Canine parvovirus type 2 (CPV-2) is a small, single-stranded DNA virus causing fatal hemorrhagic enteritis in dogs. Currently, CPV-2 has been classified into CPV-2a, CPV-2b, and CPV-2c based on genetic variation in the VP2 gene. The CPV-2c variant has become ubiquitous worldwide and gained attention for monitoring parvoviral evolution. In this study, we characterized the full-length genome sequences of CPV-2c isolates obtained from 59 dogs in Vietnam. Molecular analysis revealed that Vietnamese CPV-2c shared a common evolutionary pattern with the Asian CPV-2 clade, which is marked by genetic signature patterns in the structural and nonstructural proteins. In addition, these Vietnamese CPV-2c strains exhibited unique Thr112Ile and Ile447Met mutations in the VP1 and VP2 sequence, respectively. Interestingly, phylogenetic analysis indicated that the mutations of amino acid residues in both the structural and nonstructural genes have contributed to the emergence of a new clade, designated here as the Asia-IV clade. The substitution rates, estimated from a dataset containing 199 sequences over the last 40 years, confirmed that CPV-2 showed a high rate of nucleotide substitution, at about 2.49 x 10-4 nucleotide substitutions per site per year (nt/s/y), with VP1/2 and NS1/2 estimates of 3.06 x 10-4 and 3.16 x 10-4 nt/s/y, respectively. Even though no evidence of genetic recombination in these Vietnamese CPV-2c strains was established, potential positive selection sites were observed in both the structural and nonstructural genes, suggesting the viral evolutionary process has occurred in both the structural and nonstructural proteins. Genetic and evolutionary analysis of the full-length genome sequence is necessary to gain evolutionary insight of CPV-2. Further studies are needed to elucidate the potential role of these observed mutations in the novel Asia-IV clade.
In this study, the digital droplet polymerase chain reaction (ddPCR) was used to quantify circulating bovine papillomavirus (BPV; genus: Deltapapillomavirus) levels in blood samples from 25 healthy cows and 15 cows with chronic enzootic hematuria due to papillomavirus-associated bladder tumors. ddPCR detected the BPV DNA in 95% of all the samples (i.e., in 24 of the healthy cows and 14 of the diseased animals), whereas quantitative real time PCR (qPCR) detected it in only 57.5% of the same blood samples, with the percentage differences between ddPCR and qPCR being statistically significant (P value 0.05), according to the 2 test of Campbell and Richardson. Furthermore, ddPCR detected BPV infections by a single genotype and by multiple genotypes in 37% and 63% of the cows, respectively, whereas qPCR detected these in 16% and 16%, respectively. Of the two assays, ddPCR was the more sensitive and accurate clinical diagnostic tool, allowing the detection of otherwise undetectable BPV genotypes, and consequently, a higher number of BPV co-infections. qPCR failed to detect many BPV co-infections by multiple genotypes. Therefore, ddPCR may be an essential tool for improving diagnostic procedures, allowing the identification of the genotypic distribution of BPV and a better understanding about the territorial divergence, if any, of the BPV prevalence in different areas. No significant differences in the blood viral load estimations were observed between the two animal groups, suggesting that the bloodstream could be a site of primary infection. Finally, as BPV DNA was detected in cows affected by noninvasive urothelial tumors, including papilloma and papillary urothelial neoplasms of low malignant potential, the circulating BPVs appeared to be independent of the status of urothelial neoplasms. Therefore, unlike in humans, circulating BPVs cannot be an actual prognostic marker of urothelial tumors in cows.
Previous research has identified a relationship between climate and occurrence of SARS-CoV and MERS-CoV cases, information that can be used to reduce the risk of infection. Using COVID-19 notification and postcode data from New South Wales, Australia during the exponential phase of the epidemic in 2020, we used time-series analysis to investigate the relationship between 749 cases of locally-acquired COVID-19 and daily rainfall, 9am and 3pm temperature, and 9am and 3pm relative humidity. Lower 9am relative humidity (but not rainfall or temperature) was associated with increased case occurrence; a reduction in relative humidity of 1% was predicted to be associated with an increase of COVID-19 cases by 6.11%. During periods of low relative humidity, the public health system should anticipate an increased number of COVID-19 cases.
Tilapia lake virus (TiLV) is an emerging virus that is rapidly spreading across the world. Over the past 6 years (2014–2020), TiLV outbreaks had been reported in at least 16 countries, spanning three continents, including Asia, Africa, and America. Despite its enormous economic impact, its origin, evolution, and epidemiology are still largely poorly characterised. Here, we report eight TiLV whole genome sequences from Thailand sampled between 2014–2019. Together with publicly available sequences from various regions of the world, we estimated the origin of TiLV to be between 2003–2009, 5–10 years before the first report of the virus in Israel in 2014. Our analyses consistently showed that TiLV started to spread in 2000s, and reached its peak in 2014–2016, matching well with the timing of its first report. From 2016 onwards, the TiLV population declined steadily. This could be a result of herd immunity building up in the fish population, and / or a reflection of a better awareness of the virus coupled with a better and more cautious protocol of Tilapia importation. Despite the fact that we included all publicly available sequences, our analyses revealed long unsampled histories of TiLVs in many countries, especially towards its basal diversification. This result highlights the lack and the need for systematic surveillance of TiLV in fish.
A new pathogenic virus, COVID-19, appeared in 2019, in Wuhan, China, typically causing fever, cough, diarrhea and fatigue and significant mortality. COVID-19 has also shown about 80% genetic similarity to the Severe Acute Respiratory Symptom (SARS) virus, which is already known to be derived from a bat virus. Arterial thrombosis and venous thrombosis, variously attributed to long term patient immobilizations, inflammation, autoimmune reactions or endothelial cell damage to the blood vessels, have also been reported for COVID-19 infections. However, there is another explanation for thrombosis (blood clots) in many patients infected with COVID-19.
African swine fever (ASF) is emerging in Vietnam and poses a continuing severe threat to the swine industry. A histopathological study of clinical samples collected during the August to September 2019 outbreak of ASF was performed to determine the characteristic lesions. We analyzed samples from eight ASFV-infected farms. Histopathological results revealed the characteristic lesions of the acute to the subacute clinical form of ASF. Immunohistochemical results showed ASFV viral antigen distribution in mononuclear cells/macrophage in various organs, hepatocytes, and renal tubular epithelium. Molecular analysis of partial capsid protein 72 gene revealed that ASFV strain from the eight separate outbreaks belonged to genotype II.
Repurposing of existing antiviral drugs, immunological modulators, and supportive therapies represents a promising path toward rapidly developing new control strategies to mitigate the devastating public health consequences of the COVID-19 pandemic. A comprehensive text-mining and manual curation approach was used to comb and summarize the most pertinent information from existing clinical trials. Drugs with previous efficacy against related betacoronaviruses like SARS and MERS were also systematically evaluated as potentially promising candidates for drug repositioning.
New technologies in the field of vaccinology arise as necessity for treatment and control of many diseases. Currently modified live virus and inactivated vaccines used for Bovine Herpesvirus-1 (BoHV-1) have several disadvantages. Previous works for preventive treatment of BoHV-1 with DNA based vaccines have demonstrated the capability to induce humoral and cellular immune response. Nevertheless, it is well known that “naked” DNA induces low immunogenic response. Thus, loading of antigen encoding DNA sequences in liposomal formulations targeting dendritic cell receptors could be a promising strategy to better activate these antigen presenting cells (APC). In this work, DNA based vaccine encoding the truncated version of gD glycoprotein (pCIgD) of BoHV-1 was investigated alone and upon encapsulation on liposomal formulation coated with MANα1-2MAN-PEG-DOPE and LPS from Brucella ovis (pCIgD-Man-L) in mice and cattle assay. Results showed that the use of pCIgD-Man-L was capable to enhance the immune response in both animal models. Significant levels of humoral immunity were achieved when total antibody titers and isotypes were detected in sera and mucosa. For cellular immunity, specific viral lymphoproliferation was detected in the animals inoculated with pCIgD-Man-L. In addition, positively modulation of CD40 molecules on the surface of bovine dendritic cells (DCs) was observed when cells were stimulated and activated with vaccine formulations. When challenge assay was performed, bovines inoculated with pCIgD and liposome decorated with MANα1-2MAN-PEG-DOPE elicited better protection and diminished viral excretion. The results demonstrate the targeting of the MANα1-2MAN coated liposomes toward dendritic cells and their ability to boost the immunogenicity according to an adjuvant effect that results in long-lasting immunity. Liposome decorated with MANα1-2MAN-PEG-DOPE were for the first time tested as DNA based vaccine in cattle as preventive treatment of BoHV-1. These results open up new perspectives for the design of vaccine for the control of bovine rhinotracheitis.
Event-based surveillance (EBS) systems monitor a broad range of information sources to detect early signals of disease emergence, including new and unknown diseases. Following the emergence of a newly identified coronavirus –so-called COVID-19, in humans in December 2019 in Wuhan, China, we conducted a retrospective analysis of the capacity of three Event-Based Systems (EBS) systems (ProMED, HealthMap and PADI-web) to detect early signals of this emergence. We evaluated the changes in the online news vocabulary coinciding with the period before / after the identification of COVID-19, as well as the assessment of its contagiousness and pandemic potential. ProMED was the timeliest EBS, detecting signals one day before the official notification. At this early stage, the specific vocabulary was related to “pneumonia symptoms” and “mystery illness”. Once COVID-19 was identified, the vocabulary changed to virus family and specific COVID-19 acronyms. Our results suggest the three EBS systems are complementary regarding data sources, and all need improvements regarding timeliness. EBS methods should be adapted to the different stages of disease emergence to improve the early detection of future emergence of unknown pathogens.
The world is confronting a dire situation due to the recent pandemic of the novel coronavirus disease (2019-nCoV) with so far mortality cases of 100,000 all over the world. Currently, there are no effective enough treatment options for this previously unknown virus. The current drugs in pipline and some plausible drug are overviewed in this paper. The potential molecular targets of each steps of the 2019-nCoV drug life cycle is discussed and highlights here. Although different types of anti-viral targets are applicable for 2019-nCoV drug screenings, the more promising targets can be considered as protease and RNA polymerase. Based on the results from antiviral agents repurposing and clinical studies, the remdesivir could be an encouraging drug in the frontline to be administrated for 2019-nCoV. Much progress in understanding the 2019-nCoV the molecular details of its life cycle followed by the identification of therapeutic targets seems to be an efficient approach in discovering potential drugs.
In order to analyze the prevalence of cat viral diseases in China, including feline parvovirus (FPV), feline calicivirus (FCV), feline herpesvirus-1 (FHV-1), feline leukemia virus (FeLV), feline immunodeficiency virus (FIV) and feline infectious peritonitis virus (FIPV), a total of 1,326 samples of cats from 16 cities were investigated from 2016 to 2019. Collectively, 1,060 (79.9%) cats were tested positive for at least one virus in nucleotide detection, the positive rates of cat exposure to FeLV, FPV, FHV-1, FCV, FIV and FIPV were 59.6%, 19.2%, 16.3%, 14.2%, 1.5% and 0.5%, respectively. The prevalence of FHV-1 and FPV were dominant in winter and spring. Cats from north China showed a higher positive rate of viral infection than that of cats from south China. The virus infection is not highly correlated with age, except that FPV is prone to occur within the age of 12 months. In the serological survey, the seroprevalences of 267 vaccinated cats to FPV, FCV, FHV-1 were 83.9%, 58.3% and 44.0%, respectively. Meanwhile, the seroprevalences of 39 unvaccinated cats to FPV, FCV, FHV-1 were 76.9% (30/39), 82.4% (28/34) and 58.6% (17/29), respectively. This study demonstrated that a high prevalence of the six viral diseases in China, and the insufficient serological potency of FCV and FHV reminds the urgency for more effective vaccines.
Ranaviruses can infect both captive and wild cold-blooded vertebrates, leading to significant economic and environmental losses. With the cases of ranavirus infection increasing, many ranavirus genomic sequences were published, but little is known about ranavirus taxonomy on a whole genome level. In this study, 44 ranaviruses core genes were identified in 32 ranaviruses genome suquences by using PanX. The Neighbor joining phylogenetic trees (NJ-tree) based on 44 ranaviruses core genes and 24 iridoviridae core genes and composition vector phylogenetic tree (CV-Tree) based on whole genome were constructed. The three of phylogenetic trees showed that 32 ranavirus isolates can be divided to 4 different subspecies including GIV-like, EHNV-like, FV3-like and CMTV-like, and subspecies taxonomic position of three phylogenetic trees were consistent. However, the phylogenetic position of ToRV could not be determined if it belongs to FV3-like or CMTV-like group. Subsequently, we carried out dot plot analysis and confirmed that ToRV should belong to CMTV-like group. Based on dot plot analysis and phylogenetic trees, taxonomic classification of ranaviruses were confirmed. Finally, 4 genes which are suitable for the construction of phylogenetic tree were selected from ranavirus core genes by recombination analysis, substitution saturation analysis and single-gene phylogenetic analysis. Phylogenetic tree based on concatenated sequences of the 4 selected genes showed that classification of subspecies was identical with 3 of the phylogenetic trees. Conclusion: our results confirmed taxonomic identification of ranaviruses, the 4 selected genes used in phylogenic analysis will make taxonomic identification more convenient and accurate.
There are several routes of African swine fever (ASF) introduction into a country. Among the possible routes of entry, quarantine policies determine the possibility of introduction by legal import of live pigs and pig products. This study aimed at assessing the probability of ASF introduction through legal import of live pigs and pig products during the high risk period (HRP) using a quantitative stochastic approach during 2009-2018. The result indicates that the mean annual probability of ASF introduction by legal import of live pig was 1.58×10-7 (1.52~1.67×10-7 95% CI). The mean annual probability by legal import of pig products was 1.59×10-10 (1.55~1.64×10-10 95% CI), of which Poland assumed 87.9% of the mean annual risk. The current import quarantine policy of Korean government may be enough to block the release of the virus via legal import of live pigs and pig products, and it should be continually enforced. This result can help to elucidate source of infection and minimize the catastrophic consequences of the potential ASF reintroduction into South Korea by designing risk mitigation strategies such as risk-based selection of routes to be assessed and prevented and decreased exposure possibility by increased control of food waste and swill feeding practices.
The occurrence of mycobacterial infections in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. In addition to the well-known pathogenic members of the Mycobacterium tuberculosis - complex (MTBC), over 180 nontuberculous mycobacteria (NTM) species have been described. Although the large majority of the NTM are assumed to be non-pathogenic to most individuals, an increasing trend in NTM infections has been observed over the last decades. The reasons of such augmentation are probably more than one: improved laboratory diagnostics, an increasing number of immunocompromised patients and individuals with lung damage are some of the possible aspects. Mandibular lymph nodes of 176 hunted wild boars from the pre-Alpine region of Canton Ticino, Switzerland, were collected. Following gross inspection, each lymph node was subjected to culture and to an IS6110 based real-time PCR specific for MTBC members. Histology was performed of a selection of lymph nodes presenting gross visible lesions. Moreover, accuracy of matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry species identification was compared with sequence analysis of a combination of housekeeping genes. Mycobacteria of the MTBC were detected in five out of 176 wild boars (2.8%; CI95% 1.2 - 6.5) and were all confirmed to be Mycobacterium microti by molecular methods. In addition, based on the examined lymph nodes, NTM were detected in 57.4% (CI95% 50.0 – 64.5) of the wild boars originating from the study area. The 111 isolates belonged to 24 known species and three potentially undescribed Mycobacterium species. M. avium subsp. hominissuis thereby predominated (22.5%) and was found in lymph nodes with and without macroscopic changes. Overall, the present findings show that, with the exception of undescribed Mycobacterium species where identification was not possible (3.6%; 4/111), MALDI-TOF had a high concordance rate (90.1%; 100/111 isolates) to the sequence based reference method.
COVID-19 pandemic disease spread by SARS-COV-2 single-strand structure RNA virus belongs to the 7th generation of the coronavirus family. Following an unusual replication mechanism, its extreme ease of transmissibility has put many counties under lockdown. With a cure for the infection uncertain in the near future, the pressure currently lies in the current healthcare infrastructure, policies, government activities, and behaviour of the people to contain the virus. This research seeks to understand the spreading patterns of the COVID-19 virus through exponential growth modelling and identifies countries that have showed an initial sign of containment until 26th March 2020. Post identification of countries that have shown an initial sign of containment, predictive supervised machine learning models were built with infrastructure, environment, policies, and infection related independent variables. For the purpose, COVID-19 infection data across 42 countries were used. Logistic regression results shows a positive significant relationship of healthcare infrastructure and lockdown policies on the sign of early containment in countries. Machine learning models based on logistic regression, decision tree, random forest, and support vector machines were developed and are seen to have accuracies between 76.2% to 92.9% to predict early sign of infection containment. Other policies and activities taken by countries to contain the infection are also discussed.