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174 emerging diseases Preprints

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emerging diseases virus porcine deltacoronavirus covid-19 pdcov isolation diarrhea wildlife bacterial pathogens intergenic region variant therapeutic replication slippage rural development zoonosis/zoonotics new intervention strategies peru veterinary epidemiology immunity vaccine design ticks disease control transmission parasitic infections disease-freedom one health pathogenesis + show more tags
whole genome sequencing vaccine diagnostics african swine fever virus
Please note: These are preprints and have not been peer reviewed. Data may be preliminary. Preprints should not be relied on to guide medical practice or health-related decisions. News media reporting on preprints should stress that the research should not yet be considered conclusive.
Animals and SARS-CoV-2: Species susceptibility and viral transmission in experimental...
Emma Hobbs
Tristan Reid

Emma Hobbs

and 1 more

July 06, 2020
The current COVID-19 global pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of probable bat origin, has highlighted the ongoing need for a One Health response to emerging zoonotic disease events, which are significantly increasing over time. Understanding the human-animal interface and its relevance to disease transmission remains a critical control point for many emerging zoonoses. Determination of the susceptibility of various animal species to infection with SARS-CoV-2 and the role of animals in the epidemiology of the disease will be critical to informing appropriate human and veterinary public health responses to this pandemic. A scoping literature review was conducted to collect, evaluate and present the available research evidence regarding SARS-CoV-2 infections in animals. Experimental studies have successfully demonstrated SARS-CoV-2 infection and transmission in cats, ferrets, hamsters, bats and non-human primates under experimental settings. Dogs appear to have limited susceptibility to SARS-CoV-2, while other domestic species including pigs and poultry do not appear susceptible. Naturally occurring SARS-CoV-2 infections in animals appear uncommon, with 14 pets, 8 captive big cats and an unreported number of farmed mink testing positive to date. Infections typically appear asymptomatic in dogs, while clinical signs of respiratory and/or gastrointestinal disease tend to be mild to moderate in felines, and severe to fatal in mink. Most animal cases have been infected by close contact with COVID-19 patients. In domestic settings, viral transmission is self-limiting, however in high density animal environments there can be sustained between-animal transmission. To date, two potential cases of animal-to-human transmission are being investigated, on infected mink farms. Given the millions of COVID-19 cases worldwide and ongoing potential for further zoonotic and anthroponotic viral transmission, further research and surveillance activities are needed to definitively determine the role of animals in community transmission of SARS-CoV-2.
COVID-19 in India: Prediction of the Evolution of Coronavirus using Epidemiological M...
Muthusami Rathinasamy
Saritha K

Muthusami Rathinasamy

and 2 more

July 02, 2020
Coronavirus Disease 2019 (COVID-19) Pandemic is a big threat for all countries’ health systems. In India, the first case of coronavirus occurred in Kerala on 30 January 2020, followed by 2 more until 2 February 2020, but all three were cured, according to the World Health Organization (WHO) India situation report-2. Since this, no single case of coronavirus has been recorded across the country for a month. Nevertheless, from 2 March onwards, the number of cases rose on a regular basis. As of 21 June 2020, 410,461 confirmed cases and 13,254 total deaths, as stated in the World Health Organization (WHO) India situation report-21. This research presents significant findings about the early outbreak of COVID-19 in India. Due to the recent rapid rise in new cases of COVID-19, the pre-evolution of pandemic coronavirus is a pre-eminence in India. The susceptible-infectious-recovered (SIR) model was developed to estimate the reproductive number R0 at the early stage of the outbreak of COVID-19 and to evaluate this outbreak with available data on confirmed, deaths and recovered cases in India from 02 February 2020 to 26 June 2020.
Nucleic Acid Visualization Assay for Middle East Respiratory Syndrome Coronavirus (ME...
Pei Huang
Hongli Jin

Pei Huang

and 22 more

July 02, 2020
Since its first emergence in 2012, cases of infection with Middle East respiratory syndrome coronavirus (MERS-CoV) have continued to occur. In this study, we present two nucleic acid visualization assays that target the MERS-CoV UpE and N genes as a panel that combines reverse transcription recombinase polymerase amplification with a closed vertical flow visualization strip (RT-RPA-VF). The limit of detection was 1.2×10^1 copies/μl for the UpE assay and 1.2 copies/μl for the N assay. The two assays exhibited no cross-reactivity with multiple CoVs, including the bat severe acute respiratory syndrome related coronavirus (SARSr-CoV), the bat coronavirus HKU4, and the human coronaviruses 229E, OC43, HKU1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The RT-RPA-VF assay does not require sophisticated equipment and provides rapid detection within 30 min, so it has potential for use in surveillance and detection of MERS-CoV in low-resource settings.
COVID-19 and domestic animals: Exploring the species barrier crossing, zoonotic and r...
rajesh kumar
seetha harilal

rajesh kumar

and 6 more

July 01, 2020
To date, more than thirty animals were tested positive for SARS-CoV-2, all of them infected by humans with COVID-19. Some animal experiments suggested the possibility of an animal to animal transmission of SARS-CoV-2 and were seen in some cases of infected animals. Animal to human transmission was considered unlikely until investigations revealed the possibility of mink to human transmission of SARS-CoV-2 in the Netherlands. Studying the susceptibility of SARS-CoV-2 to domestic animals concluded that pigs, chicken, and ducks were not vulnerable to Covid-19; dogs showed less susceptibility to SARS-CoV-2 and cats as well as ferrets were seen susceptible to Covid-19. SARS-CoV-2 is seen crossing the species barrier, infecting humans from the wild with the source yet unclear, spreading from humans to humans quickly, humans to animals, animals to animals, and is likely to spread from animals to humans even though minimally. Animals appear somewhat resistant to SARS-CoV-2 transmission compared to humans who globally crossed eight million infection cases, and the infected animals mostly do not show many complications and recover quickly. Precautions are advised to prevent human to animal transmission of the virus, and in some areas, avoid animal to human spread of the virus. Further monitoring is required to assess the SARS-CoV-2 infection in animals as COVID-19 is a rapidly evolving condition worldwide.
Assessing the use of animal health platforms: user’s needs, preferences and constrain...
Juana Bianchini
Xavier Simons

Juana Bianchini

and 6 more

July 01, 2020
Animal health information systems or risk analysis tools are indispensable not only for animal health surveillance, but also to observe the evolution and risk of disease incursion into a disease-free area. Given their essential function in animal disease prevention, different international and national organizations have created their own aforementioned systems/tools. Moreover, with the increase of technology and data storage, they have become more accessible and widely used by professionals in animal and human health sciences. This study aimed to establish their preferences, needs and constraints in respect of these tools. An online survey was conducted and answered by 213 respondents from 132 countries. The respondents were animal or public health professionals in different employment sectors (mostly in government, research and university institutions) and various fields of competency (highest for animal and public health). The majority of respondents used the animal health information systems frequently and on a weekly basis, with prevention measures of diseases being regarded as the most useful information. Descriptive epidemiology is more used/needed than analytical epidemiology. Risk analysis was performed by the majority of the respondents (70%), using a qualitative approach more than a quantitative or semi-qualitative. The primary objectives was to produce risk assessment and preparedness in areas involving origin and spread of animal diseases. The features most sought after in risk assessment tools were pathways of introduction and spread assessment. The level of satisfaction was higher for the platform which is most used by the respondents. Thus, the platform choice is most likely influenced by its efficiency and functionality. Overall, these results could be taken into consideration when improving an already available platform, or when creating a new efficient tool.
ENDOPARASITES WITH POTENTIAL ZOONOTIC IN DOMESTIC DOG PUPPIES
Gisele Reginaldo
Sandra Inácio

Gisele Reginaldo

and 7 more

June 29, 2020
Gastrointestinal parasites are common in pet animals, despite the existence of therapeutic and prophylactic measures. Protozoa and helminths are of great importance for Unique Health, mainly due to their zoonotic potential. In this study, we investigated the occurrence of the main gastrointestinal parasites in domestic dog puppies in the city of Araçatuba, São Paulo. Thus, 100 fecal samples were collected from dogs up to six months of age. The samples were processed using Willis and Faust’s coproparasitological techniques and negative malachite green staining. The statistical analysis consisted of descriptive analysis. In addition, a general assessment of positivity between the techniques was carried out, in which if the animal was positive in a test it was considered positive in this criterion, due to each test being specific to a type of gastrointestinal parasite. With the results obtained it was possible to observe that animals that have age range less than or equal to six months of age had a higher occurrence for Toxocara spp. Eggs, and in some of theses animals it was possible to observe feces with normal consistency. The positivity for the parasites, by at least one of the techniques mentioned above, was: Toxocara spp. (34%); Isospora spp. (28%); Ancylostoma spp. (22%); and, Giardia spp. (8%). Thus, we concluded for the first time the occurrence of gastrointestinal parasites in domestic dog puppies less than six months of age, with detection of helminths and protozoa with zoonotic potential, being Toxocara spp. most prevalent. Finally, in our study, we diagnosed asymptomatic parasitized dogs, which may represent a risk in terms of Unique Health. Keywords: Helminths, Protozoa, Unique Health, Dogs, Diagnosis
A Three Months Study of COVID-19 in Pakistan
Jabir Ali
Hafiz Muhammad Asmar Naeem

Jabir Ali

and 6 more

June 29, 2020
COVID-19 is a new pandemic caused by SARS-CoV-2 which has created a havoc worldwide. Within no time it prevailed throughout the world compelling all countries to take emergency measures to overcome the pandemic. To overcome the disease, there is still no vaccine developed, however, different drugs are under trial. So, the only strategy to overcome the deadly virus is to avoid each and every way of contact with the already infected patients. For the assurance of avoidance policy, different countries took different measures according to their circumstances. Developing countries are much more infected than the developed ones as they already lack in fulfilling many basic necessities of life including economy. Pakistan is one of those developing countries whose economy is badly hit by following the model strategies of developed countries. So, Pakistan introduced different strategies like smart lock down, tiger force, etc. Pakistan has faced the worst peak of pandemic latter than most of the countries, so, to walk with the world in all aspects, Government should put its best efforts in the health zone to overcome COVID-19 as soon as possible.
Canine parvovirus type 2c is the dominant variant circulating in Jilin Province, Nort...
Haoyan  Jiang
Yue  Yu

Haoyan Jiang

and 12 more

June 23, 2020
To understand the current situation of canine parvovirus (CPV) epidemic strains in Jilin Province and to analyze the molecular biological characteristics and genetic evolution of the epidemic strains, 44 fecal or intestinal tissue samples detected by canine parvovirus test strips in Changchun and Liaoyuan City, Jilin Province, from February 2018 to November 2019 were collected for cloning, sequencing and genetic evolution analysis of the gene encoding the virus structural protein VP2. The results showed that 44 of the 44 samples were CPV-2 positive by PCR, among which CPV-2c was the dominant variant (70.4%). In addition, new-CPV-2a (18.2%), new-CPV-2b (9.1%) and CPV-2 (2.3%) also existed. This is the highest frequency of CPV-2c subtypes observed in canine populations in Jilin Province so far. In addition to the substitutions of Ala5Gly, Phe267Tyr, Tyr324Ile, and Gln370Arg in the VP2 protein, a novel variant with an Arg481Lys mutation was observed in a CPV-2c strain. Hence, there is a subsequent need for further and extensive epidemiological investigation and eventual adaptation of current vaccines.
Spotted fever group Rickettsiae in Dermacentor marginatus from wild boars in Italy
Giovanni Sgroi
Roberta Iatta

Giovanni Sgroi

and 6 more

June 23, 2020
Following the increase in wild boar population recorded in urban and peri-urban areas through Europe, the present survey aimed to assess the occurrence of zoonotic tick-borne bacteria in animals and their ticks collected from southern Italy, in order to evaluate the potential risk of infection for animals and humans. From October to December 2019, a total of 176 ticks collected from 93 wild boars and their spleen samples were molecularly screened for Borrelia burgdorferi sensu lato complex, Coxiella burnetii and spotted fever group (SFG) Rickettsia species. Overall, all the wild boars were infested by ticks (mean intensity, 1.9) with Dermacentor marginatus and Ixodes ricinus being identified in 99.4% and 0.6%, respectively. Out of 93 wild boars, 17 (18.3%) were infested by ticks positive to spotted fever group (SFG) Rickettsia species. Rickettsia slovaca and Rickettsia raoultii were identified in 16 (9%) and 1 (0.6%) D. marginatus, respectively, whereas a single I. ricinus (0.6%) was infected by R. slovaca. A single wild boar (1.1%) scored positive to R. slovaca. All ticks and wild boars scored negative to C. burnetii and B. burgdorferi s.l. complex. Data herein obtained suggest wild boars are involved in the dissemination of D. marginatus, especially in peri-urban settlements of the study area. An integrated management approach is advocated for wild boar population control and preventing the potential risk of tick-borne bacteria in animals and humans.
Animal Models for SARS-CoV-2 research: Systematic Review of Literature and Future Dir...
Kabita Pandey
Arpan Acharya

Kabita Pandey

and 5 more

June 22, 2020
Emerging and reemerging viral diseases can lead to devastating effects on human lives and at times also lead to economic crises. The ongoing COVID-19 pandemic due to the novel coronavirus (nCoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in Wuhan, China, has caused a global public health emergency. Still, the molecular mechanism of transmission of SARS-CoV-2, its clinical manifestations and pathogenesis is not completely understood. The global scientific community has intensified their efforts to understand the biology of SARS-CoV-2 to develop vaccines and therapeutic interventions to prevent the rapid spread of the virus and to control mortality and morbidity associated with COVID-19. To understand the pathophysiology of SARS-CoV-2, appropriate animal models that mimic the biology of human SARS-COV-2 infection is urgently needed. In this review, we outline animal models that have been used to study previous human coronaviruses (HCoVs), that includes severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Importantly, we discuss which model is appropriate for SARS-CoV-2 as well as the advantages and disadvantages of each.
Rapid emergence of African swine fever virus variants with different numbers of a tan...
Seon-Hee Kim
Song-I Lee

Seon-Hee Kim

and 7 more

June 17, 2020
African swine fever virus variants with different numbers of a 10-bp tandem repeat were isolated in South Korea soon after being identified in wild boar. The short emergence periods and sympatric distributions within a narrow geographical region suggest that the variants were sporadically generated in the pre-existing viral population.
Proposed Theory for Management of COVID_19: Thermal Shock to Viral wall Lipoprotein.
Yasser Ali

Yasser Ali

June 15, 2020
Proposed Theory for Management of COVID_19: Thermal Shock to Viral wall Lipoprotein. Abstract The global pandemic of COVID_19 is challenging the world, it pushes the health professional minds all over the world to think of a solution. Up to date there is shortage in the full information about the virus, however it is a viral RNA has lipoprotein membrane. Taking in consideration the available data and based on simple scientific facts, Author proposes a theory to be clinically investigated on a wide scale of COVID_19 infected Randomized control studies phase 2 without needing to animal studies as it depends on just hot vapor. This proposed thermal attack will eliminate a lot of viruses inside respiratory tract secretions. It literally means decreasing the COVID_19 Viruses load and allows body immune system to combat the virus with almost no or a little cytokine storm. It could decrease the spread of infection among contacts with cases infected with Corona viruses. This idea can simply quiet the morbidity and mortality curve. Keywords: COVID_19; Thermal; Destruction; Viral wall; Ventilator Setup.
Genetic evolution and epidemiological analysis of Seneca Valley virus (SVV) in China
Jinyong Zhang
He Zhang

Jinyong Zhang

and 13 more

June 11, 2020
Seneca Valley virus (SVV) is a novel Picornaviridae that is closely associated with porcine idiopathic vesicular disease (PIVD). Here, we report the detection and isolation of a novel strain of SVV, CH-GX-01-2019, from swine in Guangxi Province, China. The complete genomic sequence of CH-GX-01-2019 exhibited 93.3 - 98.9% identify with other SVV isolates at the nucleotide level. This new strain of SVV showed the highest level of similarity (98.9%) with Vietnamese strains and exhibited two consecutive mutations in the VP1 gene. Phylogenetic analysis based on the complete genome and the VP1 gene showed that Chinese forms of SVV can be divided into three clusters. We analyzed the geographical distributions of SVV strains in China and found that the epidemiology of these viruses in China is complicated; most strains are distributed predominantly in south and central China. Between 2015 and 2019, the dominant epidemic strains of Chinese SSV changed from clusters 1 and 3 to cluster 2. CH-GX-01-2019 (cluster 3) represents a recombinant strain from Colombia-2016 (cluster 2) and HB-CH-2016 (cluster 1). Our findings will enhance our understanding of the prevalence and genetic variation of SVV in the swine herds of China and provide important insights into the molecular epidemiology of SVV.
Prevalence, genetic diversity and implications for public health of Enterocytozoon bi...
Wei Zhao
Huanhuan Zhou

Wei Zhao

and 7 more

June 11, 2020
Rodents, globally overpopulated, are important source for zoonotic disease transmission to humans, including Enterocytozoon bieneusi (one of the most prevalent zoonotic pathogen). Here, we studied the prevalence and performed genetic analysis of E. bieneusi in rodents from the Hainan province of China by the amplification of the internal transcribed spacer (ITS) region of rDNA of E. bieneusi using PCR. Six hundred and three fresh fecal samples were gathered from 369 wild rats, 117 bamboo rats, 93 Asiatic brush-tailed porcupine and 24 red-bellied squirrels. The average rate of infection of E. bieneusi was 15.8% (95/603) with 18.7% (69/369) in wild rats, 11.9% (25/210) in farmed rodents and 4.2% (1/24) for red-bellied squirrels. Sixteen E. bieneusi genotypes were identified, including nine known genotypes (D, Type IV, PigEBITS7, Peru8, Peru11, ESH02, S7, EbpA and CHG5), and seven novel genotypes (HNR-I to HNR-VII). Genotype D (44.2%, 42/95) predominated, followed by PigEBITS7 (20.0%, 19/95), HNR-VII (15.8%, 15/95), Type IV (5.3%, 5/95), HNR-III (2.1%, 2/95), HNR-VI (2.1%, 2/95) and each of the remaining 10 genotypes (1.1%, 1/95). This is the first report on the identification of E. bieneusi in rodents from Hainan, China. The zoonotic potential of the identified E. bieneusi genotypes suggested that the rodents posed a serious threat to the local inhabitants. Thus, measures need to be taken to control the population of wild rats in the areas investigated in this study, along with identification of safe methods of disposal of farmed rodent feces. Additionally, the local people should be made aware of the risk of disease transmission from rodents to humans.
Association between climatic factors and COVID-19 transmission in a global South mega...
Muhammad Mainuddin Patwary
Faysal Kabir Shuvo

Muhammad Mainuddin Patwary

and 2 more

June 11, 2020
A flu-like disease (COVID-19) caused by a novel coronavirus has emerged in Wuhan, China in December, 2019 that is shortly turned into a public health concern globally. The effect of climatic variables on COVID-19 transmission is of paramount importance. However, the interactions are still controversial. This study investigated the association between climatic factors and COVID-19 spread in Dhaka megacity, Bangladesh. Data on the daily confirmed new cases of COVID-19 and climate parameters were collected from March 8, 2020 to April 30, 2020 in Dhaka City, Bangladesh. A log-linked negative binomial regression model was applied to estimate the association between climatic factors and transmission of COVID-19 cases. The daily new confirmed cases of COVID-19 were found positively associated with 14-days moving average of the daily average temperature (AvgT) and Relative Humidity (RH). Each 1°C increase of AvgT was associated with 2.76 times increase of daily confirmed new cases whereas 1% increase of RH was linked to an increase of 18% of the daily confirmed new cases of COVID-19. The study also found RH to be the stronger predictor and moderator between the AvgT and the daily cases of COVID-19 in Dhaka City. The results provide no evidence that COVID-19 could fade out itself when warmer season arrives. Thus, effective public health control measures must be implemented to prevent the further transmission of COVID-19.
COVID-19 severity declines over time
Christian Gortazar
Francisco Rodríguez del Río

Christian Gortazar

and 4 more

June 10, 2020
The first SARS-CoV-2 pandemic has affected most countries causing hundreds of thousands of deaths. Evolution of the pandemic may involve endemicity with or without significant secondary waves. We observed that disease severity (p=0.006) and duration of symptoms (p<0.001) declined over time in an isolated rural community. This decline was not driven by changes in patient age structure nor by changes in temperature or precipitations. The underlying mechanism may be relevant for COVID-19 management.
Unexpected positive correlation between human development index and risk of infection...
Kai Liu
Mu He

Kai Liu

and 2 more

June 09, 2020
In this analysis, we observed that human development index (an integrated index of life expectation, education and living standard) correlates with case rate (proportion of confirmed cases among the population) and the fatality rates of COVID-19 in Italy based on data as of May 15, 2020.
First expert elicitation of knowledge on drivers of emergence of the COVID-19 in pets
Claude Saegerman
Juana Bianchini

Claude Saegerman

and 4 more

June 08, 2020
Infection with the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) induces the coronavirus infectious disease 19 (COVID-19). Its pandemic form in human population and its probable animal origin, along with recent case reports in pets, make drivers of emergence crucial in carnivore domestic pets, especially cats, dogs and ferrets. Few data are available in these species; we first listed forty-six possible drivers of emergence of COVID-19 in pets, regrouped in eight domains (i.e. pathogen/disease characteristics, spatial-temporal distance of outbreaks, ability to monitor, disease treatment and control, characteristics of pets, changes in climate conditions, wildlife interface, human activity, and economic and trade activities). Secondly, we developed a scoring system per driver, then elicited experts (N = 33) to: (i) allocate a score to each driver, (ii) weight the drivers scores within each domain and (iii) weight the different domains between them. Thirdly, an overall weighted score per driver was calculated; drivers were ranked in decreasing order. Fourthly, a regression tree analysis was used to group drivers with comparable likelihood to play a role in the emergence of COVID-19 in pets. Finally, the robustness of the expert elicitation was verified. Five drivers were ranked with the highest probability to play a key role in the emergence of COVID-19 in pets: availability and quality of diagnostic tools, human density close to pets, ability of preventive/control measures to avoid the disease introduction or spread in a country (except treatment, vaccination and reservoir(s) control), current species specificity of the disease causing agent and current knowledge on the pathogen. As scientific knowledge on the topic is scarce and still uncertain, expert elicitation of knowledge, in addition with clustering and sensitivity analyses, is of prime importance to prioritize future studies, starting from the top five drivers. The present methodology is applicable to other emerging pet diseases.
Charateristics, clinical features, and animal contact history of COVID-19 patients in...
Yufeng YUAN
Zhen YANG

Yufeng YUAN

and 5 more

June 05, 2020
Leishenshan Hospital was an urgently built filed hospital in Wuhan only for treating coronavirus disease 2019 (COVID-19) patients. From the 8th of February it received the first cohort of patients until the closure day, 15th of April, it totally accepted 2011 COVID-19 patients including 20.9% severe and 79.1% non-severe cases with a case fatality rate (CFR) 2.2% (95%CI 1.6-3.0%). Totally 1917 (95.3%, 95%CI 94.3-96.2) patients were cured with a recovery rate of 86.2% in severe group and 100.0 % in non-severe group. On the 8th of April 2020, Wuhan city eased the lockdown policy after 76 days of the most restrict measurement ever. Herein, we collected 509 medical records from Leishenshan hospital to share some commonly interested COVID-19 clinical data.
The first isolation and whole genome characterization of Porcine Deltacoronavirus fro...
Juan More-Bayona
Mercy  Ramírez

Juan More-Bayona

and 3 more

June 04, 2020
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 positives to Porcine Deltacoronavirus with a cycle threshold (Ct) between 9-14, revealing a high viral load, while tested negatives 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. 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.
Effects of temperature on COVID-19 transmission in India
Indranil Bhattacharjee
Anuradha Deb

Indranil Bhattacharjee

and 4 more

June 04, 2020
This study analyzed the corelation between COVID-19 and temperature in India. Secondary published data from different websites is used by us. The climate indicators included in the study are maximum temperature, minimum temperature. Kendall and Spearman rank correlation tests were chosen for data analysis. We find that maximum temperature has significant relations associated with the COVID-19 pandemic. The findings of this study will help health regulators to combat COVID-19 in India and the rest of the world.
Assessing the potential transmission of major Salmonella serotypes from chicken feed...
Mickael Cargnel
Maria-Eleni Filippitzi

Mickael Cargnel

and 5 more

June 02, 2020
Vertical and horizontal transmissions of Salmonella spp. along the food chain (FC) have been reported to play an important role in the contamination of foodstuffs and of humans. This study aims first to clarify to what extend some selected major Salmonella serotypes are represented along the chicken FC and potentially transmitted from feed to humans. Then to discuss if the sampling results of the Belgian National Salmonella monitoring program may be considered as proxy to predict possible dominant serotypes and trends in humans. By using results of this programme, this study tried to highlight statistically significant differences in yearly prevalences between broilers exit status and other matrices (e.g. feed, other chicken categories, foodstuffs). Then to show up statistically significant changes from year to year prevalences in broilers exit status and to look if these changes can also be observed in the other matrices. Results have showed significant differences in yearly prevalences. They also pinpointed that the prevalence for the same serotypes could significantly vary from year to year in broilers exit status but this variation was inconsistently observed in the other matrices. These observations do not support the assumption of significant vertical and horizontal bacterial transmission along the chicken FC. Results in the national program cannot be considered as proxy. Determining the contribution of contaminated animal feed to human illness is challenging as the interplay of many factors makes it difficult. Coupling the actual programme with network analysis, source attribution and genome sequencing would be a way to explore deeper the spread of Salmonella serotypes along the FC. Belgium has put efforts to decrease Salmonella Enteritidis and Salmonella Typhimurium prevalence along the FC, but attention should be also paid to other pathogens that could fill the vacant niche left as Salmonella infantis which prevalence has been increasing in some matrices.
Emergence of European and North American mutant variants of SARS-CoV-2 in Southeast A...
Ovinu Kibria  Islam
Hassan Al-Emran

Ovinu Islam

and 5 more

June 02, 2020
The SARS-CoV-2 strain of the coronavirus is responsible for the current COVID-19 pandemic, with an ongoing toll of over 5 million infections and 333 thousand deaths worldwide within the first 5 months. Insight into the phylodynamics and mutation variants of this strain is vital to understanding the nature of its spread in different climate conditions. The incidence rate of COVID-19 is increasing at an alarming pace within subtropical Southeast Asian nations with high temperatures and humidity. To understand this spread, we analyzed 60 genome sequences of SARS-CoV-2 available in GISAID platform from 6 Southeast Asian countries. Multiple sequence alignments and maximum likelihood phylogenetic analyses were performed to analyze and characterize the non-synonymous mutant variants circulating in this region. Global mutation distribution analysis showed that the majority of the mutations found in this region are also prevalent in Europe and North America, and the concurrent presence of these mutations at a high frequency in Australia and Saudi Arabia indicate possible transmission routes. Unique spike protein and non-structural protein mutations were observed circulating within a localized area. We divided the circulating viral strains into 4 major groups and 2 sub-groups on the basis of the most frequent non-synonymous mutations. Strains with a unique set of 4 co-evolving mutations were found to be circulating at a high frequency within India, specifically, group 2 strains characterized by two co-evolving NS mutants which alter in RdRp (P323L) and spike protein (D614G) common in Europe and North America. These European and North American variants (Nextstrain clade A2) have rapidly emerged as dominant strains within Southeast Asia, increasing from a 0% presence in January to an 85% presence by May 2020. These variants may have an evolutionary advantage over their ancestral types and could present the largest threat to Southeast Asia for the coming winter.
On-site Detection of AHPND in Shrimp Farming by Probe-based Recombinase Polymerase Am...
Xiaohan Yang
Dong Yu

Xiaohan Yang

and 8 more

June 01, 2020
Acute hepatopancreatic necrosis disease (AHPND) is an important bacterial disease occurring early after stocking shrimp fry in shrimp ponds with the mortalities of 100 %. AHPND leads to significantly drop in production and brings out huge economic losses worldwide. Thus, rapid, accurate, and convenient on-site detection method is urgent need to monitor the outbreak and spreading of AHPND especially for equipment-poor areas. Application of traditional PCR-based methods is restricted due to the dependence on laboratory equipment and technicians. In this study, an improved isothermal recombinase polymerase amplification (RPA) combined lateral flow strip (LFS) assay was developed for AHPND detection by introducing a probe. The specific primers and probe were designed based on the PirAB gene, chemical modifications were labelled to improve the specificity, and mismatched bases were made to eliminate primer-dependent artifacts. In combination with crude DNA extraction by boiling for 10 min, the RPA-LFS assay could be finished within 25 min at 37-45°C and results were readable by naked eyes. The exclusivity was validated to be no cross-reactivity with 10 other common vibrio spp strains. The inclusivity was verified using 10 other VPAHPND strains isolated from infected shrimps. The limit of detection was 101 colony forming unit (CFU)/mL or 102 copies/μL and 100 CFU/10 g after 2 hours enrichment in spiked shrimp samples. The detection accuracy was evaluated in a total of 75 collected shrimp and seawater samples, which was proven to be consistent with AP4. The established RPA-LFS method provides a rapid, accurate, sensitive and equipment-free approach for on-site detection of AHPND and technical references for monitoring other pathogens in cultivation industry.
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