Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States

Although many persons in the United States have acquired immunity to COVID-19, either through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to non-immune persons so long as disease transmission continues. We can estimate when sustained disease transmission will end in a population by calculating the population-specific basic reproduction number , the expected number of secondary cases generated by an infected person in the absence of any interventions. The value of relates to a herd immunity threshold (HIT), which is given by . When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely (barring mutations allowing SARS-CoV-2 to escape immunity). Here, we report state-level estimates obtained using Bayesian inference. Maximum a posteriori estimates range from 7.1 for New Jersey to 2.3 for Wyoming, indicating that disease transmission varies considerably across states and that reaching herd immunity will be more difficult in some states than others. estimates were obtained from compartmental models via the next-generation matrix approach after each model was parameterized using regional daily confirmed case reports of COVID-19 from 21 January 2020 to 21 June 2020. Our estimates characterize the infectiousness of ancestral strains, but they can be used to determine HITs for a distinct, currently dominant circulating strain, such as SARS-CoV-2 variant Delta (lineage B.1.617.2), if the relative infectiousness of the strain can be ascertained. On the basis of Delta-adjusted HITs, vaccination data, and seroprevalence survey data, we found that no state had achieved herd immunity as of 20 September 2021.

A spatiotemporal analysis of COVID-19 transmission in Jakarta, Indonesia for pandemic decision support

With 25% confirmed cases of the country’s total number of coronavirus disease 2019 (COVID-19) on 31 January 2021, Jakarta has the highest confirmed cases of in Indonesia. The city holds a significant role as the centre of government and national economic activity for which pandemic have had a huge impact. Spatiotemporal analysis was employed to identify the current condition of disease transmission and to provide comprehensive information on the COVID-19 outbreak in Jakarta. We applied space-time analysis to visualise the pattern of COVID-19 hotspots in each time series. We also mapped area capacity of the referral hospitals covering the entire area of Jakarta to understand the hospital service range. This research was conducted in 4 stages: i) disease mapping; ii) spatial autocorrelation analysis; iii) space-time pattern analysis; and iv) areal capacity mapping. The analysis resulted in 144 sub-districts categorised as high vulnerability. Autocorrelation studies by Moran’s I identified cluster patterns and the emerging hotspot results indicated successful interventions as the number of hotspots fell in the first period of social restrictions. The results presented should be beneficial for policy makers.

Exploring the Role of Innate Lymphocytes in the Immune System of Bats and Virus-Host Interactions

Bats are reservoirs of a large number of viruses of global public health significance, including the ancestral virus for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the causative agent of coronavirus disease 2019 (COVID-19). Although bats are natural carriers of multiple pathogenic viruses, they rarely display signs of disease. Recent insights suggest that bats have a more balanced host defense and tolerance system to viral infections that may be linked to the evolutionary adaptation to powered flight. Therefore, a deeper understanding of bat immune system may provide intervention strategies to prevent zoonotic disease transmission and to identify new therapeutic targets. Similar to other eutherian mammals, bats have both innate and adaptive immune systems that have evolved to detect and respond to invading pathogens. Bridging these two systems are innate lymphocytes, which are highly abundant within circulation and barrier tissues. These cells share the characteristics of both innate and adaptive immune cells and are poised to mount rapid effector responses. They are ideally suited as the first line of defense against early stages of viral infections. Here, we will focus on the current knowledge of innate lymphocytes in bats, their function, and their potential role in host–pathogen interactions. Moreover, given that studies into bat immune systems are often hindered by a lack of bat-specific research tools, we will discuss strategies that may aid future research in bat immunity, including the potential use of organoid models to delineate the interplay between innate lymphocytes, bat viruses, and host tolerance.

The Dilemma of Reconstructive Material Choice for Orbital Floor Fracture: A Narrative Review

The aim of this study is to present a narrative review of the properties of materials currently used for orbital floor reconstruction. Orbital floor fractures, due to their complex anatomy, physiology, and aesthetic concerns, pose complexities regarding management. Since the 1950s, a myriad of materials has been used to reconstruct orbital floor fractures. This narrative review synthesises the findings of literature retrieved from search of PubMed, Web of Science, and Google Scholar databases. This narrative review was conducted of 66 studies on reconstructive materials. Ideal material properties are that they are resorbable, osteoconductive, resistant to infection, minimally reactive, do not induce capsule formation, allow for bony ingrowth, are cheap, and readily available. Autologous implants provide reliable, lifelong, and biocompatible material choices. Allogenic materials pose a threat of catastrophic disease transmission. Newer alloplastic materials have gained popularity. Consideration must be made when deliberating the use of permanent alloplastic materials that are a foreign body with potential body interactions, or the use of resorbable alloplastic materials failing to provide adequate support for orbital contents. It is vital that surgeons have an appropriate knowledge of materials so that they are used appropriately and reduce the risks of complications.

Livestock, pathogens, vectors, and their environment: a causal inference-based approach to estimating the pathway-specific effect of livestock on human African trypanosomiasis risk

Livestock are important reservoirs for many diseases, and investigation of such zoonoses has long been the focus of One Health research. However, the effects of livestock on human and environmental health extend well beyond direct disease transmission. In this retrospective ecological cohort study we use pre-existing data and methods derived from causal inference and spatial epidemiology to estimate three hypothesized mechanisms by which livestock can come to bear on human African trypanosomiasis (HAT) risk: the reservoir effect, by which infected cattle and pigs are a source of infection to humans; the zooprophylactic effect, by which preference for livestock hosts exhibited by the tsetse fly vector of HAT means that their presence protects humans from infection; and the environmental change effect, by which livestock keeping activities modify the environment in such a way that habitat suitability for tsetse flies, and in turn human infection risk, is reduced. We conducted this study in four high burden countries: at the point level in Uganda, Malawi, and Democratic Republic of Congo (DRC), and at the county-level in South Sudan. Our results indicate cattle and pigs play an important reservoir role for the rhodesiense form (rHAT) in Uganda, however zooprophylaxis outweighs this effect for rHAT in Malawi. For the gambiense form (gHAT) we found evidence that pigs may be a competent reservoir, however dominance of the reservoir versus zooprophylactic pathway for cattle varied across countries. We did not find compelling evidence of an environmental change effect.

Application of Interpretative Structural Modeling (ISM) to Determine Port Waste Management Strategies for African Swine Fever (ASF) Prevention at Tanjung Priok Port

African Swine Fever (ASF) is one of the infectious diseases affecting swine with high mortality rate. Disease transmission occurs direct and indirect. Indirect transmission through feed, virus contaminated object and swill feeding produced by ships. Ships berthing in the port of Tanjung Priok mostly comes or transits from a country which ASF exist. Among those ships, some discharge their garbage and take over into the final dumping site without any further treatment. There are many institution and a third parties involved in garbage management in the port of Tanjung Priok. This research aims is to identify an obstacle, actors and strategies in managing garbage from the ships to prevent ASF spread in the port of Tanjung Priok using Interpretative Structural Modelling (ISM). The results of this research shows the biggest obstacle in managing garbage from the ships, in order to prevent ASF spread in the port of Tanjung Priok is the absence of standard operating procedures (SOP), The most important actor is Indonesia Port Corporation II and the most important strategy is develop an integrated SOP for ship waste management. is to develop an integrated SOP for ship waste management.

COVID-19 Pandemic and Periodontal Practice: The Immunological, Clinical, and Economic Points of View

The recent global health problem, COVID-19, has had far-reaching impacts on lifestyles. Although many effective WHO-approved vaccines have been produced that have reduced the spread and severity of the disease, it appears to persist in humans for a long time and possibly forever as everyday it turns out to have new mutations. COVID-19 involves the lungs and other organs primarily through cytokine storms, which have been implicated in many other inflammatory disorders, including periodontal diseases. COVID-19 is in a close association with dental and periodontal practice from two respects: first, repeated mandatory lockdowns have reduced patient referrals to dentists and limited the dental and periodontal procedures to emergency treatments, whereas it is important to recognize the oral manifestations of COVID-19 as well as the influence of oral and periodontal disease on the severity of COVID-19. Second, dentistry is one of the high-risk professions in terms of close contact with unmasked individuals, necessitating redefining the principles of infection control. The pressures of the economic recession on patients as well as dentists add to the difficulty of resuming elective dental services. Therefore, this study is divided into two parts corresponding to what mentioned above: the first part examines the clinical and immunological associations between COVID-19 and periodontal and oral diseases, and the second part delineates the measures needed to control the disease transmission in dental clinics as well as the economic impact of the pandemic era on dental services.

Estimating The Distribution of Livestock In Space And Time: A Time-Series Contribution To Livestock Density Mapping

More than one billion people rely on livestock for income, nutrition, and social cohesion, however livestock keeping can facilitate disease transmission and contribute to climate change. While data on the distribution of livestock thus have broad utility across a range of applications, efforts to map the distribution of livestock on a large scale are limited to the Gridded Livestock of the World (GLW) project. We present a complimentary effort to map the distribution of cattle and pigs in Malawi, Uganda, Democratic Republic of Congo (DRC), and South Sudan. In contrast to GLW, which uses dasymmetric modeling applied to census data to produce time-stratified estimates of livestock counts and spatial density, our work uses complex survey data and distinct modeling methods to generate a time-series of livestock distribution, defining livestock density as the ratio of animals to humans. In addition to favorable cross-validation results and general agreement with national density estimates derived from external data on national human and livestock populations, our results demonstrate extremely good agreement with GLW-3 estimates, supporting the validity of both efforts. Our results furthermore offer a high-resolution time series result and employ a definition of density which is particularly well-suited to the study of livestock-origin zoonoses.

Prevention and Control of African Swine Fever in the Smallholder Pig Value Chain in Northern Uganda: Thematic Analysis of Stakeholders' Perceptions

African swine fever (ASF) is endemic in Uganda and considered a major constraint to pig production. In the absence of a vaccine, biosecurity is key for ASF prevention and control. To improve prevention and control on farm and community level there is need for more knowledge on current application of biosecurity practises, and better understanding of how pig value chain actors perceive prevention and control. To achieve this, a qualitative interview study involving focus group discussions (FGD) was conducted with actors from the smallholder pig value chain in northern Uganda. Six villages were purposively selected based on previous outbreaks of ASF, preliminary perceived willingness to control ASF, and the representation of several different value chain actors in the village. Results indicated that biosecurity practises such as basic hygiene routines including safe carcass handling, minimising direct and indirect contacts between pigs or between pigs and people, trade restrictions and sharing of disease information were implemented in some of the villages. Thematic analysis based on grounded theory revealed six categories of data relating to ASF prevention and control. Together these categories form a logical framework including both enablers and hindrances for ASF prevention and control. In summary participants mostly had positive perceptions of ASF biosecurity, describing measures as effective. Participants further possessed knowledge of ASF and its transmission, some of which was in line with known scientific knowledge and some not. Nevertheless, participants were hindered from preventing and controlling ASF due to biosecurity costs and a need to prioritise family livelihood over disease transmission risks, incompatibility of current biosecurity practises with local culture, traditions and social contexts and finally lack of access to veterinarians or, occasionally, low-quality veterinary services. The constraints could be addressed by applying participatory processes in designing biosecurity measures to ensure better adaptation to local cultural and social contexts.

Insect Diapause

Our highly seasonal world restricts insect activity to brief portions of the year. This feature necessitates a sophisticated interpretation of seasonal changes and enactment of mechanisms for bringing development to a halt and then reinitiating it when the inimical season is past. The dormant state of diapause serves to bridge the unfavourable seasons, and its timing provides a powerful mechanism for synchronizing insect development. This book explores how seasonal signals are monitored and used by insects to enact specific molecular pathways that generate the diapause phenotype. The broad perspective offered here scales from the ecological to the molecular and thus provides a comprehensive view of this exciting and vibrant research field, offering insights on topics ranging from pest management, evolution, speciation, climate change and disease transmission, to human health, as well as analogies with other forms of invertebrate dormancy and mammalian hibernation.