The SARS-CoV-2 virus was detected for the first time in December 2019 in Wuhan, China. Currently, this virus has spread around the world, and new variants have emerged. This new pandemic virus provoked the rapid development of diagnostic tools, therapies and vaccines to control this new disease called COVID-19. Antibody detection by ELISA has been broadly used to recognize the number of persons infected with this virus or to evaluate the response of vaccinated individuals. As the pandemic spread, new questions arose, such as the prevalence of antibodies after natural infection and the response induced by the different vaccines. In Mexico, as in other countries, mRNA and viral-vectored vaccines have been widely used among the population. In this work, we developed an indirect ELISA test to evaluate S1 antibodies in convalescent and vaccinated individuals. By using this test, we showed that IgG antibodies against the S1 protein of SARS-CoV-2 were detected up to 42 weeks after the onset of the symptoms, in contrast to IgA and IgM, which decreased 14 weeks after the onset of symptoms. The evaluation of the antibody response in individuals vaccinated with Pfizer-BioNTech and CanSinoBio vaccines showed no differences two weeks after vaccination. However, after completing the two doses of Pfizer-BioNTech and the one dose of CanSinoBio, a significantly higher response of IgG antibodies was observed in persons vaccinated with Pfizer-BioNTech than in those vaccinated with CanSinoBio. In conclusion, these results confirm that after natural infection with SARS-CoV-2, it is possible to detect antibodies for up to ten months. Additionally, our results showed that one dose of the CanSinoBio vaccine induces a lower response of IgG antibodies than that induced by the complete scheme of the Pfizer-BioNTech vaccine.

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.

Susceptibility of turkeys, chickens and chicken embryos to SARS-CoV-2 virus was evaluated by experiment inoculation. Turkeys and chickens were inoculated using a combination of intranasal, oral and ocular routes. Both turkeys and chickens did not develop clinical disease or antibodies to the virus following inoculation. Viral RNA was not detected in oral and cloacal swabs and in tissues using quantitative real-time RT-PCR. In addition, chicken embryos were inoculated using the yolk sac, intravenous, chorioallantoic membrane and allantoic cavity routes did not support replication of the virus. SARS-COV-2 virus does not affect both turkeys and chickens in the current genetic state and does not pose any potential risk to establish in both species of domestic poultry.

Summary: The unusual genetic diversity of the Omicron strain has led to speculation about its origin. The mathematical modeling platform developed for the Stockholm Paradigm (SP) indicates strongly that it has retro-colonized humans from an unidentified animal reservoir originally infected by humans. The relationship between Omicron and all other SARS-CoV-2 variants indicates oscillations among hosts, a core part of the SP. Such oscillations result from the emergence of novel variants following colonization of new hosts, replenishing and expanding the risk space for disease emergence. The SP predicts that pathogens colonize new hosts using pre-existing capacities. Those events are thus predictable to a certain extent. Novel variants emerge after a colonization and are not predictable. This makes it imperative to take proactive measures for anticipating emerging infectious diseases (EID) and mitigating their impact. The SP suggests a policy protocol to accomplish this goal. This is the DAMA Protocol: comprising DOCUMENT to detect pathogens before they emerge in new places or colonize new hosts; ASSESS to determine risk; MONITOR to detect changes in pathogen populations that increase the risk of outbreaks; and ACT to prevent outbreaks when possible and minimize their impact when they occur.

African swine fever (ASF) and classical swine fever (CSF) are two major transboundary animal diseases of swine with important socioeconomic consequences at farm, subnational and national level. The objective of this study was to evaluate the direct cost of outbreaks and their control at country/regional level in four countries: namely CSF in Colombia in 2015-2016, the retrospective cost of ASF in the Philippines in 2019 and in a province of Vietnam in 2020, and a hypothetical ASF scenario in one region in North Macedonia, using the newly developed Outbreak Costing Tool (OutCosT). The tool calculates the costs of 106 different items, broken down by up to four types of farms, and by who assumes the cost (whether veterinary services, farmers or other stakeholders). The total cost of CSF in Colombia was US$ 3.8 million of which 88% represented the cost of the vaccination campaign. For ASF, there were wide differences between countries: US$ 826,911 in Lao Cai (Vietnam), US$ 3,319,666 in North Macedonia and over US$ 58 million in the Philippines. While in the Philippines and Vietnam, 96-98% of the cost occurred in the affected farms, the highest expenditure in North Macedonia scenario was the movement control of the neighbouring and at-risk farms (77%). These important differences between countries depend on the spread of the disease, but also on the production systems affected and the measures applied. Apart from the financial cost, these diseases have other negative impacts, especially in the livelihoods of smallholder farms. The OutCosT tool also allows users to evaluate qualitatively other important aspects related to the epidemics, such as the impact on human health, the environment, animal welfare, socio-economic vulnerability, trading and political response. The main purpose of the OutCosT, which will become a FAO corporate tool, is to support country authorities to rapidly respond to ASF outbreaks by estimating the associated costs, and for advocacy purposes to mobilize resources at national or international levels.

Carnivore protoparvovirus 1 is one of the most important pathogens affecting both wild and domestic carnivores. Here, we reported the genetic characterization of canine parvovirus strains from a rescued guiña (Leopardus guigna) and domestic dogs from Chile. Guiña sequence was classified as CPV-2c and phylogenetic analysis of the complete coding genome showed that the guiña CPV-2c strain share a recent common ancestor with Chilean domestic dogs strains. These viruses presented >99% identity and showed three changes in the NS1 protein, CHL-17 V596A, CHL-71 E661K and CHL-guigna L582F. This is the first detection and genetic characterization of CPV-2c infection in guiña worldwide and one of the few comparative studies that undoubtedly determine that the source of infection were domestic dogs. The current findings highlight that guiña is a susceptible species to protoparvovirus infection and that domestic dogs represent an important thread to its conservation. The CPV cross-species transmission between domestic dogs and guiña should be taken into account for protection programs of this endangerous species.

There is growing evidence that climatic factors could influence the evolution of the current COVID-19 pandemic. Here, we build on this evidence base, focusing on the southern hemisphere summer and autumn period. The relationship between climatic factors and COVID-19 cases in New South Wales, Australia was investigated during both the exponential and declining phases of the epidemic in 2020, and in different regions. Increased relative humidity was associated with decreased cases in both epidemic phases, and a consistent negative relationship was found between relative humidity and cases. Overall, a decrease in relative humidity of 1% was associated with an increase in cases of 7-8%. Overall, we found no relationship with between cases and temperature, rainfall or wind speed. Information generated in this study confirms humidity as a driver of SARS-CoV-2 transmission.

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.

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.

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.

Using a model developed previously by the authors, a risk assessment was conducted to predict the change in the risk of ASF entering Japan as a result of the coronavirus pandemic in humans. The annual probability of ASF entering Japan was calculated to be 23% (90% prediction interval: 0-91%), 4.7% (0-24%) in February, 0.4% (0-2.1%) in March and 0.004% (0-0.01%) in April 2020 indicating a significant decline in the risk of ASF entry into Japan from China. The decline was attributed to a decline in the number of air travelers from China and amount of restaurant food.

Leishmania donovani is the causative agent of historically anthroponotic visceral leishmaniasis (VL) on the Indian subcontinent (ISC). L. donovani is transmitted by the sand fly species Phlebotomus argentipes. Our collaborative group and others have shown that sand flies trapped outside in endemic villages have fed on cattle and dogs in addition to people. Domestic animals are reservoirs for L. donovani complex spp., particularly L. infantum, in other endemic areas. Multiple studies using quantitative PCR or serological detection methods have demonstrated that goats, cattle, rats and dogs were diagnostically positive for L. donovani infection or exposure in eastern Africa, Bangladesh, Nepal and India. There is a limited understanding of the extent to which L. donovani infection of domestic animals drives transmission to other animals or humans on the ISC. Evidence from other vector-borne disease elimination strategies indicated that emerging infections in domestic species hindered eradication. The predominant lesson learned from these other situations is that non-human reservoirs must be identified, controlled and/or prevented. Massive efforts are underway for VL elimination on the Indian subcontinent. Despite these herculean efforts, residual VL incidence persists. The specter of an animal reservoir complicating elimination efforts haunts the final push toward full VL control. Better understanding of L. donovani transmission on the Indian subcontinent and rigorous consideration of how non-human reservoirs alter VL ecology are critical to sustain elimination goals.

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.

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.

Despite the recognized role of wild waterfowl in the potential dispersal and transmission of highly pathogenic avian influenza (HPAI) virus, little is known about how infection affects these birds. This lack of information limits our ability to estimate viral spread in the event of an HPAI outbreak, thereby limiting our abilities to estimate and communicate risk. Here we present telemetry data from a wild Lesser Scaup ( Aythya affinis), captured during a separate ecology study in the Chesapeake Bay, Maryland. This bird tested positive for infection with clade 2.3.4.4 HPAI virus of the A/goose/Guangdong/1/1996 (Gs/GD) H5N1 lineage (results received post-release) during the 2021-22 ongoing outbreaks in North America. While the infected bird was somewhat lighter than other adult males surgically implanted with transmitters (790g, mean=868g, n=11), it showed no clinical signs of infection at capture, during surgery, nor upon release. The bird died 3d later, pathology undetermined as the specimen was not able to be recovered. Analysis of movement data within the 3d window showed that the infected individual’s maximum and average hourly movements (3894.3m, 428.8m respectively) were noticeably lower than noninfected conspecifics tagged and released the same day (mean =21594.5m, mean =1097.9m, respectively; n=4). We identified four instances where the infected bird had direct contact (fixes located within 25m and 15 min) with another marked bird during this time. Collectively, these data suggest that the HPAI positive bird observed in this study may have been shedding virus for some period prior to death, with opportunities for direct bird to bird or environmental transmission. Although limited by low sample size and proximity to the time of tagging, we hope that these data will provide useful information as managers continue to respond to this ongoing outbreak event.

African swine fever (ASF) has spread across many countries in Europe since the introduction into Georgia in 2007. We report here on the first cases of ASF in wild boar detected in Germany close to the border with Poland. In addition to the constant risk of ASF virus (ASFV) spread through human activities, movements of infected wild boar also represent a route of introduction. Since ASF emerged in Western Poland in November 2019, surveillance efforts, in particular examination of wild boar found dead, were intensified in the regions of Germany bordering with Poland. The first case of ASF in wild boar in Germany was therefore detected by passive surveillance and confirmed on 10th September 2020. By 24th September 2020, 32 cases were recorded. Testing of samples from tissues of carcasses in different stages of decomposition yielded cycle threshold values from 18 to 36 in the OIE-recommended PCR which were comparable between the regional and national reference laboratory. Blood swabs yielded reliable results, indicating that the method is suitable also under outbreak conditions. Phylogenetic analysis of the ASFV whole-genome sequence generated from material of the first carcass detected in Germany, revealed that it groups with ASFV genotype II including all sequences from Eastern Europe, Asia and Belgium. However, some genetic markers including a 14 bp tandem repeat duplication in the O174L gene were confirmed that have so far been detected only in sequences from Poland (including Western Poland). Epidemiological investigations that include estimated postmortem intervals of wild boar carcasses of infected animals suggest that ASFV had been introduced into Germany in the first half of July 2020 or even earlier.

Monogenean infection of the internal organs is extremely rare when compared to external infections. This study describes mass mortality of Nile tilapia (Oreochromis niloticus L.) originating from co-infection with Enterogyrus spp. and Aeromonas jandaei following transport stress. The first fish deaths occurred on day 1 post-transport, while cumulative mortality reached approximately 90% by day 10 post-stocking. An atypical amount of pale (whitish) faeces floating on the surface of the water as well as typical clinical signs of motile Aeromonas septicemia, were reported. Adult monogeneans and countless eggs of monogeneans were found in the stomachs and the intestines of both moribund and dead fish, respectively. Two strains of A. jandaei were isolated from the kidneys. Scanning electron microscope microphotographs of the stomach revealed the presence of numerous monogeneans penetrating deep into the gastric tissue, and diffuse lesions filled with bacilliform bacteria. This is the first report of co-infection by Enterogyrus spp. and A. jandaei in Nile tilapia and the first report of E. coronatus, E. foratus, and E. malbergi parasitizing tilapia in Brazil. These findings indicate that synergic co-infection by Monogenean stomach parasites (E. coronatus, E. foratus, and E. malbergi) and A. jandaei may induce high mortalities in tilapia following transport stress.

After its first description in Wuhan (China), SARS-CoV-2 the agent of coronavirus disease 2019 (COVID-19) rapidly spread worldwide. Previous studies suggested that pets could be susceptible to SARS-CoV-2. Here, we investigated the putative infection of SARS-CoV-2 in 22 cats and 11 dogs from owners previously infected or suspected of being infected by SARS-CoV-2. For each animal, rectal, nasopharyngeal swabs and serum were taken. Swabs were submitted to RT-qPCR assays targeting 2 genes of SARS-CoV-2. All dogs were tested SARS-CoV-2 negative. One cat was tested positive by RT-qPCR on rectal swab. Nasopharyngeal swabs from this animal were tested negative. This cat showed mild respiratory and digestive signs. Serological analysis confirm the presence of antibodies against the SARS-CoV-2 in the two serum samples taken 10 days apart. Genome sequence analysis revealed that the cat SARS-CoV-2 belongs to the phylogenetic clade A2a like most of the French human SARS-CoV-2. This study reports for the first time the natural infection of a cat in France (near Paris) probably through their owners. There is currently no evidence that cats can spread COVID-19 and owners should not abandon their pets or compromise their welfare.