4.8 Article

Bayesian Phylogeography and Pathogenic Characterization of Smallpox Based on HA, ATI, and CrmB Genes

期刊

MOLECULAR BIOLOGY AND EVOLUTION
卷 35, 期 11, 页码 2607-2617

出版社

OXFORD UNIV PRESS
DOI: 10.1093/molbev/msy153

关键词

Variola virus; smallpox; phylogeography; epidemics; public health; biosecurity

资金

  1. NHRMC Centre for Research Excellence in Integrated Systems for Epidemic Response (ISER) [1107393]
  2. Australian Government Research Training Program Scholarship
  3. tri-university (Arizona State University, King's College London) PLuS Alliance
  4. tri-university (University of New South Wales) PLuS Alliance

向作者/读者索取更多资源

Variola virus is at risk of re-emergence either through accidental release, bioterrorism, or synthetic biology. The use of phylogenetics and phylogeography to support epidemic field response is expected to grow as sequencing technology becomes miniaturized, cheap, and ubiquitous. In this study, we aimed to explore the use of common VARV diagnostic targets hemagglutinin (HA), cytokine response modifier B (CrmB), and A-type inclusion protein (ATI) for phylogenetic characterization as well as the representativeness of modelling strategies in phylogeography to support epidemic response should smallpox re-emerge. We used Bayesian discrete-trait phylogeography using the most complete data set currently available of whole genome (n = 51) and partially sequenced (n = 20) VARV isolates. We show that multilocus models combining HA, ATI, and CrmB genes may represent a useful heuristic to differentiate between VARV Major and subclades of VARV Minor which have been associated with variable case-fatality rates. Where whole genome sequencing is unavailable, phylogeography models of HA, ATI, and CrmB may provide preliminary but uncertain estimates of transmission, while supplementing whole genome models with additional isolates sequenced only for HA can improve sample representativeness, maintaining similar support for transmission relative to whole genome models. We have also provided empirical evidence delineating historic international VARV transmission using phylogeography. Due to the persistent threat of re-emergence, our results provide important research for smallpox epidemic preparedness in the posteradication era as recommended by the World Health Organisation.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.8
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Infectious Diseases

COVID-19 outbreaks in aged-care facilities in Australia

Ashley Quigley, Haley Stone, Phi Yen Nguyen, Abrar Ahmad Chughtai, C. Raina MacIntyre

Summary: Aged-care facilities in Australia faced challenges in implementing infection control methods for respiratory outbreaks like COVID-19. Lack of research in this vulnerable setting led to a study estimating the burden of aged-care worker infections and outbreaks of COVID-19. The study revealed a higher risk of COVID-19 in aged-care facilities compared to the general population, emphasizing the need for additional prevention and control measures.

INFLUENZA AND OTHER RESPIRATORY VIRUSES (2022)

Article Public, Environmental & Occupational Health

Estimated Mask Use and Temporal Relationship to COVID-19 Epidemiology of Black Lives Matter Protests in 12 Cities

Ashley Quigley, Phi Yen Nguyen, Haley Stone, David J. Heslop, Abrar Ahmad Chughtai, C. Raina MacIntyre

Summary: Most cities' Black Lives Matter protests did not increase the incidence of COVID-19 in 2020, with high levels of mask use observed among protesters. Only Miami, which had high protest intensity and the use of tear gas, showed an increase in COVID-19 cases after one incubation period post-protest. The absence of a major epidemic surge within two incubation periods of a protest indicates that the protests did not have a significant influence on epidemic activity, except in Miami.

JOURNAL OF RACIAL AND ETHNIC HEALTH DISPARITIES (2023)

Article Public, Environmental & Occupational Health

Modeling on the Effects of Deliberate Release of Aerosolized Inhalational Bacillus anthracis (Anthrax) on an Australian Population

Valentina Costantino, Prateek Bahl, Con Doolan, Charitha de Silva, David Heslop, Xin Chen, Samsung Lim, Chandini Raina MacIntyre

Summary: This study aimed to determine the optimal mitigation strategies for an aerosolized attack with Bacillus anthracis. A plume dispersion model was used to simulate the effects of an anthrax attack in Sydney, Australia, considering weather conditions. The study found that vaccination as postexposure prophylaxis in conjunction with antibiotics is the most effective strategy to reduce deaths, especially when started early and with high adherence.

HEALTH SECURITY (2023)

Article Cardiac & Cardiovascular Systems

The impact of COVID-19 and COVID vaccination on cardiovascular outcomes

Zubair Akhtar, Mallory Trent, Aye Moa, Timothy C. Tan, Ole Froebert, C. Raina MacIntyre

Summary: COVID-19 is a risk factor for cardiovascular disease, but its vaccination can prevent it. However, COVID-19 vaccination may also cause myocarditis or pericarditis. Non-specific symptoms of COVID-19 infection may originate from the heart. This review focuses on the cardiovascular complications of COVID-19 and the impact of COVID-19 vaccination.

EUROPEAN HEART JOURNAL SUPPLEMENTS (2023)

Review Medicine, Research & Experimental

Artificial intelligence in public health: the potential of epidemic early warning systems

Chandini Raina MacIntyre, Xin Chen, Mohana Kunasekaran, Ashley Quigley, Samsung Lim, Haley Stone, Hye-young Paik, Lina Yao, David Heslop, Wenzhao Wei, Ines Sarmiento, Deepti Gurdasani

Summary: The use of AI in epidemic surveillance through automated early warnings generated from vast open-source data with minimal human intervention has the potential to bring about revolutionary and sustainable changes. AI can overcome challenges faced by weak health systems by detecting epidemic signals earlier than traditional surveillance methods, triggering early investigation and response at the regional level. However, the uptake of AI-based epidemic intelligence systems by public health authorities is low compared to clinical counterparts, highlighting the need for widespread adoption of digital open-source surveillance and AI technology for effective prevention of serious epidemics.

JOURNAL OF INTERNATIONAL MEDICAL RESEARCH (2023)

Editorial Material Biochemistry & Molecular Biology

When to update COVID-19 vaccine composition

Rebecca Grant, Jilian A. Sacks, Priya Abraham, Supamit Chunsuttiwat, Cheryl Cohen, J. Peter Figueroa, Thomas Fleming, Paul Fine, David Goldblatt, Hideki Hasegawa, C. Raina MacIntrye, Ziad A. Memish, Elizabeth Miller, Sergio Nishioka, Amadou A. Sall, Samba Sow, Oyewale Tomori, Youchun Wang, Maria D. Van Kerkhove, Marie-Ange Wambo, Homa Attar Cohen, Samuel Mesfin, James R. Otieno, Lorenzo Subissi, Sylvie Briand, David E. Wentworth, Kanta Subbarao

Summary: Vaccines for different SARS-CoV-2 variants have been authorized, but continuous monitoring is necessary to decide when vaccine antigen composition should be revised, along with clinical studies to assess vaccine effectiveness.

NATURE MEDICINE (2023)

Article Immunology

Knowledge, attitudes and practices of health care workers in a cardiology department on influenza vaccination

Elizabeth Benedict Kpozehouen, Bravien Arrudsivah, Timothy C. Tan, C. Raina Macintyre

Summary: Background: Influenza vaccination has been shown to be effective in preventing myocardial infarction, but vaccination rates are low in both adults and healthcare workers. This study aimed to understand the knowledge, attitudes, and practices of healthcare workers in a cardiology ward regarding influenza vaccination. Results revealed a lack of awareness among healthcare workers regarding the associations between influenza, vaccination, and cardiovascular health. They did not routinely discuss the benefits of influenza vaccination or recommend it to patients, possibly due to a lack of awareness, not considering it part of their job, and workload issues. Improving healthcare workers' health literacy and awareness of the benefits of vaccination may lead to better healthcare outcomes for cardiac patients.

VACCINE (2023)

Article Immunology

Informing the design of a whole of life immunisation register for Australia

Elizabeth B. Kpozehouen, Robert Menzies, Holly Seale, Julia Brotherton, C. Raina Macintyre

Summary: In 2016, Australia launched the Australian Immunisation Register (AIR), a national immunisation system covering all age groups. Recommendations from a national workshop have been integrated into the current version of AIR, improving the accuracy and validity of data. However, access to AIR data for research purposes remains limited.

VACCINE (2023)

Article Microbiology

Rhizobium Phage-Like Microvirus Genome Sequence Identified in Wastewater in Arizona, USA, in November 2020 Encodes an Endolysin and a Putative Multiheme Cytochrome c-like Protein

Ainsley R. Chapman, Jillian M. Wright, Nicole A. Kaiser, Peter M. Jones, Erin M. Driver, Rolf U. Halden, Arvind Varsani, Matthew Scotch, Temitope O. C. Faleye

Summary: This paper describes the genome of MAZ-Nov-2020, a microvirus identified from municipal wastewater in Maricopa County, Arizona, USA, in November 2020. The genome is 4,696 nucleotides long, with a GC content of 56% and a coverage of 3,641x. It encodes major capsid protein, endolysin, replication initiator protein, and two hypothetical proteins, one of which is predicted to be a membrane-associated multiheme cytochrome c.

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2023)

Article Computer Science, Information Systems

Foundational domains and competencies for baccalaureate health informatics education

Saif Khairat, Sue S. Feldman, Arif Rana, Mohammad Faysel, Saptarshi Purkayastha, Matthew Scotch, Christina Eldredge

Summary: This article presents the foundational domains and corresponding competencies developed by AMIA's Academic Forum Baccalaureate Education Committee (BEC) for undergraduate health informatics education.

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION (2023)

Article Public, Environmental & Occupational Health

Could it be monkeypox? Use of an AI-based epidemic early warning system to monitor rash and fever illness

D. Hutchinson, M. Kunasekaran, A. Quigley, A. Moa, C. R. MacIntyre

Summary: The objective of this study was to use the EPIWATCH AI system to scan open-source data and detect early warnings of infectious disease outbreaks. By analyzing a multicountry outbreak of Mpox in non-endemic countries confirmed by the World Health Organization in May 2022, the study aimed to identify signals of fever and rash-like illness and determine if they represented potential Mpox outbreaks. The EPIWATCH AI system was used to detect global signals for syndromes of rash and fever from 1 month prior to the initial case confirmation in the United Kingdom to 2 months following.

PUBLIC HEALTH (2023)

Article Infectious Diseases

Canine Parvovirus 2C Identified in Dog Feces from Poop Bags Collected from Outdoor Waste Bins in Arizona USA, June 2022

Temitope O. C. Faleye, Erin M. Driver, Devin A. Bowes, Abriana Smith, Nicole A. Kaiser, Jillian M. Wright, Ainsley R. Chapman, Rolf U. Halden, Arvind Varsani, Matthew Scotch

Summary: In this study, CPV genomes were sequenced from dog feces collected in poop bags, and a variant of CPV-2c with amino acid substitutions in NS1 and NS2 was identified in Arizona, USA in June 2022. This genome is the only CPV genome described in the USA from the 2022 season, despite reports of CPV outbreaks and fatalities in dogs. Further studies and experimental research are needed to enhance our understanding of the evolutionary process of CPV.

TRANSBOUNDARY AND EMERGING DISEASES (2023)

Review Biotechnology & Applied Microbiology

Systematic review of influenza vaccine effectiveness against laboratory-confirmed influenza among older adults living in aged care facilities

Aye Moa, Mohana Kunasekaran, Zubair Akhtar, Valentina Costantino, C. Raina Macintyre

Summary: We estimated the effectiveness of influenza vaccines in preventing laboratory-confirmed influenza among older adults in aged care. Fourteen studies were included for final review and showed considerable variation in reported vaccine effectiveness. Observational studies demonstrated VE ranging from 7.2% to 89.8%, while randomized clinical trials showed a 17% reduction in infection rates with the adjuvanted trivalent vaccine. Limitations included the small number of included studies, variations in seasons and diagnostic testing methods, and limited research on enhanced influenza vaccines in aged care settings.

HUMAN VACCINES & IMMUNOTHERAPEUTICS (2023)

Article Nursing

Healthcare Workers' SARS-CoV-2 Infections in Four Hospital Outbreaks during Delta Variant Prevalence in Sydney, Australia

Danielle Hutchinson, Mohana Kunasekaran, Haley Stone, Xin Chen, Ashley Quigley, Aye Moa, C. Raina Macintyre

Summary: The use of personal protective equipment (PPE), such as respirators, plays a significant role in reducing the risk of healthcare workers (HCWs) acquiring SARS-CoV-2 infections. However, differences in PPE guidelines across different clinical settings may leave HCWs vulnerable to infection. During periods of high community transmission, it is crucial to provide respirators to protect hospital staff.

NURSING RESEARCH AND PRACTICE (2023)

Article Public, Environmental & Occupational Health

Early pandemic use of face masks in Papua New Guinea under a mask mandate

Mark Raphael, Angela Kelly-Hanku, David Heslop, Danielle Hutchinson, Mohana Kunasekaran, Ashley Quigley, Raina Macintyred

Summary: Compliance with face mask mandates in Papua New Guinea was found to be very low, especially in outdoor settings. Individuals without face coverings and not following physical distancing guidelines are at a higher risk for COVID-19 transmission, particularly in medium- and large-sized gatherings. A new strategy is needed to enforce public health mandates and should be clearly promoted to the public.

WESTERN PACIFIC SURVEILLANCE AND RESPONSE (2023)

暂无数据