On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study.

Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.

Dating first cases of COVID-19.

Questions persist as to the origin of the COVID-19 pandemic. Evidence is building that its origin as a zoonotic spillover occurred prior to the officially accepted timing of early December, 2019. Here we provide novel methods to date the origin of COVID-19 cases. We show that six countries had exceptionally early cases, unlikely to represent part of their main case series. The model suggests a likely timing of the first case of COVID-19 in China as November 17 (95% CI October 4). Origination dates are discussed for the first five countries outside China and each continent. Results infer that SARS-CoV-2 emerged in China in early October to mid-November, and by January, had spread globally. This suggests an earlier and more rapid timeline of spread. Our study provides new approaches for estimating dates of the arrival of infectious diseases based on small samples that can be applied to many epidemiological situations.

[COVID-19 and Its Environment: From a History of Human Medicine Towards an Ecological History of Medicine?] / COVID-19 und seine Umwelt: Von einer Geschichte der Humanmedizin zu einer ökologischen Medizingeschichte?

This paper is part of the Forum COVID-19: Perspectives in the Humanities and Social Sciences. The history of medicine is mostly written as a history of human medicine. COVID-19 and other zoonotic infectious diseases, however, demand a reconsideration of medical history in terms of ecology and the inclusion of non-human actors and diverse environments. This contribution discusses possible approaches for an ecological history of medicine which satisfies the needs of several current and overlapping crises.

History of indigenous Trypanosoma cruzi infection in humans, animals and triatomines in California, USA.

This historical review highlights previously undescribed potential foci for sylvatic and domestic locally acquired Chagas disease in California. The review starts in the 1910s, when Trypanosoma cruzi was first discovered through scientific triatomine investigations. Next, the natural transition around the mid-1900s into clinical investigations of the domestic and peridomestic environments and their epidemiologic profiles is detailed. The review closes with the shift to applied genetic, diagnostic and scientific applications surrounding Chagas disease infected individuals in the state. Throughout the course of the review, transmission foci and their unique clinical and epidemiologic characteristics are described. This in-depth review has merit for clinicians, veterinarians and public health officials working with vector-borne diseases in the southwestern USA.

Pre-Columbian zoonotic enteric parasites: An insight into Puerto Rican indigenous culture diets and life styles.

The pre-Columbian Huecoid and Saladoid cultures were agricultural ethnic groups that supplemented their diets by fishing, hunting and scavenging. Archaeological deposits associated to these cultures contained a variety of faunal osseous remains that hinted at the cultures' diets. The present study identified zoonotic parasites that may have infected these two cultures as a result of their diets. We used metagenomic sequencing and microscopy data from 540-1,400 year old coprolites as well as the zooarchaeological data to recreate the possible interactions between zoonotic parasites and their hosts. Microscopy revealed Diphyllobothrium spp. and Dipylidium caninum eggs along with unidentified cestode and trematode eggs. DNA sequencing together with functional prediction and phylogenetic inference identified reads of Cryptosporidium spp., Giardia intestinalis and Schistosoma spp. The complimentary nature of the molecular, microscopy and zooarchaeology data provided additional insight into the detected zoonotic parasites' potential host range. Network modeling revealed that rodents and canids living in close proximity to these cultures were most likely the main source of these zoonotic parasite infections.

MERS-CoV in Camels but Not Camel Handlers, Sudan, 2015 and 2017.

We tested samples collected from camels, camel workers, and other animals in Sudan and Qatar in 2015 and 2017 for evidence of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. MERS-CoV antibodies were abundant in Sudan camels, but we found no evidence of MERS-CoV infection in camel workers, other livestock, or bats.

Ancient Parasite Analysis and Zoonotic Potential of Spirometra sp. in Two Related Sites from Pernambuco, Brazil.

Pathoecology studies the environmental and cultural factors that contribute to the maintenance of infections or diseases in populations. Concerning parasites, it requires the evaluation of these factors based on the presence and life cycle of these organisms. For this reason, it is possible to apply this concept in the context of ancient populations in order to understand the parasite-host dynamic or even the health consequences faced by the members of the populations. This study aimed to apply the pathoecology concept in Pedra do Tubarão and Cemitério do Caboclo archaeological sites. Six coprolite samples were analyzed and 1 was positive for Spirometra sp. eggs. Spirometra is a cestode that has copepods as the first intermediate host; amphibians, reptiles, birds, and mammals as the second intermediate hosts; and felines and canines as definitive hosts. Humans can be infected by ingesting the first or second intermediate hosts and can develop sparganosis, which can cause health consequences depending on the location of the spargana. The presence of this parasite, of a water fount near the site, where the first intermediate host can live, and the findings of the bones of some of the second intermediate hosts in these sites, suggesting dietary purposes, indicate that this infection was probably present in this population.

A brief history of bird flu.

In 1918, a strain of influenza A virus caused a human pandemic resulting in the deaths of 50 million people. A century later, with the advent of sequencing technology and corresponding phylogenetic methods, we know much more about the origins, evolution and epidemiology of influenza epidemics. Here we review the history of avian influenza viruses through the lens of their genetic makeup: from their relationship to human pandemic viruses, starting with the 1918 H1N1 strain, through to the highly pathogenic epidemics in birds and zoonoses up to 2018. We describe the genesis of novel influenza A virus strains by reassortment and evolution in wild and domestic bird populations, as well as the role of wild bird migration in their long-range spread. The emergence of highly pathogenic avian influenza viruses, and the zoonotic incursions of avian H5 and H7 viruses into humans over the last couple of decades are also described. The threat of a new avian influenza virus causing a human pandemic is still present today, although control in domestic avian populations can minimize the risk to human health. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.

Hepatitis E Virus Infection in European Brown Hares, Germany, 2007-2014.

Rabbit-associated hepatitis E viruses (HEVs) cause zoonotic infections. We investigated 2,389 hares in Germany during 2007-2014. Complete genome characterization of a hare-associated HEV strain revealed close genomic relatedness to rabbit-associated HEV strains. Although hare-specific HEV seroprevalence was low, at 2.6%, hares represent a potential source of sporadic HEV infections.

Origins of the 1918 Pandemic: Revisiting the Swine "Mixing Vessel" Hypothesis.

How influenza A viruses host-jump from animal reservoir species to humans, which can initiate global pandemics, is a central question in pathogen evolution. The zoonotic and spatial origins of the influenza virus associated with the "Spanish flu" pandemic of 1918 have been debated for decades. Outbreaks of respiratory disease in US swine occurred concurrently with disease in humans, raising the possibility that the 1918 virus originated in pigs. Swine also were proposed as "mixing vessel" intermediary hosts between birds and humans during the 1957 Asian and 1968 Hong Kong pandemics. Swine have presented an attractive explanation for how avian viruses overcome the substantial evolutionary barriers presented by different cellular environments in humans and birds. However, key assumptions underpinning the swine mixing-vessel model of pandemic emergence have been challenged in light of new evidence. Increased surveillance in swine has revealed that human-to-swine transmission actually occurs far more frequently than the reverse, and there is no empirical evidence that swine played a role in the emergence of human influenza in 1918, 1957, or 1968. Swine-to-human transmission occurs periodically and can trigger pandemics, as in 2009. But swine are not necessary to mediate the establishment of avian viruses in humans, which invites new perspectives on the evolutionary processes underlying pandemic emergence.

[Technical assistance in crisis times: Brucelosis in the country programs for Spain of the world health organization (1951-1972)]. / Ayuda técnica en tiempos de crisis: la brucelosis en los programas país para España de la organización mundial de la salud (1951-1972).

OBJECTIVE: Brucellosis was one of the most important health problems in post-Civil War Spain and in subsequent years. The objective of the study was to reconstruct the first programs that the WHO set up in this country, to address this problem, between 1951 and 1972 and their main outcomes. METHODS: On the basis of primary sources of diverse origin, especially unpublished reports on Spain from foreign experts, from the WHO Historical Archive, the contents related to the disease were analyzed, contextualizing them within the framework of both the history of Spanish Public Health during the period studied and the international public health strategies for the prevention and control of brucellosis between 1951 and 1972. RESULTS: Spain 0001 (E1), Spain 0012 (E12) programs were located. The first of them (E1), dedicated to the problem of endemoepidemic diseases (brucellosis, rabies and Q fever), developed between 1952 and 1956, offered assistance in the work of control of these diseases carried out by public health laboratories. The second was preceded by visits of experts between 1956-1958 and formally started in 1969 and ended in 1972. This program was specifically devoted to the fight against brucellosis and included the start-up of laboratory and epidemiological work, the training of specialists, vaccination experiences in goats and sheep and the initiation of studies on immunizations in humans. CONCLUSIONS: The presence of consultants and experts from the WHO, from the highest scientific authority in the field of brucellosis such as Sandford Elberg or Martin Kaplan, was decisive in, at least, two aspects: first, to have an external view that would allow to know the reality of the Spanish health situation in the matter of the control of this zoonosis and, secondly, to start up and develop laboratory techniques and training of specialists with the aim of creating, at least, a center of reference for the preparation of vaccines, which the experts placed, ideally, in the National School of Health in Madrid.

OBJETIVO: La brucelosis fue uno de los más importantes problemas de salud en la España de la postguerra civil y en los años posteriores. El objetivo del estudio fue reconstruir los primeros programas que la OMS puso en marcha en este país, para abordar dicho problema, entre 1951 y 1972 y sus consecuencias. METODOS: Sobre la base de fuentes primarias de diversa procedencia, en especial, informes inéditos sobre España de expertos extranjeros, procedentes del Archivo Histórico de la OMS, se analizaron los contenidos relativos a la enfermedad, contextualizándolos tanto en el marco de la historia de la salud pública española del periodo objeto de estudio como en el de las estrategias a nivel internacional desarrolladas en este campo. RESULTADOS: Se localizaron los programas España 0001 (E1) y España 0012 (E12). El primero de ellos (E1), dedicado al problema de las enfermedades endemo-epidémicas (brucelosis, rabia y fiebre Q), desarrollado entre 1952 y 1956, ofreció asistencia en las labores de control de estas enfermedades llevadas a cabo por los laboratorios de salud pública. El segundo, precedido de visitas de expertos, entre 1956-1958, se inició formalmente en 1969 y finalizó en 1972, se consagró específicamente a la lucha contra la brucelosis e incluyó la puesta en marcha de trabajos de laboratorio y epidemiológicos, formación de especialistas, experiencias vacunales en ganado caprino y ovino e inicios de estudios sobre inmunizaciones en humanos. CONCLUSIONES: La presencia de consultores y expertos de la OMS de la máxima autoridad científica en el campo de la brucelosis, como Sandford Elberg o Martin Kaplan, fue decisiva en dos aspectos al menos, en primer lugar, para poder disponer de una mirada externa que permitiera conocer la realidad de la situación sanitaria española en el tema del control de dicha zoonosis y, en segundo lugar, para la puesta en marcha y el desarrollo de técnicas de laboratorio y de formación de especialistas con el objetivo de crear, al menos, un centro de referencia para la confección de vacunas, que los expertos situaban, de forma idónea, en la Escuela Nacional de Sanidad en Madrid.

Entangled histories of plague ecology in Russia and the USSR.

During the mid-twentieth century, Soviet scientists developed the "natural focus" theory-practice framework to explain outbreaks of diseases (such as bubonic plague) endemic to wild animals and transmitted to humans. Focusing on parasitologist-physician Evgeny N. Pavlovsky and other field scientists' work in the Soviet borderlands, this article explores how the natural focus framework's concepts and practices were entangled in political as well as material ecologies of knowledge and practice. We argue that the very definition of endemic plague incorporated both hands-on materialist experience (including the identification of microbes/pathogens, insects/vectors, and mammals/reservoirs) and ideological concepts that supported Soviet colonization ("improving" hinterlands, "controlling natural focuses of disease," and "sanitizing" landscapes). Theorizing and fighting plague assisted with the goals of controlling and improving landscapes and peoples in southern Russia and Central Asia. The history of the natural focus framework illustrates how Soviet disease ecology co-developed with the needs of local and central political powers in the Soviet borderlands.

Toxocara eggs in an 18th century Franciscan from Portugal. The challenge of differentiating between parasitism and chance in Paleoparasitology.

In 2005, an adult male was excavated in the cloister of the former Convent of the Holy Spirit, in the Franciscan Province of Holy Mary of Arrábida, Lisbon district. From the anterior part of the sacrum, a darker organic agglomeration was collected and studied for intestinal parasites. Samples were rehydrated with Lycopodium tablets in a Na3PO4 5% solution for 72h, followed by the swirl technique. Organic material was concentrated at 2500rpm. At least 20 slides of each sample were examined using a light/polarized microscope. A control sample from outside the pelvis revealed no biological remains. A sample collected inside the pelvic girdle was positive for pollen grains, other plant remains and Toxocara eggs, perhaps T. cati (2766 eggs/gram sediment). This finding, although exciting, cannot be explained in a simple way because humans are not definitive hosts for Toxocara species. Ingestion of feces-contaminated food or water, geophagy, or true infection are hypotheses considered in this study, which demonstrates the difficulty of interpreting the presence of animal parasites in human remains. This is the first time Toxocara eggs are found associated with human remains.

Apex Predators, Rockshelters, and Zoonoses in the Patagonian Holocene.

Carnivorous mammals are a trophic guild with an important role in the dissemination of parasite infective stages (larvae, eggs, cysts, and oocysts). In the present study, new samples of coprolites attributed to carnivorous mammals, obtained from 2 archaeological caves, were analyzed for the presence of parasites with the aim to increase the knowledge about parasites in rockshelters that could have spread to humans and other mammals. To this purpose, fragments of 3 coprolites from Cerro Casa de Piedra, cave 5 and cave 7, were examined. Coprolites were rehydrated in aqueous trisodium phosphate and processed by spontaneous sedimentation. High parasite richness was observed and new parasite species for archaeological contexts were found. The parasitological findings in Puma concolor coprolites associated with caves suggest the importance of these carnivores in the dissemination of parasites in areas with high re-use of space and steady conditions of temperature, humidity, and radiation.

Historical Aspects of Echinococcosis.

Echinococcosis is a zoonosis whose history dates back to antiquity. This article provides an overview on the general history of echinococcosis, including the elucidation of Echinococcus life cycles and the long controversy on the aetiology of the cystic and alveolar forms of echinococcosis (CE and AE), lasting about 100years since the middle of the 19th century. Furthermore, selected historical aspects of some fields of echinococcosis research are discussed and compared with our current knowledge, such as geographic distribution and epidemiology of CE (Echinococcus granulosus) and AE (Echinococcus multilocularis), clinical aspects and pathology, diagnosis in humans and animals, treatment (with focus on chemotherapy), control and basic research. A short paragraph is devoted to the neotropical forms of echinococcosis, caused by Echinococcus vogeli and Echinococcus oligarthrus. In this context the achievements of some ancestral pioneers of echinococcosis research are particularly highlighted and appreciated. Finally, the role of associations, international organizations (World Health Organization and others) and international working groups in echinococcosis research and control is briefly outlined. The retrospective reveals both the admirable achievements of our ancestors and the scientific progress of more recent times. But, it also shows the gaps in our knowledge, skills and resources that we need to control or even eradicate echinococcosis.