of these isolates revealed a high recombination rate of 27.7% (17/54), and showed that recombination occurred mainly in the ORF1 region. This shows that the prevalence of PCV2 has clearly decreased in recent years and that PCV2d has become a predominant genotype since 2008. In addition, frequent recombination events were observed in the PCV2 isolates from Hunan, China.

Detection of PCV2e strains in Southeast China

Porcine circovirus 2 (PCV2) has been prevalent in swine herds in China since 2002, causing severe economic loss to the pig industry. The number of live pigs in southeast China is > 20 million. Since information on the genetic variation of PCV2 in the Fujian province is limited, the objective of the present work was to investigate the epidemiological and evolutionary characteristics of PCV2 in southeast China from 2013 to 2017. Of the 685 samples collected from 90 different swine herds from 2013 to 2017, 356 samples from 84 different swine herds were positive for PCV2. PCV2a, PCV2b, PCV2d, and PCV2e co-existed in the Fujian province, with PCV2d being the predominant circulating strain in swineherds and PCV2e being reported for the first time in China. Strikingly, PCV2-FJ-water DNA comes from contaminated river water and not infected animals. Sequence comparison among all isolates indicated that 95 isolates shared approximately 78.7%–100% nucleotide identity and 74.5%–100% amino acid identity for open reading frame 2 (ORF2). Amino acid alignment showed that the Cap protein of PCV2e differed markedly from those of PCV2a, PCV2b, PCV2c, and PCV2d. These results indicated that various PCV2 genotypes exist in China, and that PCV2 is continuously evolving, leading to rapid emergence of new variant stains.

Phylogenetic analysis of two goat-origin PCV2 isolates in China

Complete genome characterization of non-porcine origin Porcine circovirus type 2 (PCV2) was first described in 2014 in China. In the present study, we first identified PCV2 nucleotides in goat samples and the prevalence of PCV2 in goat was 6.15%. However, only two new strains, Goat2014-4 and Goat2014-5, could be completely sequenced. The genome of the strain Goat2014-4, which collected from the goat infected with PPRV, contains 1766 nt; strain Goat2014-5, which originated from a healthy goat, is comprised of 1767 nt. The results showed that they shared the highest nucleotide identity with BDH and the lowest similarity with DK1980PMWSfree strain and they belonged only to genotype PCV2d. Meanwhile, they shared higher homology with porcine-origin PCV2 strains than others. Moreover, a detailed analysis of the capsid amino acid sequences revealed that there were distinct differences for goat2014-4 (708 bp) and goat2014-5 (705 bp); strain Goat2014-4 showed an elongation of two amino acids, and strains Goat2014-5 showed an elongation of one amino acid compared with other reference strains. This is the first report of the genetic analysis of goat-origin PCV2 isolates. It also provides an additional supported evidence for cross-species transmission of PCV2.

Genetic analysis of porcine circovirus type 2 from pigs affected with PMWS in Chile reveals intergenotypic recombination

Background

Porcine circovirus type 2 (PCV2) is a very small, non-enveloped and icosahedral virus, with circular single stranded DNA genome. This virus is the most ubiquitous and persistent pathogen currently affecting the swine industry worldwide. PCV2 has been implicated as the major causative agent of postweaning multisystemic wasting syndrome (PMWS), a disease which is characterized by severe immunosuppressive effects in the porcine host. Worldwide PCV2 isolates have been classified into four different genotypes, PCV2a, PCV2b, PCV2c and PCVd. The goal of this work was to conduct the first phylogenetic analysis of PCV2 in Chile.

Methods

PCV2 partial ORF2 sequences (462 nt) obtained from 29 clinical cases of PMWS in 22 Chilean intensive swine farms, covering over the 90% of the local pork-production, were analyzed.

Results

14% and 52% of sequences belonged to the genotypes PCV2a and PCV2b, respectively. Surprisingly, 34% of sequences were PCV2a/PCV2d recombinant viruses.

Conclusions

Our findings suggested that a novel cluster of Chilean sequences emerged resulting from intergenotypic recombination between PCV2a and PCV2d.

Genetic diversity and evolutionary characteristics of type 2 porcine reproductive and respiratory syndrome virus in southeastern China from 2009 to 2014

The objective of this study was to assess the genetic diversity of porcine reproductive and respiratory syndrome virus circulating in Fujian province (southeastern China). Based on 53 ORF5 nucleotide sequences collected from nine sites, both highly pathogenic (sublineage 8.7) and lineage 1 strains were circulating in Fujian in 2009-2014 along with lineages 3 and 5.1. Notably, the lineage 1 strains were closely related to the NADC30 strain circulating in North America and were the predominant strains in 2014. In addition, we found that nonstructural protein 2 (NSP2) was the most variable nonstructural protein in Fujian isolates, with a 36-amino-acid (aa) insertion and seven different deletions detected in the 53 sequences examined. Similarly, analysis of GP5 amino acid sequences showed that the isolates were highly variable in primary neutralizing epitopes. Interesting, FJ3.2 and FJ7-2 strains have the mutation N44K, but they exhibited high replication and high titers in MARC-145 and PAM cells. The complete genome sequences determined for 12 type 2 isolates were 82.1-99.3% identical and were 15,016-15,407 nucleotides (nt), in length excluding the poly(A) tail. The strains also shared 88.2-99.4% identity with strain VR2332 (the prototype North American strain), 83.4-99.2% identity with strain JXA1 (the prototype high-pathogenicity Chinese strain), 88.2-97.1% identity with strain CH-1a (the prototype classical Chinese strain), and 82.9-97.1% identity with strain NADC30 (the prototype NADC30-like strain). Strikingly, phylogenetic and molecular evolutionary analyses indicated that strain FJW05 is a spontaneous recombinant between a circulating lineage 1 virus and the vaccine strain JXA1-R, which is derived from the highly pathogenic strain JXA-1. Collectively, the data highlight the epidemiology of porcine reproductive and respiratory syndrome in Fujian and may aid in selecting a suitable vaccine for use on pig farms.

Recombination in JXA1-R vaccine and NADC30-like strain of porcine reproductive and respiratory syndrome viruses

Porcine reproductive and respiratory syndrome (PRRS) is considered one of the most devastating swine diseases worldwide, resulting in immense economic losses. PRRS virus (PRRSV) has undergone rapid evolution since its first recognition in 1990s. In the present study, a PRRSV strain named FJXS15 causing high morbidity and mortality was isolated from piglets and sows from a farm participating in vaccination in China. Phylogenetic and molecular evolutionary analyses revealed that FJXS15 was highly similar to the JXA1-R vaccine strain (a live attenuated virus vaccine strain derived from the highly pathogenic PRRSV JXA1) in the ORF1a (nt 901-)-ORF4 (-nt 419) coding regions, as well as to FJZ03 (lineage 1, NADC30-like) in the 5'-UTR, ORF5a-ORF7 coding regions, and 3'-UTR, suggestive of a natural recombination event. Recombination analyses showed that recombination events occurred in two inter-lineage recombination events between Lineages 1 and 8 based on based on classification system (Shi et al., 2010), and two recombination breakpoints at positions 1-1092 and 13771-15537 of the sequence alignment (with reference to the VR-2332 strain). Animal experiments demonstrated that FJXS15-infected animals had more severe histopathological lung lesions than did JXA1-R-infected and control groups. A 25% mortality rate was found in FJXS15-infected piglets, which was similar to that found with other Chinese HP-PRRSV strains. Thus, the recombinant virus is a highly virulent PRRSV. Moreover, this report provides evidence for inter-subgenotypic recombination between the JXA1-R vaccine virus and a circulating Lineage 1 virus.

Molecular Detection of Pseudorabies Virus (PrV), Porcine Parvovirus (PPV) and Porcine Circovirus 2 (PCV2) in Swine in Republic of Montenegro

The presence of pseudorabies virus (PrV), porcine parvovirus (PPV) and porcine circovirus 2 (PCV2) was examined in sixty samples (spleen and lymph nodes) and thirty samples of sacral ganglia collected from non-vaccinated swine by virus isolation and polymerase chain reaction (PCR). Using PCR method PrV was detected in three samples, PPV in seven samples and six samples were found positive for PCV2. The phylogenetic analysis of the nucleotide sequences of three PrV isolates identified in this study showed high similarity and significant clustering within the PrV genotype I strains such as Kaplan and Bartha isolated from pigs in Hungary, strain Becker isolated in USA and strain Kolchis isolated in Greece. The nucleotide sequences of two PPV isolates showed high level of similarity with the strain Challenge isolated from pigs in UK, strain Kresse isolated in USA and strains 77 and LZ isolated in China. The phylogenetic analysis of the nucleotide sequences of two PCV2 isolates showed high level of similarity and significant clustering within genotype PCV2b strains such as NIVS-3, NIVS-5 and NIVS-6 isolated in Serbia, strain 3959 isolated in Austria, strain PM165 isolated from pigs in Brasil, and strain XT2008 isolated in China. The results of our study present the molecular characterization of PrV, PPV and PCV2 identified in swine in Republic of Montenegro. Besides that, these results confirmed that PCR is a very useful method for rapid detection of these viruses in subclinically infected swine.

Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay

Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility.

Antigenic Determinants of Possible Vaccine Escape by Porcine Circovirus Subtype 2b Viruses

Currently available commercial vaccines against porcine circovirus strain 2 (PCV2) solely target the PCV2a genotype. While PCV2 vaccines are highly effective in preventing clinical signs, PCV2b has dominated over the PCV2a genotype in prevalence, corresponding with the introduction of PCV2a vaccines. A recently emerged PCV2b recombinant with an additional amino acid in the capsid protein, designated the mutant PCV2b (mPCV2b), is cause for concern due to its increased virulence and rapid spread. The accumulation of recent evidence for the increased genetic diversity in PCV2 suggests that current vaccines against PCV2a may be inducing selection pressure and driving viral evolution. In this study, the hypothesis that differences in key immune epitopes between the PCV2a vaccine strains, a classical PCV2b strain called PCV2b 41513 obtained from a vaccine-failure case, and mPCV2b strains could promote vaccine escape was tested using immuno-informatic tools. In the major viral proteins, 9 of the 18 predicted swine leukocyte antigens (SLA) class-I epitopes, 8 of the 22 predicted SLA class-II epitopes, and 7 of the 25 predicted B cell epitopes varied between the vaccine and field strains. A majority of the substitutions in both the T- and B-cell epitopes were located in the capsid protein. Some B- and T-cell epitopes that were identified as immunogenic in the vaccine strain were not identified as epitopes in the field strains, indicating a subtle shift in the antigenic profile of the field strains. Several nonconserved epitopes had both predicted B- and T-cell functions. Therefore, substitutions in the dual epitopes could affect both arms of the immune response simultaneously, causing immune escape. Our findings support further rational design of PCV2 vaccines to increase the current threshold of protection.

First identification of Porcine Circovirus Type 2b mutant in pigs from Uruguay

Porcine Circovirus Type 2 (PCV2) is a worldwide distributed virus and is considered an important emerging pathogen related to several distinct disease syndromes in pigs. PCV2 strains are classified into three genotypes: PCV2a, with five subtypes (2A-2E), PCV2b with three subtypes (1A-1C) and PCV2c, only found in Denmark. Recently, several reports suggested the circulation of newly emerging PCV2b mutants (mPCV2b) isolated from pigs with PCVAD in cases of suspected vaccine failure. In this work, we report for the first time the identification of mPCV2b in pigs from Uruguay, providing an additional evidence of a global circulation. Complete genome characterization and phylogenetic analysis reveal that Uruguayan strains, as well as mPCV2b previously reported are closely related to other sequences already classified as PCV2b-1C. Furthermore, results showed that mPCV2b presented different genetic markers in the capsid protein compared with classical PCV2a/b strains. Further investigation about antigenic shift of the mPCV2b strains including the Uruguayan isolates is needed.

Recurrent positive selection and heterogeneous codon usage bias events leading to coexistence of divergent pigeon circoviruses

The capsid genes from 14 pigeon circovirus (PiCV) sequences, collected from Taiwan between 2009 and 2010, were sequenced and compared with 14 PiCV capsid gene sequences from GenBank. Based on pairwise comparison, PiCV strains from Taiwan shared 73.9-100% nucleotide identity and 72-100% amino acid identity with those of the 14 reported PiCV sequences. Phylogenetic analyses revealed that Taiwanese PiCV isolates can be grouped into two clades: clade 1 comprising isolates from Belgium, Australia, USA, Italy and China, and clade 2 showing close relation to isolates from Germany and France. Recurrent positive selection was detected in clade 1 PiCV lineages, which may contribute to the diversification of predominant PiCV sequences in Taiwan. Further observations suggest that synonymous codon usage variations between PiCV clade 1 and clade 2 may reflect the adaptive divergence on translation efficiency of capsid genes in infectious hosts. Variation in selective pressures acting on the evolutionary divergence and codon usage bias of both clades explains the regional coexistence of virus sequences congeners prevented from competitive exclusion within an island such as Taiwan. Our genotyping results also provide insight into the aetiological agents of PiCV outbreak in Taiwan and we present a comparative analysis of the central coding region of PiCV genome. From the sequence comparison results of 28 PiCVs which differs in regard to the geographical origin and columbid species, we identified conserved regions within the capsid gene that are likely to be suitable for primer selection and vaccine development.

Synonymous codon usage in TTSuV2: analysis and comparison with TTSuV1

Two species of the DNA virus Torque teno sus virus (TTSuV), TTSuV1 and TTSuV2, have become widely distributed in pig-farming countries in recent years. In this study, we performed a comprehensive analysis of synonymous codon usage bias in 41 available TTSuV2 coding sequences (CDS), and compared the codon usage patterns of TTSuV2 and TTSuV1. TTSuV codon usage patterns were found to be phylogenetically conserved. Values for the effective number of codons (ENC) indicated that the overall extent of codon usage bias in both TTSuV2 and TTSuV1 was not significant, the most frequently occurring codons had an A or C at the third codon position. Correspondence analysis (COA) was performed and TTSuV2 and TTSuV1 sequences were located in different quadrants of the first two major axes. A plot of the ENC revealed that compositional constraint was the major factor determining the codon usage bias for TTSuV2. In addition, hierarchical cluster analysis of 41 TTSuV2 isolates based on relative synonymous codon usage (RSCU) values suggested that there was no association between geographic distribution and codon bias of TTSuV2 sequences. Finally, the comparison of RSCU for TTSuV2, TTSuV1 and the corresponding host sequence indicated that the codon usage pattern of TTSuV2 was similar to that of TTSuV1. However the similarity was low for each virus and its host. These conclusions provide important insight into the synonymous codon usage pattern of TTSuV2, as well as better understangding of the molecular evolution of TTSuV2 genomes.