Isolation of Angola-like Marburg virus from Egyptian rousette bats from West Africa.

Marburg virus (MARV) causes sporadic outbreaks of severe Marburg virus disease (MVD). Most MVD outbreaks originated in East Africa and field studies in East Africa, South Africa, Zambia, and Gabon identified the Egyptian rousette bat (ERB; Rousettus aegyptiacus) as a natural reservoir. However, the largest recorded MVD outbreak with the highest case-fatality ratio happened in 2005 in Angola, where direct spillover from bats was not  shown. Here, collaborative studies by the Centers for Disease Control and Prevention, Njala University, University of California, Davis USAID-PREDICT, and the University of Makeni identify MARV circulating in ERBs in Sierra Leone. PCR, antibody and virus isolation data from 1755 bats of 42 species shows active MARV infection in approximately 2.5% of ERBs. Phylogenetic analysis identifies MARVs that are similar to the Angola strain. These results provide evidence of MARV circulation in West Africa and demonstrate the value of pathogen surveillance to identify previously undetected threats

Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security

Functional study of TFIIH and the mechanisms of transcription and DNA repair

La régulation de l'expression des gènes et la réparation de l'ADN sont deux mécanismes essentiels à la survie de la cellule. La transcription des gènes de classe II codant pour les protéines est un mécanisme complexe faisant intervenir une myriade de protéines dont l'ARN polymérase II (ARNP II) et six facteurs généraux de la transcription (TFIIA, B, D, E, F et H). La réparation par excision de nucléotides (NER) permet l'élimination des lésions distordant l'ADN, c'est un mécanisme crucial pour le maintien de l'information génétique. Il fait également intervenir plus d'une vingtaine de protéines qui, pour certaines, se retrouvent mutées chez les patients atteints de maladies génétiques rares. Le facteur général de transcription TFIIH joue aussi un rôle dans l'étape d'ouverture de l'ADN autour de la lésion lors de la NER.Au cours de mon travail doctoral, j'ai entrepris dans un premier temps de détailler le rôle intrinsèque des différentes sous-unités du facteur TFIIH, et plus particulièrement de la sous-unité p44. J'ai ainsi pu montrer que la partie carboxy-terminale de cette protéine jouait un rôle dans la cohésion du complexe TFIIH mais aussi dans son activité d'échappée du promoteur lors de l'initiation de la transcription. Puis, dans un second temps, je me suis intéressé au mécanisme reliant la transcription à la réparation, nommé transcription couplée à la réparation. J'ai ainsi pu montrer qu'une ARNP II bloquée par une lésion cisplatine sur le brin transcrit de l'ADN se retrouve éjectée de l'ADN de façon ATP mais non réparation dépendante.Genes regulation and DNA repair are two processes vital to cell survival. Transcription of class II genes (mostly protein coding genes) is a complex process involving the functions of many proteins, among them the RNA polymerase II (RNAP II) and six general transcription factors (TFIIA, B, D, E, F and H). Nucleotide excision repair (NER) is a mechanism whereby DNA lesions are eliminated. It's a key mechanism for the maintenance of genetic information. More than twenty proteins participate in this reaction. Mutation in some of them give rise to DNA repair genetic disorders. The general transcription factor TFIIH plays also a role in DNA melting around the lesion during the NER reaction.During my PhD study, I first study the role of different TFIIH subunits, especially the p44 subunit. I was able to show that the carboxy-terminal domain of this protein is important for TFIIH cohesion but also promoter escape activity of TFIIH. Then I focused my attention on the mechanism that link transcription and DNA repair: transcription coupled repair. I was able to show that an RNAP II blocked by a cisplatin lesion on the transcribed DNA strand is ejected from the template in an ATP but not a repair dependent manner

Etude fonctionnelle de TFIIH et des mécanismes de transcription et de réparation de l’ADN

La régulation de l’expression des gènes et la réparation de l’ADN sont deux mécanismes essentiels à la survie de la cellule. La transcription des gènes de classe II codant pour les protéines est un mécanisme complexe faisant intervenir une myriade de protéines dont l’ARN polymérase II (ARNP II) et six facteurs généraux de la transcription (TFIIA, B, D, E, F et H). La réparation par excision de nucléotides (NER) permet l’élimination des lésions distordant l’ADN, c’est un mécanisme crucial pour le maintien de l’information génétique. Il fait également intervenir plus d’une vingtaine de protéines qui, pour certaines, se retrouvent mutées chez les patients atteints de maladies génétiques rares. Le facteur général de transcription TFIIH joue aussi un rôle dans l’étape d’ouverture de l’ADN autour de la lésion lors de la NER. Au cours de mon travail doctoral, j’ai entrepris dans un premier temps de détailler le rôle intrinsèque des différentes sous-unités du facteur TFIIH, et plus particulièrement de la sous-unité p.44. J’ai ainsi pu montrer que la partie carboxy-terminale de cette protéine jouait un rôle dans la cohésion du complexe TFIIH mais aussi dans son activité d’échappée du promoteur lors de l’initiation de la transcription. Puis, dans un second temps, je me suis intéressé au mécanisme reliant la transcription à la réparation, nommé transcription couplée à la réparation. J’ai ainsi pu montrer qu’une ARNP II bloquée par une lésion cisplatine sur le brin transcrit de l’ADN se retrouve éjectée de l’ADN de façon ATP mais non réparation dépendante

Functional study of TFIIH and the mechanisms of transcription and DNA repair

La régulation de l'expression des gènes et la réparation de l'ADN sont deux mécanismes essentiels à la survie de la cellule. La transcription des gènes de classe II codant pour les protéines est un mécanisme complexe faisant intervenir une myriade de protGenes regulation and DNA repair are two processes vital to cell survival. Transcription of class II genes (mostly protein coding genes) is a complex process involving the functions of many proteins, among them the RNA polymerase II (RNAP II) and six gene

Fate of RNA polymerase II stalled at a cisplatin lesion

Elongating RNA polymerase II blocked by DNA damage in the transcribed DNA strand is thought to initiate the transcription-coupled repair process. The objective of this study is to better understand the sequence of events that occurs during repair from the time RNA polymerase II first encounters the lesion. This study establishes that an immobilized DNA template containing a unique cisplatin lesion can serve as an in vitro substrate for both transcription and DNA repair. RNA polymerase II is quantitatively stalled at the cisplatin lesion during transcription and can be released from the template, along with the nascent transcript, in an ATP-dependent manner. RNA polymerase II stalled at a lesion and containing a dephosphorylated repetitive carboxyl-terminal domain (CTD) appears to be more sensitive toward release. However, a dephosphorylated CTD can become readily phosphorylated in front of the lesion by CTD kinases in the presence of ATP. The observation that RNA polymerase II and transcript release occurs in a TFIIH-deficient repair extract but not in a reconstituted repair system demonstrates that disassembly of the elongation complex can occur independently of the repair process and vice versa. Indeed, the presence of RNA polymerase II at the lesion does not prevent dual incision from occurring. Finally, we also propose that the Cockayne's syndrome B protein factor, believed to be the mammalian transcription repair coupling factor, is neither involved in transcript release nor required for dual incision in the presence of lesionstalled RNA polymerase II in vitro. More likely, it prevents RNA polymerase from backing up when it encounters the lesion. The ability to transcribe and repair the same damaged DNA molecule fixed on beads, along with the fact that the reaction conditions can be freely altered, provides a powerful tool to study the fate of RNA polymerase II blocked on the cisplatin lesion

Coronaviruses Detected in Bats in Close Contact with Humans in Rwanda.

Bats living in close contact with people in Rwanda were tested for evidence of infection with viruses of zoonotic potential. Mucosal swabs from 503 bats representing 17 species were sampled from 2010 to 2014 and screened by consensus PCR for 11 viral families. Samples were negative for all viral families except coronaviruses, which were detected in 27 bats belonging to eight species. Known coronaviruses detected included the betacorona viruses: Kenya bat coronaviruses, Eidolon bat coronavirus, and Bat coronavirus HKU9, as well as an alphacoronavirus, Chaerephon Bat coronavirus. Novel coronaviruses included two betacorona viruses clustering with SARS-CoV, a 2d coronavirus, and an alphacoronavirus

Correction: Detection of novel coronaviruses in bats in Myanmar.

[This corrects the article DOI: 10.1371/journal.pone.0230802.]

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

Rationale There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear. Objectives We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis. Methods Samples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing. Measurements and Main Results Improved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing. Conclusions This study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

Rationale There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear. Objectives We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis. Methods Samples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing. Measurements and Main Results Improved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing. Conclusions This study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs