Ten millennia of hepatitis B virus evolution.

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.

The origins of viral infection sleuth.

The events of the past year have underscored the serious and rapid threat that emerging viruses pose to global health. However, much of the rapid progress in understanding and combating SARS-CoV-2 was made possible because of the decades of important groundwork laid from researchers studying other emergent infectious diseases. The 2021 John Dirks Canada Gairdner Global Health award recognizes the contributions of Joseph Sriyal Malik Peiris and Yi Guan toward understanding the origins and options for control of newly emerging infectious disease outbreaks in Asia, notably zoonotic influenza and severe acute respiratory syndrome (SARS). Cell's Nicole Neuman corresponded with Yi Guan about his path to becoming a viral infection sleuth and the challenges of understanding emerging pathogens and their origins. Excerpts of their exchange are included here.

[The challenge of (re)emerging diseases, the limits of the biomedical response and the new paradigm of global health]. / El desafío de las enfermedades (re)emergentes, los límites de la respuesta biomédica y el nuevo paradigma de salud global.

"Emerging and reemerging infectious diseases" pose a growing threat to the hegemony of biomedicine, raising questions about whether its discourse and practices can handle the global challenge they represent. The construction of this new nosological category is analyzed in this article, which examines some notable examples of the impact of (re)emerging diseases on public health, food security and human development on a global scale. It discusses irresponsible practices by sectors of the pharmaceutical and agricultural industries which led to the emergence and spread of these diseases; and points to some crucial failures of approach and time management in global health policies on HIV/AIDS, with disastrous consequences for sub-Saharan Africa.

Las "enfermedades infecciosas emergentes y reemergentes" constituyen una creciente amenaza para la hegemonía de la biomedicina, al suscitar no pocos interrogantes sobre la idoneidad de su discurso y prácticas para afrontar el desafío global que representan. Se analiza el proceso de construcción de esta nueva categoría nosológica, y se examinan ejemplos destacados del impacto de las enfermedades (re)emergentes en la salud pública, la seguridad alimentaria y el desarrollo humano a escala global. Se refiere a prácticas irresponsables de sectores de la industria farmacéutica y agropecuaria, determinantes en su desencadenamiento y diseminación; y a algunos fallos cruciales de enfoque y manejo de los tiempos en las políticas de salud global en relación al VIH/sida con desastrosas consecuencias para el África subsahariana.

El desafío de las enfermedades (re)emergentes, los límites de la respuesta biomédica y el nuevo paradigma de salud global / The challenge of (re)emerging diseases, the limits of the biomedical response and the new paradigm of global health

Resumen Las "enfermedades infecciosas emergentes y reemergentes" constituyen una creciente amenaza para la hegemonía de la biomedicina, al suscitar no pocos interrogantes sobre la idoneidad de su discurso y prácticas para afrontar el desafío global que representan. Se analiza el proceso de construcción de esta nueva categoría nosológica, y se examinan ejemplos destacados del impacto de las enfermedades (re)emergentes en la salud pública, la seguridad alimentaria y el desarrollo humano a escala global. Se refiere a prácticas irresponsables de sectores de la industria farmacéutica y agropecuaria, determinantes en su desencadenamiento y diseminación; y a algunos fallos cruciales de enfoque y manejo de los tiempos en las políticas de salud global en relación al VIH/sida con desastrosas consecuencias para el África subsahariana.

Abstract "Emerging and reemerging infectious diseases" pose a growing threat to the hegemony of biomedicine, raising questions about whether its discourse and practices can handle the global challenge they represent. The construction of this new nosological category is analyzed in this article, which examines some notable examples of the impact of (re)emerging diseases on public health, food security and human development on a global scale. It discusses irresponsible practices by sectors of the pharmaceutical and agricultural industries which led to the emergence and spread of these diseases; and points to some crucial failures of approach and time management in global health policies on HIV/AIDS, with disastrous consequences for sub-Saharan Africa.

Presence of Antibodies Against Haemophilus influenzae Serotype a in Alaska Before and After the Emergence of Invasive Infections.

BACKGROUND: Haemophilus influenzae bacteria can cause asymptomatic carriage and invasive disease. Haemophilus influenzae serotype a (Hia) is an emerging cause of invasive disease in Alaska, with greatest burden occurring among rural Alaska Native (AN) children. The first case of invasive Hia (iHia) in Alaska was reported in 2002; however, it is unclear how long the pathogen has been in Alaska. METHODS: We quantified immunoglobulin G antibodies against Hia (anti-Hia) in 839 banked serum samples from Alaska residents, comparing antibody concentrations in samples drawn in the decades before (1980s and 1990s) and after (2000s) the emergence of iHia. We also assessed serum antibody concentration by age group, region of residence, and race. RESULTS: The anti-Hia was >0.1 µg/mL in 88.1% (348 of 395) and 91.0% (404 of 444) of samples from the decades prior and after the emergence of Hia, respectively (P = .17). No significant differences in antibody levels were detected between people from rural and urban regions (1.55 vs 2.08 µg/mL, P = .91 for age ≥5) or between AN and non-AN people (2.50 vs 2.60 µg/mL, P = .26). CONCLUSIONS: Our results are consistent with widespread Hia exposure in Alaska predating the first iHia case. No difference in Hia antibody prevalence was detected between populations with differing levels of invasive disease.

Measles virus and rinderpest virus divergence dated to the sixth century BCE.

Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. Although it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. We sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the divergence date of measles virus and rinderpest virus. This divergence date represents the earliest possible date for the establishment of measles in human populations. Our analyses show that the measles virus potentially arose as early as the sixth century BCE, possibly coinciding with the rise of large cities.

[Epidemics: lessons from History]. / Épidémies: Leçons d'Histoire.

TITLE: Épidémies: Leçons d'Histoire. ABSTRACT: Jusqu'au milieu du XVIIIe siècle, l'espérance de vie était de 25 ans dans les pays d'Europe, proche alors de celle de la préhistoire. À cette époque, nos ancêtres succombaient, pour la plupart, à une infection bactérienne ou virale, quand la mort n'était pas le résultat d'un épisode critique, comme la guerre ou la famine. Un seul microbe suffisait à terrasser de nombreuses victimes. L'épidémie de SARS-CoV-2 est là pour nous rappeler que ce risque est désormais à nouveau d'actualité. Si son origine zoonotique par la chauve-souris est probable, la contamination interhumaine montre son adaptation rapide à l'homme et permet d'évoquer ainsi la transmission des épidémies, qu'elle soit ou non liée à des vecteurs, ces derniers pouvant représenter dans d'autres occasions un des maillons de la chaîne.

Emerging and reemerging respiratory viral infections up to Covid-19

Infectious diseases remain as the significant causes of human and animal morbidity and mortality, leading to extensive outbreaks and epidemics. Acute respiratory viral diseases claim over 4 million deaths and cause millions of hospitalizations in developing countries every year. Emerging viruses, especially the RNA viruses, are more pathogenic since most people have no herd immunity. The RNA viruses can adapt to the rapidly changing global and local environment due to the high error rate of their polymerases that replicate their genomes. Currently, coronavirus disease 2019 (COVID-19) is determined as an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was first identified in 2019 in Wuhan. Herein we discuss emerging and reemerging respiratory viral infections till to SARS-CoV-2.

Pre-vaccine rotavirus surveillance in Buenos Aires, Argentina. Characterization of an emergent G1P[8] strain associated to fatal cases in 2014.

Group A rotaviruses (RVA) are the most frequent etiological agents causing severe diarrhea in infants and surveillance of genotype, and genetic characteristics of circulating strains are necessary in order to evaluate vaccine programs. The objectives of this work were to describe G and P genotype from 2012 through 2014 in Buenos Aires, Argentina completing an overview of 19 years of genotype surveillance in our region and to characterize an emerging G1P[8] strain associated with severe cases and five fatalities in 2014. We performed genotyping by RT-PCR. The sequencing of several genes, phylogenetic analyses, and comparative epidemiological data were used to know the origin and phylogenetic relationships of the emerging G1P[8] strain. Along with this report, 19 years of continuous RVA genotype surveillance in Argentina in the pre-vaccine era was covered. During the last year of this surveillance, 2014, a significantly increased incidence of RVA associated gastroenteritis was related to the reemergence of G1P[8] strains, being these ones detected in low frequency in the last nine years. Interestingly, the patients affected were significantly older when compared with those from the last six seasons. Additionally, phylogenetic analysis of several genes infer that these G1P[8] strains were closely related to Asian strains circulating during 2012 and 2013. In addition to this, the suggested extra continental origin for the 2014 G1P[8] strains and the very low circulation of G1 type during nine years probably explain the increased incidence and severity in the gastroenteritis cases and the particular epidemiologic characteristics. In conclusion, this work gives us a whole panorama of the pre-vaccine era of the RVA molecular epidemiology in the most populated region of Argentina. In this way, this work inspires us to continue with this type of studies in the post-vaccination era.

[A Mythological Anamnesis: from AIDS Spiders to the Bats of Ebola or Covid-19 - Revised Version of the Paper Presented at the Colloquium "Cultural and Social Perspectives on Epidemics", musée du quai Branly-Jacques-Chirac, June 27, 2019]. / Une anamnèse mythologique : des araignées du sida aux chauves-souris d'Ebola ou de la Covid-19 ­ Version remaniée de la communication présentée au colloque Regards culturels et sociaux autour des épidémies, musée du quai Branly-Jacques-Chirac le 27 juin 2019.

This article focuses on some representations of the origin of AIDS and Ebola in Burkina Faso, against a new background of Covid-19 which began in early 2020 in connection with two animals: the spider and the bat. These are also, if not first and foremost, heroes of oral literature (from tales to myths) from this region of West Africa. It is up to anthropologists to explore the meandering symbolism and imagination of these liminal animals that move back and forth between the worlds inhabited by humans and the "bush" worlds of non-humans. Here arises a mythological anamnesis. These "trickster" animals challenge categories and understanding of both virologists and anthropologists.

Cet article porte sur quelques représentations de l'origine du sida et d'Ebola en pays lobi burkinabè, avec la Covid-19 en nouvel arrière-plan depuis le début de l'année 2020, en lien avec deux animaux : l'araignée et la chauve-souris. Ce sont aussi, voire d'abord, des héros de la littérature orale (des contes aux mythes) de cette région d'Afrique de l'Ouest. Des anthropologues ont exploré les méandres des symboliques et des imaginaires de ces animaux liminaires qui vont et viennent entre les mondes habités par les humains et les univers de « brousse ¼ des non-humains. Une anamnèse mythologique est mise à jour. Ces animaux rusés se jouent de nos catégories et de notre entendement, virologues et anthropologues ici confondus.

Batrachochytrium dendrobatidis infection in amphibians predates first known epizootic in Costa Rica.

Emerging infectious diseases are a growing threat to biodiversity worldwide. Outbreaks of the infectious disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), are implicated in the decline and extinction of numerous amphibian species. In Costa Rica, a major decline event occurred in 1987, more than two decades before this pathogen was discovered. The loss of many species in Costa Rica is assumed to be due to Bd-epizootics, but there are few studies that provide data from amphibians in the time leading up to the proposed epizootics. In this study, we provide new data on Bd infection rates of amphibians collected throughout Costa Rica, in the decades prior to the epizootics. We used a quantitative PCR assay to test for Bd presence in 1016 anuran museum specimens collected throughout Costa Rica. The earliest specimen that tested positive for Bd was collected in 1964. Across all time periods, we found an overall infection rate (defined as the proportion of Bd-positive individuals) of 4%. The number of infected individuals remained relatively low across all species tested and the range of Bd-positive specimens was shown to be geographically constrained up until the 1980s; when epizootics are hypothesized to have occurred. After that time, infection rate increased three-fold, and the range of specimens tested positive for Bd increased, with Bd-positive specimens collected across the entire country. Our results suggest that Bd dynamics in Costa Rica are more complicated than previously thought. The discovery of Bd's presence in the country preceding massive declines leads to a number of different hypotheses: 1) Bd invaded Costa Rica earlier than previously known, and spread more slowly than previously reported; 2) Bd invaded multiple times and faded out; 3) an endemic Bd lineage existed; 4) an earlier Bd lineage evolved into the current Bd lineage or hybridized with an invasive lineage; or 5) an earlier Bd lineage went extinct and a new invasion event occurred causing epizootics. To help visualize areas where future studies should take place, we provide a Bd habitat suitability model trained with local data. Studies that provide information on genetic lineages of Bd are needed to determine the most plausible spatial-temporal, host-pathogen dynamics that could best explain the epizootics resulting in amphibian declines in Costa Rica and throughout Central America.

Hospital-Associated Multicenter Outbreak of Emerging Fungus Candida auris, Colombia, 2016.

Candida auris is an emerging multidrug-resistant fungus that causes hospital-associated outbreaks of invasive infections with high death rates. During 2015-2016, health authorities in Colombia detected an outbreak of C. auris. We conducted an investigation to characterize the epidemiology, transmission mechanisms, and reservoirs of this organism. We investigated 4 hospitals with confirmed cases of C. auris candidemia in 3 cities in Colombia. We abstracted medical records and collected swabs from contemporaneously hospitalized patients to assess for skin colonization. We identified 40 cases; median patient age was 23 years (IQR 4 months-56 years). Twelve (30%) patients were <1 year of age, and 24 (60%) were male. The 30-day mortality was 43%. Cases clustered in time and location; axilla and groin were the most commonly colonized sites. Temporal and spatial clustering of cases and skin colonization suggest person-to-person transmission of C. auris. These cases highlight the importance of adherence to infection control recommendations.

Carbapenem-Resistant Pseudomonas aeruginosa at US Emerging Infections Program Sites, 2015.

Pseudomonas aeruginosa is intrinsically resistant to many antimicrobial drugs, making carbapenems crucial in clinical management. During July-October 2015 in the United States, we piloted laboratory-based surveillance for carbapenem-resistant P. aeruginosa (CRPA) at sentinel facilities in Georgia, New Mexico, Oregon, and Tennessee, and population-based surveillance in Monroe County, NY. An incident case was the first P. aeruginosa isolate resistant to antipseudomonal carbapenems from a patient in a 30-day period from any source except the nares, rectum or perirectal area, or feces. We found 294 incident cases among 274 patients. Cases were most commonly identified from respiratory sites (120/294; 40.8%) and urine (111/294; 37.8%); most (223/280; 79.6%) occurred in patients with healthcare facility inpatient stays in the prior year. Genes encoding carbapenemases were identified in 3 (2.3%) of 129 isolates tested. The burden of CRPA was high at facilities under surveillance, but carbapenemase-producing CRPA were rare.

Emergent Invasive Group A Streptococcus dysgalactiae subsp. equisimilis, United States, 2015-2018.

The term group A Streptococcus is considered synonymous for the species Streptococcus pyogenes. We describe an emergent invasive S. dysgalactiae subspecies equisimilis lineage that obtained the group A antigen through a single ancestral recombination event between a group C S. dysgalactiae subsp. equisimilis strain and a group A S. pyogenes strain.

Using Big Data to Monitor the Introduction and Spread of Chikungunya, Europe, 2017.

With regard to fully harvesting the potential of big data, public health lags behind other fields. To determine this potential, we applied big data (air passenger volume from international areas with active chikungunya transmission, Twitter data, and vectorial capacity estimates of Aedes albopictus mosquitoes) to the 2017 chikungunya outbreaks in Europe to assess the risks for virus transmission, virus importation, and short-range dispersion from the outbreak foci. We found that indicators based on voluminous and velocious data can help identify virus dispersion from outbreak foci and that vector abundance and vectorial capacity estimates can provide information on local climate suitability for mosquitoborne outbreaks. In contrast, more established indicators based on Wikipedia and Google Trends search strings were less timely. We found that a combination of novel and disparate datasets can be used in real time to prevent and control emerging and reemerging infectious diseases.