The raw case fatality rate (CFR, reported number of COVID-19 deaths divided by the number of cases) is a useful indicator to quantify the severity or treatment efficacy in a locality. In many countries, the pandemic showed a two-wave pattern now, namely the daily reported cases once reached a low level and now went up. To our knowledge, no study has compared the CFR for the two waves. In this work, we report that in 53 countries or regions with the highest deaths, the CFR is reduced in 43 countries or regions in the on-going second wave. We discussed the possible reasons. Also, we compare the two-wave pattern of COVID-19 with the weekly influenza positive tests. The influenza activity in pre-pandemic era provided an indicator for climate in a country, since it is well-known that influenza is driven by weather. The sharp drop in 2020 influenza activity is an indicator of the effects of social distancing.
Numerous unknown factors influence anthrax epidemiology in multi-host systems, especially at wildlife/livestock/human interfaces. Serology tests for anti-anthrax antibodies in carnivores are useful tools in identifying the presence or absence of Bacillus anthracis in a range. These were employed to ascertain if the disease pattern followed the recognized high and low risk anthrax zonation in Zimbabwe and also to establish if anthrax was absent from Hwange National Park in which there has been no reported outbreaks. African lions (Panthera leo) (n= 114) drawn from -free-range protected areas and captive game parks located in recognized high and low risk zones across Zimbabwe were tested for antibodies to anthrax PA antigen using the ELISA immunoassay. A random selection of 27 lion sera samples comprising 17 sero-positive and 10 sero-negative sera were further tested in the species-independent toxin neutralization assay (TNA) in order to validate the former as a surveillance tool for anthrax in African lions. Using the ELISA-PA immunoassay, 21.9% (25/114) of the lions tested positive for antibodies to anthrax. Seropositivity was recorded in all study areas and there was no significant difference (p= 0.852) in seropositivity between lions in high and low risk anthrax zones. Also, there was no significant difference (McNemar’s χ2 = 0.9, p = 0.343) in the proportion of lions testing positive to anti-PA anthrax antibodies on ELISA-PA immunoassay compared to the TNA, with fair agreement between the two tests [Kappa (K) statistic = 0.30; 0.08
The activity of influenza A at the end of 2019 was higher than previous two years in children younger than 6 years old in Wuhan, China. The 2019-20 seasonal influenza winter outbreak preceded the COVID-19 outbreak, with a higher and earlier peak than that of the 2017-18 and 2018-19 seasons. We speculate this could be due to the earlier CNY holiday season in 2019-20 than in previous two years. We compared these results with those of two previous studies to further discuss the possible interference between influenza and COVID-19 in young children.
Abstract: Armadillos are specialist diggers and their burrows are used to find food, seek shelter and protect their pups. These burrows can also be shared with dozens of vertebrate and invertebrate species and; consequently, their parasites including the zoonotics. The aim of this study was to diagnose the presence of zoonotic parasites in four wild-caught armadillo species from two different Brazilian ecosystems, the Cerrado (Brazilian savanna) and the Pantanal (wetland). The investigated parasites and their correspondent diseases were: Toxoplasma gondii (toxoplasmosis), Trypanosoma cruzi (Chagas disease), Leishmania spp., (leishmaniasis), Paracoccidioides spp. (Paracoccidioidomicosis) and Mycobacterium leprae (Hansen’s disease). Forty-three free-living armadillos from Pantanal and seven road-killed armadillos from the Cerrado were sampled. Trypanosoma cruzi DTU TcIII were isolated from 2 out of 43 (4.65%) armadillos, including one of them also infected with Trypanosoma rangeli. Antibodies anti-T. gondii were detected in 13 out of 43 (30.2%) armadillos. All seven armadillos from Cerrado tested positive for Paracoccidioides brasiliensis DNA, in the lungs, spleen, liver and ear fragments. Also, by molecular analysis, all 43 individuals were negative for M. leprae and Leishmania spp. Armadillos were infected by T. cruzi, T. rangeli, P. brasiliensis, and presented seric antibodies to T. gondii, highlighting the importance of those armadillos could have in the epidemiology of zoonotic parasites. Key words: Cingulata, Trypanosoma cruzi, Toxoplasma gondii, Paracoccidioides brasiliensis, Mycobacterium leprae, Leishmania sp.
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.
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.
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.
The objective of the study was to define and then evaluate an early decision indicator (EDI) trigger that operated within the first 5 weeks of a response that would indicate a large outbreak of FMD was developing, in order to be able to inform control options within an adaptive management framework. To define the trigger, a previous dataset of 10,000 simulated FMD outbreaks in New Zealand, controlled by the standard stamping-out approach, was re-analysed at various time points between days 11–35 of each response. The two predictive metrics adopted comprised the mean third quartiles of cumulative numbers of infected premises (IPs) at weekly time points, and estimated dissemination rate (EDR) values indicating sustained spread, specifically > 2.0 between days 11-14 or > 1.5 at any time point between days 15–35 of the response. To evaluate the trigger, the trigger was parameterized within the InterSpread Plus modelling framework, and a new series of simulation generated. The trigger was treated like a series of diagnostic tests that were applied during days 11–35 of each simulated outbreak, and its results recorded and then compared to the final size of each outbreak. The performance of the test was then evaluated across the population of outbreaks, and the sensitivity (Se), specificity (Sp), positive predictive value (PPV) and negative predictive value (NPV) calculated. The Se, Sp, PPV and NPV for predicting large outbreaks were 0.997, 0.513, 0.404 and 0.998 respectively. The study showed that the complex EDI incorporating both the cumulative number of IPs and EDR was very sensitive to detecting large outbreaks, although not all outbreaks predicted to be large were so, whereas outbreaks predicted to be small invariably were small. Therefore, it shows promise as a tool that could support an adaptive management approach to FMD control.
Coronavirus (CoV) pandemics have become a huge threat to the public health worldwide in the recent decades. Typically, severe acute respiratory syndrome CoV (SARS-CoV) caused SARS pandemic in 2003 and SARS-CoV-2 caused the ongoing COVID-19 pandemic. Both viruses have been reported to originate from bats. Thus, direct or indirect interspecies transmission from bats to humans is required for the viruses to cause pandemics. Receptor utilization is a key factor determining the host range of viruses which is critical to the interspecies transmission. Angiotensin converting enzyme 2 (ACE2) is the receptor of both SARS-CoV and SARS-CoV-2, but only ACE2s of certain animals can be utilized by the viruses. Here, we employed pseudovirus cell-entry assay to evaluate the receptor-utilizing capability of ACE2s of 20 animals by the two viruses and found that SARS-CoV-2 utilized less ACE2s than SARS-CoV, indicating a narrower host range of SARS-CoV-2. Especially, SARS-CoV-2 tended not to use murine or non-mammal ACE2s. Meanwhile, pangolin CoV, another SARS-related coronavirus highly homologous to SARS-CoV-2 in its genome, yet showed similar ACE2 utilization profile with SARS-CoV rather than SARS-CoV-2. To clarify the mechanism underlying the receptor utilization, we compared the amino acid sequences of the 20 ACE2s and found 5 amino acid residues potentially critical for ACE2 utilization, including the N-terminal 20th and 42nd amino acids that may determine the different receptor utilization of SARS-CoV, SARS-CoV-2 and pangolin CoV. Our studies promote the understanding of receptor utilization of pandemic coronaviruses, potentially contributing to the virus tracing, intermediate host screening and epidemic prevention for pathogenic coronaviruses.
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.
Tracing and isolation of close contacts is used to control outbreaks of coronavirus disease 2019 (COVID-19) in China. However, risk factors associated with occurrence of COVID-19 among close contacts have not been well described. 106 household contacts were included in this study, of whom 19 were developed into COVID-19 cases and the secondary attack rate was 17.9%. Multivariable analysis showed increasing risk of occurrence of COVID-19 among household contacts associated with female of index patients (Adjusted Hazard Ratio [aHR] = 5.61, 95%CI = 1.51-20.83), critical disease of index patients ([aHR] = 7.58, 95%CI = 1.66-34.66), effective contact duration with index patients >2 days ([aHR] = 4.21, 95%CI = 1.29-13.73), and effective contact duration >11 days ([aHR] = 17.88, 95%CI = 3.26-98.01).The sex and disease severity of index COVID-19 patients, and longer effective contact duration with COVID-19 confirmed cases could help epidemiologists to identify potential COVID-19 case among household contacts at an early stage.
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.
Hirudo nipponia is not only an important economic pillar for farmers, but is also a precious raw material for medicinal materials. However, in recent years, H. nipponia suffered from diseases with symptoms including systemic edema and hyperemia. It has not yet been demonstrated which pathogen causes this disease and whether this could be transmitted to humans. In this study, Klebsiella pneumoniae was isolated and identified from diseased H. nipponia and the pathogenicity of the isolated strain was confirmed. Furthermore, by comparing the sequence of the pathogen isolated from leeches to the same pathogen infecting humans, we identified that the isolated strain is a threat to human health. This work emphasizes the importance of the first discovery of pathogenic bacteria from leeches similar to human pathogens, as well as the need for identifying comorbidities for both humans and aquatic animals.
Bovine tuberculosis (bTB) prevalence substantially increased over the past two decades with relatively high impact on large dairy herds, raising the concern of regulatory authorities and industry stakeholders, and threatening animal and public health. Lack of resources, together with the economic and social consequences of whole-herd stamping-out, makes depopulation an impractical disease control alternative in these herds. The increase in bTB-prevalence was associated with demographic and management changes in the dairy industry in Uruguay, reducing the efficacy of the current control program (i.e. status quo) based on intradermal serial testing with caudal fold- and comparative cervical- tuberculin test-and slaughter of reactors (CFT-CCT). Here, we aimed to assess the epidemiological effectiveness of six alternative control scenarios based on test-and-slaughter of positive animals, using mathematical modeling to infer bTB-within-herd dynamics. We simulated six alternative control strategies consisting of testing adult cattle (>1 year) in the herd every three months using one test (in-vivo or in-vitro) or a combination in parallel of two tests (CFT, interferon-gamma release assay –IGRA- or Enzyme-linked immunosorbent assay). Results showed no significant differences overall in the time needed to reach bTB-eradication (median ranging between 61 to 82 months) or official bovine tuberculosis-free status (two consecutive negative herd-tests) between any of the alternative strategies and the status quo (median ranging between 50 and 59 months). However, we demonstrate how alternative strategies can significantly reduce bTB-prevalence when applied for restricted periods (6, 12, or 24 months), and in the case of IGRAc (IGRA using peptide-cocktail antigens), without incurring on higher unnecessary slaughter of animals (false-positives) than the status quo in the first 6 months of the program (P-value <0.05). Enhanced understanding bTB-within-herd dynamics with the application of different control strategies help to identify optimal strategies to ultimately improve bTB-control and -eradication from dairies in Uruguay and similar endemic settings.
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.
The outbreak of COVID-19 as a pandemic has shaken the global health system and economy by their roots. This epidemic is still spreading and showing no signs of decreasing trend. Vaccination is the only effective and economical means to control this pandemic. A number of research institutions and pharmaceutical companies have plunged into the race of vaccine development against COVID-19 which are in various stages of development. An intriguing fact of coronavirus infections is that in every decade of 21st century there is a new major coronavirus epidemic viz. SARS in 2002, MERS in 2012, and now COVID-19; and such epidemics are expected in future too. Since, maximum biological characteristics of SARS-CoV-2 are still obscure the scientists are relying on the information available on SARS-CoV and to some extent on MERS-CoV for designing and development of COVID-19 vaccines. But there is a need of vigorous testing for immunogenicity, safety, efficacy, and level of protection conferred in the hosts. This review focuses on the challenges and prospects of vaccine development against COVID-19. It highlights seriousness, bottlenecks in vaccine development, possible vaccine candidates, different vaccine strategies, safety evaluation issues, and vaccine production process pertaining to COVID-19 based on the knowledge acquired on SARS and MERS vaccine development in the past.
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.