A total infectome approach to understand the etiology of infectious disease in pigs

PMAP-37: A versatile cathelicidin for neutralizing bacteria and viruses

Antimicrobial peptides (AMPs), such as cathelicidins, show dual functionality by directly combating pathogens and indirectly eliminating them through stimulation of the immune system, generating interest in their therapeutic potential. Pigs have a large set of 11 cathelicidins, of which PMAP-37 is relatively understudied compared to some of the better-known cathelicidins. This study describes the effectiveness of PMAP-37 against both bacteria and viruses. PMAP-37 exhibited potent in vitro antimicrobial activity against both Gram-positive (Bacillus globigii) and Gram-negative bacteria (Escherichia coli) with minimum bactericidal concentrations (MBCs) of 2.5 and 5 μM, respectively. PMAP-37 caused a rapid permeabilization of E. coli's outer and inner membranes within 5 min, indicating its efficacy in disrupting bacterial cell membranes. Furthermore, PMAP-37 neutralized nitric oxide production in a macrophage cell line stimulated with various forms of LPS, Lipid A, or LTA in a dose-dependent manner. Flow cytometric analysis confirmed PMAP-37's capacity to inhibit LPS binding to macrophages, while zeta potential analysis showed the peptide's capacity to neutralize the negative charge of both the E. coli membrane and LPS micellular surfaces. Interestingly, PMAP-37 also exhibited antiviral activity against an important porcine pathogen, the porcine epidemic diarrhea virus (PEDV). These findings underscore the multifunctional properties of PMAP-37, and provide potential leads for future therapeutic use within the pig industry.

Diseases associated with antimicrobial use in pig farms and risk factors thereof: A cross-sectional study in the Netherlands

BACKGROUND

Current antimicrobial use (AMU) in Dutch pig farms is driven by herd health status, as only therapeutic AMU is permitted. This study focused on weaners and sows with suckling piglets to examine the diseases associated with i) overall AMU (measured in Defined Daily Dosage Animal per year - DDDA/Y), ii) use/not use of specific antimicrobial classes, iii) total consumption of specific antimicrobial classes (in DDDA/Y), and iv) farm characteristics linked to the occurrence of diseases that require AMU.

METHODS

Cross-sectional data on AMU, disease aetiologies for group treatments, and farm characteristics were collected from 154 Dutch pig farms, representing the situation in 2019. Associations between disease occurrence as a predictor and AMU (overall and by antimicrobial class) as an outcome were analyzed using multivariable generalized linear regression models. Subsequently, mixed-effects conditional Random Forest analysis was used to identify farm characteristics associated with these diseases.

RESULTS

Group treatments for musculoskeletal/neurological diseases (MNDs) in suckling piglets, and individual treatments (of unknown aetiology) in sows and suckling piglets, were significantly associated with total AMU there. AMU in weaners was significantly associated with respiratory diseases, MNDs, and individual treatments. Tetracyclines and penicillins were primarily used for respiratory diseases and MNDs in weaners, respectively, and for MNDs in sows and suckling piglets. Having a clear separation between clean and dirty outdoor areas in the farm and using boars from own production for estrus detection were both protective against occurrence of respiratory conditions in weaners, whereas PRRS vaccination in suckling piglets was a risk factor. Streptococcus suis vaccination in sows and fully slatted floors were both risk factors for MNDs in weaners, whereas being an organic farm was protective. Use of disinfecting powders in sows increased MNDs risk in suckling piglets and sows, and a longer lactation period was protective against respiratory diseases and MNDs in weaners.

CONCLUSIONS

Respiratory diseases and MNDs in weaners appeared as the primary aetiologies for antimicrobial group treatments on Dutch pig farms. Prioritizing farm practices that enhance biosecurity and animal welfare is crucial for controlling these diseases and, consequently, reducing AMU.

Discovery of viruses and bacteria associated with swine respiratory disease on farms at a nationwide scale in China using metatranscriptomic and metagenomic sequencing

Respiratory disease (RD) is a worldwide leading threat to the pig industry, but there is still limited understanding of the pathogens associated with swine RD. In this study, we conducted a nationwide genomic surveillance on identifying viruses, bacteria, and antimicrobial resistance genes (ARGs) from the lungs of pigs with RD in China. By performing metatranscriptomic sequencing combined with metagenomic sequencing, we identified 21 viral species belonging to 12 viral families. Among them, porcine reproductive and respiratory syndrome virus, influenza A virus, herpes virus, adenovirus, and parvovirus were commonly identified. However, emerging viruses, such as Getah virus and porcine respiratory coronaviruses, were also characterized. Apart from viruses, a total of 164 bacterial species were identified, with Streptococcus suis, Mycoplasma hyorhinis, Mycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida being frequently detected in high abundances. Notably, Escherichia coli, Enterococcus faecalis, Staphylococcus aureus, and Klebsiella pneumoniae were also highly detected. Our further analysis revealed a complex interaction between the identified pathogens in swine RD. We also conducted retrospectively analyses to demonstrate the prevalent viral genotypes or bacterial serotypes associated with swine RD in China. Finally, we identified 48 ARGs, which conferred resistance to 13 predicted antimicrobial classes, and many of these ARGs were significantly associated with a substantial number of mobile genetic elements, including transposons (e.g., tnpAIS1, tnpA1353, int3, and ISCau1) and plasmids (e.g., Col(BS512), Col(YC)]. These findings will contribute to further understanding the etiology, epidemiology, and microbial interactions in swine RD, and may also shed a light on the development of effective vaccines.IMPORTANCEIn this study, we identified viruses and bacteria from the lungs of pigs with RD in China at a nationwide farm scale by performing metatranscriptomic sequencing combined with metagenomic sequencing. We also demonstrated the complex interactions between different viral and/or bacterial species in swine RD. Our work provides a comprehensive knowledge about the etiology, epidemiology, and microbial interactions in swine RD and data reference for the research and development of effective vaccines against the disease.

Evolving spectrum of Pneumocystis host specificity, genetic diversity, and evolution

Following over a century's worth of research, our understanding of Pneumocystis has significantly expanded in various facets, spanning from its fundamental biology to its impacts on animal and human health. Its significance in public health has been underscored by its inclusion in the 2022 WHO fungal priority pathogens list. We present this review to summarize pivotal advancements in Pneumocystis epidemiology, host specificity, genetic diversity and evolution. Following a concise discussion of Pneumocystis species classification and divergence at the species and strain levels, we devoted the main focus to the following aspects: the epidemiological characteristics of Pneumocystis across nearly 260 mammal species, the increasing recognition of coinfection involving multiple Pneumocystis species in the same host species, the diminishing host specificity of Pneumocystis among closely related host species, and the intriguingly discordant evolution of certain Pneumocystis species with their host species. A comprehensive understanding of host specificity, genetic diversity, and evolution of Pneumocystis can provide important insights into pathogenic mechanisms and transmission modes. This, in turn, holds the potential to facilitate the development of innovative strategies for the prevention and control of Pneumocystis infection.

Recombinant characterization and pathogenicity of a novel L1C RFLP-1-4-4 variant of porcine reproductive and respiratory syndrome virus in China

Porcine reproductive and respiratory syndrome (PRRS) is one of the most significant diseases affecting the pig industry worldwide and is caused by the PRRS virus (PRRSV), which has complex genetic variation due to frequent mutations, indels, and recombination. The emergence of PRRSV L1C.5 in 2020 in the United States has raised worldwide concerns about PRRSV with the RFLP 1-4-4 pattern and lineage 1C. However, studies on the pathogenic characteristics, epidemiological distribution, and effectiveness of vaccines against PRRSV with L1C and RFLP1-4-4 pattern in China are still insufficient. In this study, a novel recombinant variant of PRRSV with RFLP 1-4-4 and lineage 1C features, different from L1C.5 in the United States, was isolated in China in 2021. In pathogenicity experiments in specific pathogen-free piglets or farm piglets, 60-100% of artificially infected experimental piglets died with high fever and respiratory symptoms. Inflammatory cytokine and chemokine levels were upregulated in infected piglets. A commercially modified live vaccine against highly pathogenic PRRSV did not provide effective protection when the vaccinated piglets were challenged with the novel L1C-1-4-4 variant. Therefore, this strain merits special attention when devising control and vaccine strategies. These findings suggest that extensive joint surveillance is urgently needed and that vaccine strategies should be updated to prevent the disease from spreading further.

Demographic and zoological drivers of infectome diversity in companion cats with ascites

Cats (Felidae) have become an integral part of many households. However, our understanding of the full spectrum of pathogens affecting cats (referred to as the infectome) is limited, mainly due to the inadequacy of commonly used diagnostic tools in capturing the complete diversity of potential pathogens and the prevalence of pathogen co-infections. In this study, we employed a meta-transcriptomic approach to simultaneously characterize the infectome contributing to different disease syndromes and to investigate spatial, demographic, and ecological factors influencing pathogen diversity and community composition in a cohort of 27 hospitalized cats and seven stray cats. We identified 15 species of pathogens, with Candidatus Rickettsia tarasevichiae and Tritrichomonas foetus representing potential spillover risks. Importantly, although most cases of ascites hyperplasia were explained by coinfection with multiple pathogens, we identified the potential novel clinical outcomes of M. aubagnense infection among cats. We demonstrated that the increase in infectome diversity can be explained by a variety of predictors including age growth, temperature increase, and a higher proportion of females, with age growth presenting the strongest effect. Fine-scale analysis indicated that a higher diversity of infectomes were harbored in young cats rather than adult ones. Our results demonstrated that most feline diseases are better explained by the presence of virus-bacteria or virus-virus coinfection. This study serves as a timely endorsement for clinical diagnosis by vets to consider the cause of a disease based on a panel of cryptical co-infecting pathogens rather than on individual infectious agents.

IMPORTANCE

Frequent studies reported the risks of cats as an intermediate host of zoonotic pathogens (e.g., SARS-CoV-2). Cats have a physically close interaction with their owners through activities like petting, kissing, and being licked on the cheek and hands. However, there are still limited studies that systematically investigate the infectome structure of cats. In this study, we employed a meta-transcriptomics approach to characterize 15 species of pathogens in cats, with Candidatus Rickettsia tarasevichiae first characterizing infection in diseased cats. Most feline diseases were better explained by the presence of virus-bacteria or virus-virus coinfection. The increase in infectome diversity could be influenced by a variety of predictors including age growth, temperature increase, and a higher proportion of females. A higher diversity of pathogens was harbored in young cats rather than adults. Importantly, we showed the value of linking the modern influx of meta-transcriptomics with comparative ecology and demography and of utilizing it to affirm that ecological and demographic variations impact the total infectome.

Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease

Companion animals such as cats and dogs harbor diverse microbial communities that can potentially impact human health due to close and frequent contact. To better characterize their total infectomes and assess zoonotic risks, we characterized the overall infectomes of companion animals (cats and dogs) and evaluated their potential zoonotic risks. Meta-transcriptomic analyses were performed on 239 samples from cats and dogs collected across China, identifying 24 viral species, 270 bacterial genera, and two fungal genera. Differences in the overall microbiome and infectome composition were compared across different animal species (cats or dogs), sampling sites (rectal or oropharyngeal), and health status (healthy or diseased). Diversity analyses revealed that viral abundance was generally higher in diseased animals compared to healthy ones, while differences in microbial composition were mainly driven by sampling site, followed by animal species and health status. Disease association analyses validated the pathogenicity of known pathogens and suggested potential pathogenic roles of previously undescribed bacteria and newly discovered viruses. Cross-species transmission analyses identified seven pathogens shared between cats and dogs, such as alphacoronavirus 1, which was detected in both oropharyngeal and rectal swabs albeit with differential pathogenicity. Further analyses showed that some viruses, like alphacoronavirus 1, harbored multiple lineages exhibiting distinct pathogenicity, tissue, or host preferences. Ultimately, a systematic evolutionary screening identified 27 potential zoonotic pathogens in this sample set, with far more bacterial than viral species, implying potential health threats to humans. Overall, our meta-transcriptomic analysis reveals a landscape of actively transcribing microorganisms in major companion animals, highlighting key pathogens, those with the potential for cross-species transmission, and possible zoonotic threats.

IMPORTANCE

This study provides a comprehensive characterization of the entire community of infectious microbes (viruses, bacteria, and fungi) in companion animals like cats and dogs, termed the "infectome." By analyzing hundreds of samples from across China, the researchers identified numerous known and novel pathogens, including 27 potential zoonotic agents that could pose health risks to both animals and humans. Notably, some of these zoonotic pathogens were detected even in apparently healthy pets, highlighting the importance of surveillance. The study also revealed key microbial factors associated with respiratory and gastrointestinal diseases in pets, as well as potential cross-species transmission events between cats and dogs. Overall, this work sheds light on the complex microbial landscapes of companion animals and their potential impacts on animal and human health, underscoring the need for monitoring and management of these infectious agents.

The use of oral fluids and sock samples for monitoring key pathogens in pig populations for surveillance purposes

Despite the prevalence of co-infections and the association of over 50 viral and 46 bacterial pathogens with pig diseases, little is known about their simultaneous occurrence, particularly in commercial pig farming environments where health programs are in place. To address this knowledge gap, this study aimed to evaluate the pathogen threshold of respiratory and enteric pathogens in pig herds using the Pork MultiPath™ (PMP1 and PMP2, respiratory and enteric respectively) technology, which detects multiple pathogens simultaneously in a single reaction with high sensitivity and specificity. In this study the most prevalent respiratory pathogens, Mycoplasma hyrohinis, Pasteurella multocida, and Haemophilus parasuis detected by PMP1 were effectively controlled during the nursery stage through strategic treatment with tiamulin. Even though the major respiratory incidences were reduced, the recorded coughing and sneezing rates were associated with the levels of H. parasuis and M. hyrohinis, which were set at 1356 and 1275 copies/reaction, respectively. In addition, one of the identified co-infection patterns indicated a strong relationship between the occurrence of H. parasuis and M. hyorhinis at the sample and pen levels, highlighting the high likelihood of detecting these two pathogens together. Testing with enteric panel PMP2 revealed that the most frequently detected virulence factors during the early nursery stage were Escherichia coli genes for toxins - ST1, ST2, and fimbriae - F4 and F18. Moreover, a co-infection with Rotavirus B and C was often observed during the nursery stage, and a strong positive correlation between these two markers has been identified. Additionally, the levels of several markers, namely E. coli F4, F5, F18, LT, ST1, and ST2, have been associated with a higher likelihood of sickness in pig populations. In addition, the onset of Brachyspira pilosicoli during the nursery and grower stages was found to be associated with an increased risk of diarrhoea, with a set threshold at around 500 copies/reaction. Although simultaneous detection of multiple pathogens is not yet widely used in the pig industry, it offers a significant advantage in capturing the diversity and interactions of co-infections. Testing pooled samples with Pork MultiPath™ is cost-effective and practical to regularly monitor the health status of pig populations.

Meta-Transcriptomic Analysis Reveals Novel RNA Viruses in Polychaetes Perinereis

Perinereis species are essential benthonic animals in coastal ecosystems and have significant roles as live feed in aquaculture, owing to their high-protein and low-fat nutritional profile. Despite their ecological importance, the viral communities associated with these organisms need to be better understood. In this study, we generated 2.6 × 108 reads using meta-transcriptomic sequencing and de novo assembled 5.3 × 103 virus-associated contigs. We identified 12 novel RNA viruses from two species, Perinereis aibuhitensis and P. wilsoni, which were classified into four major viral groups: Picobirnaviridae, Marnaviridae, unclassified Picornavirales, and unclassified Bunyavirales. Our findings revealed the hidden diversity of viruses and genome structures in Perinereis, enriching the RNA virosphere and expanding the host range of Picobirnaviridae, Marnaviridae, and Bunyavirales. This study also highlighted the potential biosecurity risk of the novel viruses carried by Perinereis to aquaculture.

Development of Highly Efficient Universal Pneumocystis Primers and Their Application in Investigating the Prevalence and Genetic Diversity of Pneumocystis in Wild Hares and Rabbits

Despite its ubiquitous infectivity to mammals with strong host specificity, our current knowledge about Pneumocystis has originated from studies of merely 4% of extant mammalian species. Further studies of Pneumocystis epidemiology across a broader range of animal species require the use of assays with high sensitivity and specificity. To this end, we have developed multiple universal Pneumocystis primers targeting different genetic loci with high amplification efficiency. Application of these primers to PCR investigation of Pneumocystis in free-living hares (Lepus townsendii, n = 130) and rabbits (Oryctolagus cuniculus, n = 8) in Canada revealed a prevalence of 81% (105/130) and 25% (2/8), respectively. Genotyping analysis identified five and two variants of Pneumocystis from hares and rabbits, respectively, with significant sequence divergence between the variants from hares. Based on phylogenetic analysis using nearly full-length sequences of the mitochondrial genome, nuclear rRNA operon and dihydropteroate synthase gene for the two most common variants, Pneumocystis in hares and rabbits are more closely related to each other than either are to Pneumocystis in other mammals. Furthermore, Pneumocystis in both hares and rabbits are more closely related to Pneumocystis in primates and dogs than to Pneumocystis in rodents. The high prevalence of Pneumocystis in hares (P. sp. 'townsendii') suggests its widespread transmissibility in the natural environment, similar to P. oryctolagi in rabbits. The presence of multiple distinct Pneumocystis populations in hares contrasts with the lack of apparent intra-species heterogeneity in P. oryctolagi, implying a unique evolution history of P. sp. 'townsendii' in hares.

Natural co-infection of pigs with African swine fever virus and porcine reproductive and respiratory syndrome virus in India

Porcine reproductive and respiratory syndrome (PRRS) and African swine fever (ASF) are economically important diseases of pigs throughout the world. During an outbreak, all age groups of animals except piglets < 1 month of age were affected with symptoms of high fever, cutaneous hemorrhages, vomition with blood, diarrhea, poor appetite, ataxia, and death. The outbreak was confirmed by the detection of the N gene of the porcine reproductive and respiratory syndrome virus (PRRSV) and the VP72 gene of the African swine fever virus (ASFV) by PCR in representative blood samples from affected pigs followed by Sanger sequencing. Mixed infection was also confirmed by simultaneous detection of both the viruses using multiplex PCR. Phylogenetic analysis of both the viruses revealed that the outbreak was related to ASFV and PRRSV strains from China which were also closely related to the PRRSV and ASFV strains from the recent outbreak from India. The study confirmed the involvement of genotype II of ASFV and genotype 2 of PRRSV in the present outbreak. Interestingly, PRRSV associated with the present outbreak was characterized as a highly pathogenic PRRSV. Therefore, the present study indicates the possibility of future waves or further outbreaks of these diseases (PRRS and ASF) in this region. This is the first report of ASFV and PRRSV co-infection in pigs from India.

A survey of fecal virome and bacterial community of the diarrhea-affected cattle in northeast China reveals novel disease-associated ecological risk factors

Limited information on the virome and bacterial community hampers our ability to discern systemic ecological risk factors that cause cattle diarrhea, which has become a pressing issue in the control of disease. A total of 110 viruses, 1,011 bacterial genera, and 322 complete viral genomes were identified from 70 sequencing samples mixed with 1,120 fecal samples from 58 farms in northeast China. For the diarrheic samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, and geographic distribution in relation to different disease-associated ecological factors; the abundance of identified viruses and bacteria was significantly correlated with the host factors of clinical status, cattle type, and age, and with environmental factors such as aquaculture model and geographical location (P < 0.05); a significant interaction occurred between viruses and viruses, bacteria and bacteria, as well as between bacteria and viruses (P < 0.05). The abundance of SMB53, Butyrivibrio, Facklamia, Trichococcus, and Turicibacter was significantly correlated with the health status of cattle (P < 0.05). The proportion of BRV, BCoV, BKV, BToV, BoNoV, BoNeV, BoAstV, BEV, BoPV, and BVDV in 1,120 fecal samples varied from 1.61% to 12.05%. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. A genome-based phylogenetic analysis revealed high variability of 10 bovine enteric viruses. The bovine hungarovirus was initially identified in both dairy and beef cattle in China. This study elucidates the fecal virome and bacterial community signatures of cattle affected by diarrhea, and reveals novel disease-associated ecological risk factors, including cattle type, cattle age, aquaculture model, and geographical location.IMPORTANCEThe lack of data on the virome and bacterial community restricts our capability to recognize ecological risk factors for bovine diarrhea disease, thereby hindering our overall comprehension of the disease's cause. In this study, we found that, for the diarrheal samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, configuration, and geographic distribution in relation to different disease-associated ecological factors. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. Our study aims to uncover novel ecological risk factors of bovine diarrheal disease by examining the pathogenic microorganism-host-environment disease ecology, thereby providing a new perspective on the control of bovine diarrheal diseases.

Meta-Analysis and Systematic Literature Review of the Genus Pneumocystis in Pet, Farm, Zoo, and Wild Mammal Species

A systematic literature search on Pneumocystis in 276 pet, farm, zoo, and wild mammal species resulted in 124 publications originating from 38 countries that were analyzed descriptively and statistically, for which inclusion and exclusion criteria were exactly defined. The range of recorded Pneumocystis prevalence was broad, yet in half of the citations a prevalence of ≤25% was documented. Prevalence was significantly dependent on the method used for Pneumocystis detection, with PCR revealing the highest percentages. Pet animals showed the lowest median Pneumocystis prevalence, followed by farm, wild, and zoo animals. In contrast, pet and farm animals showed higher proportions of high-grade infection levels compared to zoo and wild mammals. Only in individual cases, all of them associated with severe Pneumocystis pneumonia, was an underlying immunosuppression confirmed. Acquired immunosuppression caused by other diseases was frequently discussed, but its significance, especially in highly immunosuppressive cases, needs to be clarified. This meta-analysis supported a potential influence of the social and environmental factors of the host on Pneumocystis transmission in wildlife, which must be further elucidated, as well as the genetic diversity of the fungus.

Complex interplay between PRRSV-1 genetic diversity, coinfections and antimicrobial use influences performance parameters in post-weaning pigs

Porcine reproductive and respiratory syndrome (PRRS) is one of the main diseases of pigs, leading to large economic losses in swine production worldwide. PRRSV high mutation rate and low cross-protection between strains make PRRS control challenging. Through a semi-longitudinal approach, we analysed the relationships among performance parameters, PRRSV-1 genetic diversity, coinfections and antimicrobial use (AMU) in pig nurseries. We collected data over the course of five years in five PRRS-positive nurseries belonging to an Italian multisite operation, for a total of 86 batches and over 200,000 weaners involved. The farm experienced a severe PRRS outbreak in the farrowing unit at the onset of the study, but despite adopting vaccination of all sows, batch-level losses in nurseries in the following years remained constantly high (mean±SE: 11.3 ± 0.5 %). Consistently with previous studies, our phylogenetic analysis of ORF 7 sequences highlighted the peculiarity of strains circulating in Italy. Greater genetic distances between the strain circulating in a weaners' batch and strains from the farrowing unit and the previous batch were associated with increased mortality (p < 0.0001). All the respiratory and enteric coinfections contributed to an increase in losses (all p < 0.026), with secondary infections by Streptococcus suis and enteric bacteria also inducing an increase in AMU (both p < 0.041). Our findings highlight that relying solely on sows' vaccination is insufficient to contain PRRS losses, and the implementation of rigorous biosecurity measures is pivotal to limit PRRSV circulation among pig flows and consequently minimise the risk of exposure to genetically diverse strains that would increase production costs.

Detection of porcine circovirus 2, porcine parvovirus 1, and torque teno sus virus k2a in wild boars from northeastern Patagonia, Argentina

Wild boars can act as a reservoir of pathogenic viruses that affect the pig industry. Here, we assessed the presence of porcine circovirus 2, porcine parvovirus 1, and torque teno sus virus k2a in wild boars in northeastern Patagonia (Argentina). Total DNA was extracted from the tonsils of 27 animals (collected between early 2016 and mid-2019) and used to prepare sample pools, which were subjected to viral detection through two-round PCR assays. Sequencing of the amplification products and phylogenetic analysis confirmed the occurrence of all of the aforementioned infectious agents.

Polymerase chain reaction-based detection of coinfecting DNA viruses in Vietnamese pigs in 2017 and 2021

Background and Aim: Many studies have reported on the phenomenon of co-infections involving two or more pathogens (bacteria or viruses) over the past few years. However, very few studies on this issue were conducted in Vietnam. Therefore, this study aimed to determine the circulation of single and multiple porcine parvovirus (PPV) (e.g., PPV1, PPV2, PPV3, and PPV4), porcine bocavirus (PBoV), and torque teno virus (TTV) (TTV1 and TTV2) infections in Vietnamese pigs. Materials and Methods: A total of 174 porcine circovirus 2-positive samples from pigs (n = 86 for 2017 and n = 88 for 2021), including from the sera and internal organs, across 11 provinces were examined by polymerase chain reaction. Results: This study demonstrated the wide distribution of DNA viruses among pig farms in Vietnam in 2021, with the detection rate for PPV ranging from 3.4% to 27.3% among PPV1-PPV4. Moreover, the detection rates of TTV genotypes were confirmed to be 14.8% (TTV1) and 63.6% (TTV2), respectively, and the positive rate of PBoV was 65.9%. The most frequent combinations were double and triple infections. Double infection was found in 16/86 (18.6%) in 2017 and 26/88 (29.5%) in 2021, while triple infection was found at 19/86 (22.1%) in 2017 and 26/88 (29.5%) in 2021. The incidence of simultaneous detection of more than three viruses was low. Conclusion: These results provide at least partial information about the occurrence of three viruses, including PPV (including PPV1 to 4), PBoV, and TTV (TTV1 and TTV2), in pigs. Determination of particular viruses in pigs will help to prevent the porcine respiratory disease complex caused by DNA viruses in Vietnamese pigs in the future.