We report a COVID-19 case with unprecedented viral complexity. In the first severe episode, two different SARS-CoV-2 strains (superinfection) were identified within a week. Three months after discharge, patient was readmitted and was infected in a nosocomial outbreak with a different strain, suffering a second milder COVID-19 episode.

Host immune response as well as virulence factors are key in disease susceptibility. There are no known association studies of HLA class I and II alleles with chikungunya (CHIKV) infection in Latin American population. We aim to identify Human Leukocyte Antigen (HLA) alleles present in patients with CHIKV infection when compared to healthy controls, as well as allele association with the clinical spectrum of the disease. A cross-sectional analysis nested in a community cohort was carried out. We included patients 18 years and older with serological confirmation of CHIKV infection. HLA typing of HLA-A, HLA-B and HLA-DRB1 alleles was performed. Two-by-two tables were used to establish associations between allele presence and clinical characteristics. Data from 65 patients with confirmed CHIKV infection were analyzed for HLA typing. CHIKV infection was associated with the presence of HLA-A*68, HLA-B*35, HLA-DRB*01, HLA-DRB1*04 and HLA-DRB1*13 alleles with statistical significance when compared to healthy subjects. A statistically significant relationship was found between the presence of rash in the face or the abdomen and the presence of HLA-DRB1*04. Our study demonstrated that in our cohort, HLA type I as well as type II alleles are associated with CHIKV infection, and specifically an HLA type II allele with dermatological symptoms. Further research is needed to set a path for future investigation on genes outside the HLA system to improve knowledge in the pathophysiology of CHIKV infection and its host-pathogen interaction.

Introduction: The Coronavirus Disease 2019 (COVID-19) pandemic has had a variable worldwide impact, likely related to country-level characteristics. In this ecological study, we explored the association of COVID-19 case rates (per 100,000 people) and death rates (per 100,000 people) with country-level population health characteristics, economic and human development indicators, and habitat-related variables. Methods: To calculate country-level COVID-19 case and death rates, the number of cases and deaths were extracted from the Johns Hopkins Coronavirus Resource Center for 2020. Country-level population health characteristics, economic and human development indicators, and habitat-related variables were extracted from several publicly available online sources of international organizations. Results were tabulated according to world zones and country economies. Univariate and multivariable linear regression analyses were performed to examine determinants of COVID-19 case rates and death rates. Results: A total of 187 countries and territories were analyzed, with an aggregate COVID-19 case rate of 779 per 100,000 people, a death rate of 19 per 100,000 people, and a case-fatality rate of 2.4%. For country-level population health characteristics, a higher percentage rate of adults with obesity and a higher percentage rate of adults with high blood pressure was independently associated with a higher COVID-19 case rate, and a higher percentage rate of adults with obesity was associated with a higher COVID-19 death rate. For country-level economic and human development indicators, only a higher gross domestic product percentage rate spent on total health expenditure and a higher human development index was independently associated with a higher COVID-19 case rate and death rate. A higher percentage of urban population was independently associated with a higher COVID-19 death rate, whereas a higher income per capita was independently associated with a lower COVID-19 death rate. For country-level habitat-related variables, a higher average household size and a higher percentage rate of population with primary reliance on polluting fuels and technologies was independently associated with a lower COVID-19 case rate and death rate whereas a higher percentage rate of households with at least one-member age 65 years or over was associated with a higher case rate and death rates. Conclusion: This ecological study informs the need to develop country-specific public health interventions to better target populations at high risk for COVID-19, and test environmental interventions to prevent indoor transmission of SARS-CoV-2, taking into consideration population health characteristics, economic and human development indicators, and habitat-related variables that are unique to each country.

The emergence of drug-resistant tuberculosis (DR-TB) is becoming a challenge to the national TB control programs including Ethiopia. Different risk factors are associated with the emergence of DR-TB. Identifying these risk factors in a local setting is important to strengthen the effort to prevent and control DR-TB. Thus, this study aimed to assess the risk factors associated with drug-resistant TB in Ethiopia. The Preferred Reporting Items for Systematic Reviews and Meta-analysis checklist was followed to conduct this study. We systematically searched the articles from electronic databases and gray literature sources. We used the Joanna Briggs Institute Critical Appraisal tools to assess the quality of studies. Data were analyzed using STATA version 15. We estimated the pooled OR along with 95%CI for each risk factor. The heterogeneity of the studies was assessed using the forest plot and I 2 heterogeneity test. Besides, we explored the presence of publication bias through visual inspection of the funnel plot and Egger’s regression test. After intense searching, we found 2238 articles, and 27 eligible studies were included in the final analysis. Based on the pooled analysis of the odds ratio, unemployment (OR; 2.71, 95% CI; 1.64, 3.78), having a history of the previous TB (OR; 4.83, 95% CI; 3.02, 6.64), having contact with a known TB patient (OR; 1.72, 95% CI; 1.05, 2.40), having contact with a known MDR-TB patient (OR; 2.54, 95% CI; 1.46, 3.63), and having pulmonary TB (OR; 1.80, 95% CI; 1.14, 2.45) were found to be the risk factors of drug-resistant TB. While older age TB patients (OR; 0.77, 95% CI; 0.60, 0.95) including age above 45 years OR; (0.76, 95% CI; 0.55, 0.97), and males (OR; 0.86, 95% CI; 0.76, 0.97) were found to had lower risk of DR-TB compared to their counterparts. A previous history of TB treatment is a major risk factor for acquiring DR-TB in Ethiopia that might be due to poor adherence during the first-line anti TB treatment. Besides, having contact with a known TB patient, having contact with a known MDR-TB patient, having pulmonary TB, and being unemployed were the risk factors of DR-TB in Ethiopia. Thus, active screening of TB contacts for DR-TB might help to detect DR-TB cases as early as possible and could help to mitigate its further transmission across the community.

Rift Valley fever virus (RVFV) is a mosquito-borne pathogen with significant human and veterinary health consequences that periodically emerges in epizootics. RVF causes fetal loss and death in ruminants and in humans can lead to liver and renal disease, delayed-onset encephalitis, retinitis, and in some cases severe hemorrhagic fever. A live attenuated vaccine candidate (DDVax), was developed by the deletion of the virulence factors NSs and NSm from a clinical isolate, ZH501, and has proven safe and immunogenic in rodents, pregnant sheep and non-human primates. Deletion of NSm also severely restricted mosquito midgut infection and inhibited vector-borne transmission. To demonstrate environmental safety, this study investigated the replication, dissemination and transmission efficiency of DDVax in mosquitoes following oral exposure compared to RVFV strains MP-12 and ZH501. Infection and dissemination profiles were also measured in mosquitoes 7 days after feeding on goats inoculated with DDvax or MP-12. Hypothesis: DDVax should infect mosquitoes at significantly lower rates than other RVF strains and, due to lack of NSm, be transmission incompetent. Exposure of Ae. aegypti and Cx. tarsalis to 6-8 log 10 plaque forming units (PFU)/mL DDVax by artificial bloodmeal resulted in significantly reduced DDVax infection rates in mosquito bodies compared to controls. Plaque assays indicated negligible transmission of infectious DDVax in Cx. tarsalis saliva (1/140 sampled) and none in Ae aegypti saliva (0/120). Serum from goats inoculated with DDVax or MP-12 did not harbor detectable infectious virus by plaque assay at 1, 2, or 3 days-post-inoculation; infectious virus was, however, recovered from mosquito bodies that fed on goats vaccinated with MP-12 (13.8% and 4.6%, respectively), but strikingly, DDvax positive mosquito bodies were greatly reduced (4%, and 0%, respectively). Furthermore, DDVax did not disseminate to legs/wings in any of the goat-fed mosquitoes.  Collectively, these results are consistent with a beneficial environmental safety profile .

As social media becomes an ever-increasing staple of everyday life and a growing percentage of people turn to community driven platforms as a primary source of information, the data created from these posts can provide a new source of information from which to better understand an event in near real-time. The 2018-2020 outbreak of virulent Newcastle Disease (vND) in Southern California is the third outbreak of vND in Southern California within a 50-year time span. These outbreaks are thought to be primarily driven by non-commercial poultry (i.e. backyard and game fowl) in the region. Here we employed a commercial “web crawling” tool between June of 2018 and July of 2020 which encompassed the majority of the outbreak in order to collect all available online mentions of virulent Newcastle Disease (vND) in relation to the outbreak. A total of 2,498 posts in English and Spanish were returned using a Boolean logic-based string search. While the number of posts was relatively small, their impact as measured by the number of visitors to the website and the number of people viewing the post (where provided) was much larger. Using views as a metric, Twitter was identified as the most significant source of comments over blogs, forums and other news sites. Posts with negative sentiment were found to have a larger audience relative to posts with a positive sentiment. In addition, posts with negative sentiment peaked in May of 2019 which preceded the formation of the anti-depopulation group Save Our Birds (SOB). As the usage and impact of social media grows, the ability to utilize tools to analyze social media may improve both response and outreach-based strategies for various disease outbreaks including vND in Southern California which has a large non-commercial poultry population.

Toxoplasmosis is a zoonotic disease caused by the ubiquitous coccidia Toxoplasma gondii. Rodents play an important role in maintaining its life cycle, as they are one of the main diet sources for felids (wild and domestic), the unique definitive hosts. However, reports of toxoplasmosis in porcupines (Rodentia Order) are uncommon, with gaps concerning its pathophysiology. South America is the continent with the greatest genetic diversity of rodents and T. gondii. A free-ranging hairy dwarf porcupine was admitted to a wildlife rescue center with a history of trauma. During rehabilitation, the animal presented neurological symptoms (sporadic episodes of hind limbs paresis) and died five months later. The main findings during necropsy were brain congestion and severe incisor overgrowth associated with maxillary perforation. The histopathological exam showed moderate encephalitis, with variable-sized round cysts, positive for PAS stain and immunohistochemistry for T. gondii. Additionally, two cysts were observed in the medulla of the adrenal gland. Molecular techniques were performed to characterize the parasite load by qPCR (Cq=30) and the genotype by PCR-RFLP with 11 markers, which revealed a new genotype. This case adds to the body of knowledge in comparative pathology of Neotropical Rodentia and reports a new genotype circulating in South America.

NADC34-like PRRSV strains were first detected in China in 2017, with epidemic potential. In this study, the phylogenetic, epidemic, and recombinant properties of NADC34-like PRRSV in China were evaluated comprehensively. From 2020 to October 2021, 82 NADC34-like PRRSV isolates were obtained from 433 PRRSV-positive clinical samples. These strains accounted for 11.5% and 28.6% of positives in 2020 and 2021, respectively, and have spread to eight provinces. We selected 15 samples for whole-genome sequencing, revealing genome lengths of 15,009 to 15,113 nt. Phylogenetic analysis revealed that Chinese NADC34-like strains cluster with American sublineage 1.5 strains and do not form an independent branch. Recombination analysis revealed that six of fifteen complete genome sequences derived from recombination between NADC34-like and NADC30-like or HP-PRRSV; they all recombined with local strains in China, exhibiting a complex recombination pattern. Partial Nsp2 sequence alignment showed that nine of fifteen isolates have a continuous 100-aa deletion (similar to IA/2014/NADC34); other isolates have a 131-aa discontinuity deletion (similar to NADC30). Five of them also have additional amino acid deletions, all of which are reported for the first time here. In the last two years, NADC34-like PRRSV has become one of the main epidemic strains in some areas of China; it has changed significantly, its homology has decreased significantly, and it has undergone complex recombination with local Chinese strains. These results are of great significance for understanding the current epidemic situation of PRRSV in China.

Livestock trading through live animal markets are potential pathways for the introduction and spread of economically important pathogens like the African swine fever virus (ASFV) to new areas in several countries. Due to the high demand for live pigs in Nigeria both for restocking and slaughter, live pigs are sold at designated live pig markets (LPM) in the country. This involves movement of pigs over long distances. Despite, reports of ASF outbreaks following restocking of pigs bought from LPMs, there is paucity of information on the role of LPMs in the epidemiology of ASF. In this study, data and pig samples (whole blood, sera, tissue) were collected from 4 selected LPMs in Nigeria (Dawaki, Katsit, Numan & Pandam) between 2019 and 2020. Samples were analysed by polymerase chain reaction (PCR) and Enzyme-linked Immunosorbent Assay (ELISA). Four genes of ASFV positive samples were characterized to identify the circulating genotypes. Results revealed trade activities involving transportation of pigs from these selected markets to 42 major cities and towns in thirteen (13) States of Nigeria. PCR results revealed an overall ASF prevalence of 10.77% (66/613). ASFV was confirmed by PCR in all the selected LPMs with a prevalence rate of 3.13%-23.81%. The phylogeny revealed genotype I and serogroup 4 based on the p72 protein that encodes the B646L gene and the EP402R gene encoding the CD2V. While sequence analysis of CVR of B602L gene revealed 8 tetrameric repeats variants, six of which have never been reported in Nigeria. Analysis of sera samples recorded a seroprevalence of 6.9% (16/217) within the study period. Findings from this study show that LPM are hotspots and channels for transmission and continuous spread of ASFV in Nigeria. Therefore, for ASF to be controlled in Nigeria, disease surveillance and regulation at LPMs are critical.

Porcine Deltacoronavirus is a newly emergent enteric pathogen affecting swine farms worldwide. It has been detected in several countries in Europe, Asia and North America; yet, it has not been reported in South America. In November 2019, an enteric disease outbreak in a pig farm located in San Martin, Peru; was reported along with submission of three intestinal samples from pigs who succumbed to the disease. Samples were processed for molecular detection by qRT-PCR, viral isolation and further sequencing analysis. A taqman-based RT-PCR was performed to differentiate among the most relevant swine enteric coronaviruses described to date. All samples were positive to Porcine Deltacoronavirus with a cycle threshold (Ct) value between 9-14, revealing a high viral load, while testing negative to Porcine Epidemic diarrhea and Transmissible Gastroenteritis viruses. Following detection, viral isolation was performed using PK-15 and Vero cell lines. After 5 days of inoculation, no cytopathic effect was observed. A second blind passage allowed the observation of cytopathic effect on PK-15 cells, while it remained absent in Vero cells. A fluorescence test using an anti-N monoclonal antibody confirmed viral replication. One sample was processed for whole genome sequencing (NGS). In short, raw reads were imported into CLC genomics and assembled de novo. Out of 479k reads generated from the sample, 436k assembled into a 25501 bp contig which was 99.5% identical to a reference Porcine Deltacoronavirus strain from US within the North American phylogroup. Yet, there are relevant differences at the nucleotide and amino acid levels compared to previously described Porcine Deltacoronavirus strains. Altogether, our findings represent the first report of Porcine Deltacoronavirus in South America, its genomic characterization, which provides information of its evolutionary origin. Thus, this study offers new insights into the molecular epidemiology of Porcine Deltacoronavirus infections in the swine industry.

Mongolia and Eastern Siberia, Russia are border regions in Asia with high incidence of tuberculosis (TB). In this study, we aimed to investigate MDR -TB transborder transmission with a focus on endemic and epidemic Mycobacterium tuberculosis clones and drug resistance patterns. M. tuberculosis strains (291 from Mongolia and 754 from Russia) were collected within cross-sectional population-based surveys in 2010-2016. DNA was genotyped in 24 MIRU-VNTR loci and by PCR testing of the key SNP markers to discriminate within Beijing genotype. In total, 1045 isolates were divided into 435 MIRU-types that were assigned to Lineage 2 (Beijing isolates) and Lineage 4 (Ural, Haarlem, Latin-American-Mediterranean [LAM], S, and unclassified isolates). Beijing genotype was dominant in both countries, but most of Russian and all Mongolian Beijing strains belonged to different subtypes of the modern Beijing sublineage with only negligible overlap between the two countries. In particular, the Beijing types #342-32, #3819-32, #1773-32 (Asian African 2 group) were found only in Mongolia. LAM was the most common non-Beijing genotype (11.0% in Mongolia and 14.7% in Russia) and its isolates mostly belonged to LAM-RUS branch. MDR rate was higher in Russia compared to Mongolia among newly diagnosed patients: 29.4% versus 4.2% (p < 0.001) but similar and high in the retreatment subgroups (65.8% and 67.4%, respectively). In Russian collection, a higher MDR rate was observed in (i) Beijing compared to non-Beijing (47.5% versus 38.8%, p = 0.03), (ii) Beijing B0/W148 subtype compared to Beijing Central Asian/Russian subtype (64.5% versus 39.3%, p <0.001). In Mongolia, MDR rate was similar in Beijing (29.7%) and non-Beijing (27.5%) genotypes. In conclusion, population structures of the Beijing genotype in Mongolia and Russian borderline regions differ significantly including specific patterns of drug resistance. In contrast, largely overlapping LAM subtypes may correlate with historical endemic circulation of the LAM-RUS branch in Northern Eurasia.

Against the backdrop of the second wave of COVID-19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole genome sequences of SARS CoV-2 circulating in India from 1 st January 2021 to 31 st August 2021. In the 43,102 SARS-CoV-2 genomic sequences analysed, we have identified 24, 260 mutations in the S protein, based on which 265 pango lineages could be categorised. The dominant lineage in most of the 28 states of India and its 8 union territories was B.1.617.2 (the delta variant). However, the states Madhya Pradesh, Jammu & Kashmir, and Punjab had B.1.1.7 (alpha variant) as the major lineage, while the Himachal Pradesh state reported B.1.36 as the dominating lineage. A detailed analysis of various domains of S protein was carried out for detecting mutations having a prevalence of >1%; 70, 18, 7, 3, 9, 4, and 1 (N=112) such mutations were observed in the N -terminal domain, receptor binding domain, C -terminal domain, fusion peptide region, heptapeptide repeat (HR)-1 domains, signal peptide domain, and transmembrane region, respectively. However, no mutations were recorded in the HR-2, and cytoplasmic domains of the S protein. Interestingly, 13.39% (N=15) of these mutations were reported to increase the infectivity and pathogenicity of the virus; 2%(N=3) were known to be vaccine breakthrough mutations; and 0.89%(N=1) were known to escape neutralising antibodies. Biological significance of 82% (N=92) of the reported mutations is yet unknown. As SARS-CoV-2 variants are emerging rapidly, it is critical to continuously monitor local viral mutations to understand national trends of virus circulation. This can tremendously help in designing better preventive regimens in the country, and avoid vaccine breakthrough infections.

CDC estimates 1 million dogs are imported into the United States annually. With the movement of large numbers of animals into the United States the risk of disease importation is a concern, especially for emerging diseases. Dogs that arrive to the United States ill or dead are investigated by public health authorities to ensure dogs are not infected with diseases of concern (such as rabies). We identified factors associated with illness and death in imported dogs and estimated the initial investigation cost to public health authorities. Dog importation data from the CDC’s Quarantine Activity Reporting System were reviewed from 2010–2018. The date of entry, country of origin, port of entry, transportation method, and breed were extracted to examine factors associated with illness and death in dogs during international travel. Costs for public health investigations were estimated from data collected by the Bureau of Labor Statistics and Office of Personal Management. Death or illness was more likely to occur in brachycephalic breeds (aOR=3.88, 95%CI 2.74–5.51). Transportation of dogs via cargo (aOR=2.41, 95%CI 1.57–3.70) or as checked baggage (aOR=5.74, 95%CI 3.65–9.03) were also associated with death or illness. On average, 19 dog illnesses or deaths were reported annually from 2010–2018. The estimated annual cost to public health authorities to conduct initial public health assessments ranged from $2,071–$104,648. Current regulations do not provide adequate resources or mechanisms to monitor the rates of morbidity and mortality of imported dogs. There are growing attempts to assess animal welfare and communicable disease importation risks; however, responsibility for dogs’ health and well-being is overseen by multiple agencies. A joint federal agency approach to identify interventions that reduce dog morbidity and mortality during flights while continuing to protect U.S. borders from public health and foreign animal disease threats could be beneficial.

Indirect costs of animal disease outbreaks often significantly exceed the direct costs. Despite their importance, indirect costs remain poorly characterised due to their complexity. In this study, we developed a framework to assess the indirect costs of a hypothetical African Swine Fever outbreak in Switzerland. We collected data through international and national stakeholder interviews, analysis of national disease control regulations and industry data. We developed a framework to capture the resulting qualitative and quantitative data, categorise the impacts of these regulations, and rank the impacts in order of importance. We then developed a spreadsheet model to calculate the indirect costs of one category of control measure for an individual group of stakeholders. We developed a decision tree model to guide the most economically favourable implementation plan for a given control measure category, under different outbreak scenarios. Our results suggest that the most important measure/impact categories were ‘Transport logistics’, ‘Consumer demand’, ‘Prevention of wild boar and domestic pig contact’ and ‘Slaughter logistics’. In our hypothetical scenario, the greatest costs associated with ‘Prevention of wild boar and domestic pig contact’ were due to assumed partial or total depopulation of pig farms in order to reduce herd size to comply with the simulated control regulations. The model also provides suggestions on the most economically favourable strategy to reduce contact between wild boar and domestic pigs in control areas depending on the duration of the outbreak. Our approach provides a new framework to integrate qualitative and quantitative data to guide disease control strategy. This method could be useful in other countries and for other diseases, including in data- and resource-poor settings, or areas with limited experience of animal disease outbreaks.

Foot-and-mouth disease (FMD) is endemic in India, where circulation of serotypes O, A and Asia 1 is frequent. In the past two decades, many of the most widespread and significant FMD lineages globally have emerged from the South Asia region. Here, we provide an epidemiological assessment of the ongoing mass vaccination programs in regard to post-vaccination monitoring and outbreak occurrence. The objective of this study was to quantify the spatiotemporal dynamics of FMD outbreaks and to assess the impact of the mass vaccination program between 2008 to 2016 with available antibody titer data from the vaccination monitoring program, alongside other risk factors that facilitate FMD spread in the country. We first conducted a descriptive analysis of epidemiological outcomes of governmental vaccination programs in India, focusing on antibody titer data from >1 million animals sampled as part of pre- and post-vaccination monitoring and estimates of standardized incidence ratios calculated from reported outbreaks per state/administrative unit. The percent of animals with inferred immunological protection (based on ELISA) was highly variable across states, but there was a general increase in the overall percent of animals with inferred protection through time. In addition, the number of outbreaks in a state was negatively correlated with the percent of animals with inferred protection. Because standardized incidence ratios of outbreaks were heterogeneously distributed over the course of eight years, we analyzed the distribution of reported FMD outbreaks using a Bayesian space-time model to map high-risk areas. This model demonstrated a ~50% reduction in the relative risk of outbreaks in states that were part of the vaccination program. In addition, states that did not have an international border experienced reduced risk of FMD outbreaks. These findings help inform risk-based control strategies for India as the country progresses towards reducing reported clinical disease.

RT-PCR is currently the standard diagnostic method to detect symptomatic and asymptomatic individuals infected with SARS-CoV-2. However, RT-PCR results are not immediate and may falsely be negative before an infected individual sheds viral particle in the upper airway where swabs are collected. Infected individuals emit volatile organic compounds (VOCs) in their breath and sweat that are detectable by trained dogs. Here we evaluate the diagnostic accuracy of dog detection against SARS-CoV-2 infection. Fifteen dogs previously trained at two centres in Australia were presented to axillary sweat specimens collected from known SARS-CoV-2 human cases and non-cases. The true infection status of the cases and non-cases were confirmed based on RT-PCR results as well as clinical presentation. Across dogs, the overall diagnostic sensitivity (DSe) was 95.6% (95%CI: 93.6%-97.6%) and diagnostic specificity (DSp) was 98.1% (95%CI: 96.3%-100.0%). The DSp decreased significantly with non-case specimens sourced from UAE ( P-value < 0.001). The location of evaluation did not impact the detection performances. The accuracy of detection varied across dogs and experienced dogs revealed a marginally better DSp ( P-value = 0.003). The potential and limitations of this alternative detection tool are discussed.

African swine fever (ASF), considered as the most dreadful swine disease due to its very high mortality, emerged in India in 2020. The complete genome analysis of ASF viruses isolated during the first outbreaks in India showed a few unique non-synonymous mutations in MGF 369-11L, MGF 505-4R, K205R and B263R genes. Frame shiftsin the protein coding sequences were observed in DP60R, ASFV-G_ACD 00190, MGF 110-10-L- MGF110-14L fusion, MGF 360-14L and I267L genes of Indian ASFVs as compared to ASFV/Georgia/2007. Complete genome based phylogenetic analysis of p72-genotype-II viruses showed the clustering of Indian isolates with ASFV/Wuhan/2019 in a separate clade. Phylogenetic analysis of concatenated sequences of 14 open reading frames (ORF) having single nucleotide polymorphisms (SNP) showed distinct grouping of Indian ASFVs with other Asian ASFVs.Thisis the first complete genome characterization of ASF viruses isolated from domestic pigs in India. The resultsindicate that number of Tandem Repeat Sequence in the intergenic region between I73R and I329L genes, and the 14 ORFs with SNP reported in this study could be the genetic determinants to differentiate the closely related p72-genotype II viruses circulating in Asia.

Viruses of veterinary significance such as African swine fever virus, are known to survive for extended periods in plant-based feed ingredients imported into North America. To reduce the likelihood of virus introduction, high-risk ingredients, such as oil seed meals, are stored in designated facilities for extended periods under controlled environmental conditions to minimize viral infectivity prior to use in diets. While 30 days has become a standard storage period, the required ambient temperature to inactivate viruses during this time is not known. To address the question, 1-metric ton totes of conventional soybean meal were inoculated with PRRSV 144 lineage 1C variant and SVA prior to storage for 30 days at 23.9º C, 15.5º C, or 10º C, and feeding to pigs. Virus infectivity was evaluated through detection of viral RNA in oral fluid samples, along with clinical signs. Results indicated that inactivation of both viruses occurred in soy stored at 23.9º C. In contrast, SVA infectivity was observed in soy stored at both 15.5º C and 10º C, while PRRSV 144 L1C variant infectivity was only observed in soy stored at 10º C. These results suggest that a storage period of 30-days and a temperature of 23.9º C are required to reduce the risk of virus contaminated plant-based feed ingredients, such as soybean meal.