Last data update: May 20, 2024. (Total: 46824 publications since 2009)
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Estimating causes of death where there is no medical certification: evolution and state of the art of verbal autopsy
Chandramohan D , Fottrell E , Leitao J , Nichols E , Clark SJ , Alsokhn C , Cobos Munoz D , AbouZahr C , Di Pasquale A , Mswia R , Choi E , Baiden F , Thomas J , Lyatuu I , Li Z , Larbi-Debrah P , Chu Y , Cheburet S , Sankoh O , Mohamed Badr A , Fat DM , Setel P , Jakob R , de Savigny D . Glob Health Action 12/28/2021 14 1982486 Over the past 70 years, significant advances have been made in determining the causes of death in populations not served by official medical certification of cause at the time of death using a technique known as Verbal Autopsy (VA). VA involves an interview of the family or caregivers of the deceased after a suitable bereavement interval about the circumstances, signs and symptoms of the deceased in the period leading to death. The VA interview data are then interpreted by physicians or, more recently, computer algorithms, to assign a probable cause of death. VA was originally developed and applied in field research settings. This paper traces the evolution of VA methods with special emphasis on the World Health Organization's (WHO)'s efforts to standardize VA instruments and methods for expanded use in routine health information and vital statistics systems in low- and middle-income countries (LMICs). These advances in VA methods are culminating this year with the release of the 2022 WHO Standard Verbal Autopsy (VA) Toolkit. This paper highlights the many contributions the late Professor Peter Byass made to the current VA standards and methods, most notably, the development of InterVA, the most commonly used automated computer algorithm for interpreting data collected in the WHO standard instruments, and the capacity building in low- and middle-income countries (LMICs) that he promoted. This paper also provides an overview of the methods used to improve the current WHO VA standards, a catalogue of the changes and improvements in the instruments, and a mapping of current applications of the WHO VA standard approach in LMICs. It also provides access to tools and guidance needed for VA implementation in Civil Registration and Vital Statistics Systems at scale. |
Global phylogeography and evolutionary history of Shigella dysenteriae type 1.
Njamkepo E , Fawal N , Tran-Dien A , Hawkey J , Strockbine N , Jenkins C , Talukder KA , Bercion R , Kuleshov K , Kolínská R , Russell JE , Kaftyreva L , Accou-Demartin M , Karas A , Vandenberg O , Mather AE , Mason CJ , Page AJ , Ramamurthy T , Bizet C , Gamian A , Carle I , Sow AG , Bouchier C , Wester AL , Lejay-Collin M , Fonkoua MC , Le Hello S , Blaser MJ , Jernberg C , Ruckly C , Mérens A , Page AL , Aslett M , Roggentin P , Fruth A , Denamur E , Venkatesan M , Bercovier H , Bodhidatta L , Chiou CS , Clermont D , Colonna B , Egorova S , Pazhani GP , Ezernitchi AV , Guigon G , Harris SR , Izumiya H , Korzeniowska-Kowal A , Lutyńska A , Gouali M , Grimont F , Langendorf C , Marejková M , Peterson LA , Perez-Perez G , Ngandjio A , Podkolzin A , Souche E , Makarova M , Shipulin GA , Ye C , Žemličková H , Herpay M , Grimont PA , Parkhill J , Sansonetti P , Holt KE , Brisse S , Thomson NR , Weill FX . Nat Microbiol 2016 1 16027 Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease. |
A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis.
Miotto P , Tessema B , Tagliani E , Chindelevitch L , Starks AM , Emerson C , Hanna D , Kim PS , Liwski R , Zignol M , Gilpin C , Niemann S , Denkinger CM , Fleming J , Warren RM , Crook D , Posey J , Gagneux S , Hoffner S , Rodrigues C , Comas I , Engelthaler DM , Murray M , Alland D , Rigouts L , Lange C , Dheda K , Hasan R , Ranganathan UDK , McNerney R , Ezewudo M , Cirillo DM , Schito M , Köser CU , Rodwell TC . Eur Respir J 2017 50 (6) A clear understanding of the genetic basis of antibiotic resistance in Mycobacterium tuberculosis is required to accelerate the development of rapid drug susceptibility testing methods based on genetic sequence.Raw genotype-phenotype correlation data were extracted as part of a comprehensive systematic review to develop a standardised analytical approach for interpreting resistance associated mutations for rifampicin, isoniazid, ofloxacin/levofloxacin, moxifloxacin, amikacin, kanamycin, capreomycin, streptomycin, ethionamide/prothionamide and pyrazinamide. Mutation frequencies in resistant and susceptible isolates were calculated, together with novel statistical measures to classify mutations as high, moderate, minimal or indeterminate confidence for predicting resistance.We identified 286 confidence-graded mutations associated with resistance. Compared to phenotypic methods, sensitivity (95% CI) for rifampicin was 90.3% (89.6-90.9%), while for isoniazid it was 78.2% (77.4-79.0%) and their specificities were 96.3% (95.7-96.8%) and 94.4% (93.1-95.5%), respectively. For second-line drugs, sensitivity varied from 67.4% (64.1-70.6%) for capreomycin to 88.2% (85.1-90.9%) for moxifloxacin, with specificity ranging from 90.0% (87.1-92.5%) for moxifloxacin to 99.5% (99.0-99.8%) for amikacin.This study provides a standardised and comprehensive approach for the interpretation of mutations as predictors of M. tuberculosis drug-resistant phenotypes. These data have implications for the clinical interpretation of molecular diagnostics and next-generation sequencing as well as efficient individualised therapy for patients with drug-resistant tuberculosis. |
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.
Arias A , Watson SJ , Asogun D , Tobin EA , Lu J , Phan MVT , Jah U , Wadoum REG , Meredith L , Thorne L , Caddy S , Tarawalie A , Langat P , Dudas G , Faria NR , Dellicour S , Kamara A , Kargbo B , Kamara BO , Gevao S , Cooper D , Newport M , Horby P , Dunning J , Sahr F , Brooks T , Simpson AJH , Groppelli E , Liu G , Mulakken N , Rhodes K , Akpablie J , Yoti Z , Lamunu M , Vitto E , Otim P , Owilli C , Boateng I , Okoror L , Omomoh E , Oyakhilome J , Omiunu R , Yemisis I , Adomeh D , Ehikhiametalor S , Akhilomen P , Aire C , Kurth A , Cook N , Baumann J , Gabriel M , Wölfel R , Di Caro A , Carroll MW , Günther S , Redd J , Naidoo D , Pybus OG , Rambaut A , Kellam P , Goodfellow I , Cotten M . Virus Evol 2016 2 (1) vew016 To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts. |
The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology (preprint)
Chu HY , Boeckh M , Englund JA , Famulare M , Lutz B , Nickerson DA , Rieder M , Starita LM , Shendure J , Bedford T , Adler A , Brandstetter E , Frazer CD , Han PD , Gulati RK , Hadfield J , Jackson M , Kiavand A , Kimball LE , Lacombe K , Logue JK , Lyon VR , Newman KL , Sibley TR , Zigman Suchsland M , Wolf C . medRxiv 2020 2020.03.02.20029595 Introduction Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterize, and potentially contain new and emerging influenza strains at a population level. The objective of this study is to use data gathered simultaneously from community and hospital sites to develop a model of how influenza enters and spreads in a population.Methods and Analysis Starting in the 2018-19 season, we have been enrolling individuals with acute respiratory illness from community sites throughout the Seattle metropolitan area, including clinics, childcare facilities, Seattle-Tacoma International Airport, workplaces, college campuses, and homeless shelters. At these sites, we collect clinical data and mid-nasal swabs from individuals with at least two acute respiratory symptoms. Additionally, we collect residual nasal swabs and data from individuals who seek care for respiratory symptoms at four regional hospitals. Samples are tested using a multiplex molecular assay, and influenza whole genome sequencing is performed for samples with influenza detected. Geospatial mapping and computational modeling platforms are in development to characterize the regional spread of influenza and other respiratory pathogens.Ethics and Dissemination The study was approved by the University of Washington’s Institutional Review Board. Results will be disseminated through talks at conferences, peer-reviewed publications, and on the study website (www.seattleflu.org).Strengths and limitations of this study- Large-scale multiple-arm study of respiratory illness characterization with collection of samples from individuals in the community as well as in ambulatory care and hospital settings- Integration of sociodemographic, clinical, and geospatial data on a regional level- Multiplex molecular testing for multiple viral and bacterial pathogens and whole genome sequencing of influenza for detailed molecular epidemiologic characterization and transmission mapping- Geographically and socioeconomically diverse sampling of community-based acute respiratory illnessesCompeting Interest StatementAmanda Adler, Elisabeth Brandstetter, Michael Famulare, Chris D. Frazar, Peter D. Han, Reena K. Gulati, James Hadfield, Michael L. Jackson, Anahita Kiavand, Louise E. Kimball, Kirsten Lacombe, Jennifer Logue, Victoria Lyon, Kira L. Newman, Thomas R. Sibley, Jay Shendure, Lea Starita, Monica L. Zigman Suchsland, and Caitlin Wolf declare no competing interests. Helen Y Chu receives research support from Sanofi, Cepheid, and Genentech/Roche and is a consultant for Merck. Janet Englund receives research support to her institution from Astrazeneca, GlaxoSmithKline, Merck, and Novavax and is a consultant for Sanofi Pasteur and Meissa Vaccines.Funding StatementThe Seattle Flu Study is funded through the Brotman Baty Institute. The funder was not involved in the design of the study, does not have any ownership over the management and conduct of the study, the data, or the rights to publishAuthor DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable YesThe data will be accessed only by authorized individuals on the study team. Access to deidentified, aggregated data and analysis code will be publicly available on the study web page (www.seattleflu.org). http://www.seattleflu.org |
%svy_freqs: A generic SAS macro for cross-tabulation between a factor and a by-group variable given a third variable and creating publication-quality tables using data from complex surveys (preprint)
Muthusi Jacques , Mwalili Samuel , Young Peter . bioRxiv 2019 771303 Introduction In epidemiological studies, cross-tabulations are a simple but important tool for understanding the distribution of socio-demographic characteristics among study participants. They become more useful when comparisons are presented using a by-group variable such as key demographic characteristic or an outcome status; for instance, sex or the presence or absence of a disease status. Most available statistical analysis software can easily perform cross-tabulations, however, output from these must be processed further to make it readily available for review and use in a publication. In addition, performing three-way cross-tabulations of complex survey data such as those required to show the distribution of disease prevalence across multiple factors and a by-group variable is not easily implemented directly using available standard procedures of commonly used statistical software.Methods We developed a generic SAS macro, %svy_freqs, to create quality publication-ready tables from cross-tabulations between a factor and a by-group variable given a third variable using survey or non-survey data. The SAS macro also performs classical two-way cross-tabulations and refines output into publication-quality tables. It provides extra features not available in existing procedures such as ability to incorporate parameters for survey design and replication-based variance estimation methods, performing validation checks for input parameters, transparently formatting character variable values into numeric ones and allowing for generalizability.Results We demonstrate the application of the SAS macro in the analysis of data from the 2013-2014 National Health and Nutrition Examination Survey (NHANES), a complex survey designed to assess the health and nutritional status of adults and children in the United States (U.S.).Conclusion The SAS code use to develop the macro is simple yet comprehensive, easy to follow, straightforward for the end user and simple for a SAS programmer to extend. The SAS macro has shown to shorten turn-around time for statistical analysis, eliminate errors when preparing output, and support reproducible research. |
Comparative genomics of the major parasitic worms (preprint)
International Helminth Genomes Consortium , Coghlan Avril , Tyagi Rahul , Cotton James A , Holroyd Nancy , Rosa Bruce A , Tsai Isheng Jason , Laetsch Dominik R , Beech Robin N , Day Tim A , Hallsworth-Pepin Kymberlie , Ke Huei-Mien , Kuo Tzu-Hao , Lee Tracy J , Martin John , Maizels Rick M , Mutowo Prudence , Ozersky Philip , Parkinson John , Reid Adam J , Rawlings Neil D , Ribeiro Diogo M , Seshadri Swapna Lakshmipuram , Stanley Eleanor , Taylor David W , Wheeler Nicolas J , Zamanian Mostafa , Zhang Xu , Allan Fiona , Allen Judith E , Asano Kazuhito , Babayan Simon A , Bah Germanus , Beasley Helen , Bennett Hayley M , Bisset Stewart A , Castillo Estela , Cook Joseph , Cooper Philip J , Cruz-Bustos Teresa , Cuéllar Carmen , Devaney Eileen , Doyle Stephen R , Eberhard Mark L , Emery Aidan , Eom Keeseon S , Gilleard John S , Gordon Daria , Harcus Yvonne , Harsha Bhavana , Hawdon John M , Hill Dolores E , Hodgkinson Jane , Horák Petr , Howe Kevin L , Huckvale Thomas , Kalbe Martin , Kaur Gaganjot , Kikuchi Taisei , Koutsovoulos Georgios , Kumar Sujai , Leach Andrew R , Lomax Jane , Makepeace Benjamin , Matthews Jacqueline B , Muro Antonio , O’Boyle Noel Michael , Olson Peter D , Osuna Antonio , Partono Felix , Pfarr Kenneth , Rinaldi Gabriel , Foronda Pilar , Rollinson David , Gomez Samblas Mercedes , Sato Hiroshi , Schnyder Manuela , Scholz Tomáš , Shafie Myriam , Tanya Vincent N , Toledo Rafael , Tracey Alan , Urban Joseph F , Wang Lian-Chen , Zarlenga Dante , Blaxter Mark L , Mitreva Makedonka , Berriman Matthew . bioRxiv 2017 236539 Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we compare the genomes of 81 nematode and platyhelminth species, including those of 76 parasites. From 1.4 million genes, we identify gene family births and hundreds of large expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We use a wide-ranging in silico screen to identify and prioritise new potential drug targets and compounds for testing. We also uncover lineage-specific differences in core metabolism and in protein families historically targeted for drug development. This is the broadest comparative study to date of the genomes of parasitic and non-parasitic worms. It provides a transformative new resource for the research community to understand and combat the diseases that parasitic worms cause. |
Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study
Pneumonia Etiology Research for Child Health Study Group , O'Brien Katherine L , Levine Orin S , Knoll Maria Deloria , Feikin Daniel R , DeLuca Andrea N , Driscoll Amanda J , Fancourt Nicholas , Fu Wei , Haddix Meredith , Hammitt Laura L , Higdon Melissa M , Kagucia E Wangeci , Karron Ruth A , Li Mengying , Park Daniel E , Prosperi Christine , Shi Qiyuan , Wu Zhenke , Zeger Scott L , Watson Nora L , Crawley Jane , Murdoch David R , Brooks W Abdullah , Endtz Hubert P , Zaman Khalequ , Goswami Doli , Hossain Lokman , Jahan Yasmin , Chisti Mohammod Jobayer , Howie Stephen R C , Ebruke Bernard E , Antonio Martin , McLellan Jessica L , Machuka Eunice M , Shamsul Arifin , Zaman Syed M A , Mackenzie Grant , Scott J Anthony G , Awori Juliet O , Morpeth Susan C , Kamau Alice , Kazungu Sidi , Ominde Micah Silaba , Kotloff Karen L , Tapia Milagritos D , Sow Samba O , Sylla Mamadou , Tamboura Boubou , Onwuchekwa Uma , Kourouma Nana , Toure Aliou , Sissoko Seydou , Madhi Shabir A , Moore David P , Adrian Peter V , Baillie Vicky L , Kuwanda Locadiah , Mudau Azwifarwi , Groome Michelle J , Mahomed Nasreen , Simões Eric A F , Baggett Henry C , Thamthitiwat Somsak , Maloney Susan A , Bunthi Charatdao , Rhodes Julia , Sawatwong Pongpun , Akarasewi Pasakorn , Thea Donald M , Mwananyanda Lawrence , Chipeta James , Seidenberg Phil , Mwansa James , Somwe Somwe Wa , Kwenda Geoffrey , Anderson Trevor P , Mitchell Joanne L . Lancet 2019 394 (10200) 757-779 BACKGROUND: Pneumonia is the leading cause of death among children younger than 5 years. In this study, we estimated causes of pneumonia in young African and Asian children, using novel analytical methods applied to clinical and microbiological findings. METHODS: We did a multi-site, international case-control study in nine study sites in seven countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. All sites enrolled in the study for 24 months. Cases were children aged 1-59 months admitted to hospital with severe pneumonia. Controls were age-group-matched children randomly selected from communities surrounding study sites. Nasopharyngeal and oropharyngeal (NP-OP), urine, blood, induced sputum, lung aspirate, pleural fluid, and gastric aspirates were tested with cultures, multiplex PCR, or both. Primary analyses were restricted to cases without HIV infection and with abnormal chest x-rays and to controls without HIV infection. We applied a Bayesian, partial latent class analysis to estimate probabilities of aetiological agents at the individual and population level, incorporating case and control data. FINDINGS: Between Aug 15, 2011, and Jan 30, 2014, we enrolled 4232 cases and 5119 community controls. The primary analysis group was comprised of 1769 (41·8% of 4232) cases without HIV infection and with positive chest x-rays and 5102 (99·7% of 5119) community controls without HIV infection. Wheezing was present in 555 (31·7%) of 1752 cases (range by site 10·6-97·3%). 30-day case-fatality ratio was 6·4% (114 of 1769 cases). Blood cultures were positive in 56 (3·2%) of 1749 cases, and Streptococcus pneumoniae was the most common bacteria isolated (19 [33·9%] of 56). Almost all cases (98·9%) and controls (98·0%) had at least one pathogen detected by PCR in the NP-OP specimen. The detection of respiratory syncytial virus (RSV), parainfluenza virus, human metapneumovirus, influenza virus, S pneumoniae, Haemophilus influenzae type b (Hib), H influenzae non-type b, and Pneumocystis jirovecii in NP-OP specimens was associated with case status. The aetiology analysis estimated that viruses accounted for 61·4% (95% credible interval [CrI] 57·3-65·6) of causes, whereas bacteria accounted for 27·3% (23·3-31·6) and Mycobacterium tuberculosis for 5·9% (3·9-8·3). Viruses were less common (54·5%, 95% CrI 47·4-61·5 vs 68·0%, 62·7-72·7) and bacteria more common (33·7%, 27·2-40·8 vs 22·8%, 18·3-27·6) in very severe pneumonia cases than in severe cases. RSV had the greatest aetiological fraction (31·1%, 95% CrI 28·4-34·2) of all pathogens. Human rhinovirus, human metapneumovirus A or B, human parainfluenza virus, S pneumoniae, M tuberculosis, and H influenzae each accounted for 5% or more of the aetiological distribution. We observed differences in aetiological fraction by age for Bordetella pertussis, parainfluenza types 1 and 3, parechovirus-enterovirus, P jirovecii, RSV, rhinovirus, Staphylococcus aureus, and S pneumoniae, and differences by severity for RSV, S aureus, S pneumoniae, and parainfluenza type 3. The leading ten pathogens of each site accounted for 79% or more of the site's aetiological fraction. INTERPRETATION: In our study, a small set of pathogens accounted for most cases of pneumonia requiring hospital admission. Preventing and treating a subset of pathogens could substantially affect childhood pneumonia outcomes. FUNDING: Bill & Melinda Gates Foundation. |
Comparative genomics of the major parasitic worms
International Helminth Genomes Consortium , Coghlan Avril , Tyagi Rahul , Cotton James A , Holroyd Nancy , Rosa Bruce A , Tsai Isheng Jason , Laetsch Dominik R , Beech Robin N , Day Tim A , Hallsworth-Pepin Kymberlie , Ke Huei-Mien , Kuo Tzu-Hao , Lee Tracy J , Martin John , Maizels Rick M , Mutowo Prudence , Ozersky Philip , Parkinson John , Reid Adam J , Rawlings Neil D , Ribeiro Diogo M , Seshadri Swapna Lakshmipuram , Stanley Eleanor , Taylor David W , Wheeler Nicolas J , Zamanian Mostafa , Zhang Xu , Allan Fiona , Allen Judith E , Asano Kazuhito , Babayan Simon A , Bah Germanus , Beasley Helen , Bennett Hayley M , Bisset Stewart A , Castillo Estela , Cook Joseph , Cooper Philip J , Cruz-Bustos Teresa , Cuéllar Carmen , Devaney Eileen , Doyle Stephen R , Eberhard Mark L , Emery Aidan , Eom Keeseon S , Gilleard John S , Gordon Daria , Harcus Yvonne , Harsha Bhavana , Hawdon John M , Hill Dolores E , Hodgkinson Jane , Horák Petr , Howe Kevin L , Huckvale Thomas , Kalbe Martin , Kaur Gaganjot , Kikuchi Taisei , Koutsovoulos Georgios , Kumar Sujai , Leach Andrew R , Lomax Jane , Makepeace Benjamin , Matthews Jacqueline B , Muro Antonio , O’Boyle Noel Michael , Olson Peter D , Osuna Antonio , Partono Felix , Pfarr Kenneth , Rinaldi Gabriel , Foronda Pilar , Rollinson David , Gomez Samblas Mercedes , Sato Hiroshi , Schnyder Manuela , Scholz Tomáš , Shafie Myriam , Tanya Vincent N , Toledo Rafael , Tracey Alan , Urban Joseph F , Wang Lian-Chen , Zarlenga Dante , Blaxter Mark L , Mitreva Makedonka , Berriman Matthew . Nat Genet 2019 51 (1) 163-174 Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report a broad comparative study of 81 genomes of parasitic and non-parasitic worms. We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We reveal extensive lineage-specific differences in core metabolism and protein families historically targeted for drug development. From an in silico screen, we have identified and prioritized new potential drug targets and compounds for testing. This comparative genomics resource provides a much-needed boost for the research community to understand and combat parasitic worms. |
Surveillance Indicators for Women's Preconception Care
Surveillance and Research Workgroup and Clinical Workgroup of the National Preconception Health and Health Care Initiative , Adamski Alys , Bernstein Peter S , Boulet Sheree L , Chowdhury Farah M , D’Angelo Denise V , Coonrod Dean V , Frayne Daniel J , Kroelinger Charlan , Morgan Isabel A , Okoroh Ekwutosi M , Olson Christine K , Robbins Cheryl L , Verbiest Sarah . J Womens Health (Larchmt) 2020 29 (7) 910-918 Background: Limited surveillance of preconception care (PCC) impedes states' ability to monitor access and provision of quality PCC. In response, we describe PCC indicators and the evaluation process used to identify a set of PCC indicators for state use. Materials and Methods: The Surveillance and Research Workgroup and Clinical Workgroup of the National Preconception Health and Health Care Initiative used a systematic process to identify, evaluate, and prioritize PCC indicators from nationwide public health surveillance systems that Maternal and Child Health (MCH) programs can use for state-level surveillance using the Pregnancy Risk Assessment Monitoring System (PRAMS) and Behavioral Risk Factor Surveillance System (BRFSS). For each indicator, we assessed target population, prevalence, measurement simplicity, data availability, clinical utility, and whether it was related to the 10 prioritized preconception health indicators. We also assessed relevance to clinical recommendations, Healthy People (HP)2020 objectives, and the National Quality Forum measures. Lastly, we considered input from stakeholders and subject matter experts. Results: Eighty potential PCC indicators were initially identified. After conducting evaluations, obtaining stakeholder input, and consulting with subject matter experts, the list was narrowed to 30 PCC indicators for states to consider using in their MCH programs to inform the need for new strategies and monitor programmatic activities. PRAMS is the data source for 27 of the indicators, and BRFSS is the data source for three indicators. Conclusions: The identification and evaluation of population-based PCC indicators that are available at the state level increase opportunities for state MCH programs to document, monitor, and address PCC in their locales. |
Innovations in public health surveillance: updates from a forum convened by the WHO Hub for Pandemic and Epidemic Intelligence, 2 and 3 February 2022.
Morgan Oliver , Redies Isabel , Beatriz Leiva Rioja Zoila , Brownstein John , George Dylan , Golding Josie , Hanefeld Johanna , Horby Peter , Lee Christopher , Mikhailov Danil , Philip Wolfgang , Scarpino Samuel , Kifle Tessema Sofonias , Ihekweazu Chikwe . Euro Surveill 2022 27 (15) In the 2 years since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) there has been an unprecedented collective effort from the academic, public, and private sectors to advance surveillance for pandemic preparedness and response. The coronavirus disease (COVID-19) pandemic has created momentum that will define the future of public health intelligence. On 2 and 3 February 2022, the World Health Organization (WHO) Hub for Pandemic and Epidemic Intelligence convened a meeting of a small group of surveillance innovators to share insights and approaches about their initiatives and future directions. The meeting served as an opportunity for participants to share updates about their work, to explore potential for collaboration, exchange ideas, cross-fertilise our work and discuss challenges in the field of surveillance. Although the group of attendees was not geographically representative of the global surveillance community, the meeting was the first in a planned series of exchanges convened by the WHO Pandemic Hub that will generate dialogue among global thought leaders and new voices in the surveillance community. In this first convening we discussed several themes, including what is meaningful collaboration for success; how to bring the public back into public health; what are individual-centred approaches; how new kinds of data have new privacy concerns; how government structures affect the functioning of surveillance systems; how to inform the decisionmaking process; cross-scaling and down-scaling tools and technologies; investing in human talent and future practitioners; and achieving sustainability into surveillance. In this meeting report, we summarise the discussions on innovations in public health surveillance and provide a list with references and links to the organisations and initiatives represented at the meeting. |
Human plague: An old scourge that needs new answers.
Vallès X , Stenseth NC , Demeure C , Horby P , Mead PS , Cabanillas O , Ratsitorahina M , Rajerison M , Andrianaivoarimanana V , Ramasindrazana B , Pizarro-Cerda J , Scholz HC , Girod R , Hinnebusch BJ , Vigan-Womas I , Fontanet A , Wagner DM , Telfer S , Yazdanpanah Y , Tortosa P , Carrara G , Deuve J , Belmain SR , D'Ortenzio E , Baril L . PLoS Negl Trop Dis 2020 14 (8) e0008251 Yersinia pestis, the bacterial causative agent of plague, remains an important threat to human health. Plague is a rodent-borne disease that has historically shown an outstanding ability to colonize and persist across different species, habitats, and environments while provoking sporadic cases, outbreaks, and deadly global epidemics among humans. Between September and November 2017, an outbreak of urban pneumonic plague was declared in Madagascar, which refocused the attention of the scientific community on this ancient human scourge. Given recent trends and plague's resilience to control in the wild, its high fatality rate in humans without early treatment, and its capacity to disrupt social and healthcare systems, human plague should be considered as a neglected threat. A workshop was held in Paris in July 2018 to review current knowledge about plague and to identify the scientific research priorities to eradicate plague as a human threat. It was concluded that an urgent commitment is needed to develop and fund a strong research agenda aiming to fill the current knowledge gaps structured around 4 main axes: (i) an improved understanding of the ecological interactions among the reservoir, vector, pathogen, and environment; (ii) human and societal responses; (iii) improved diagnostic tools and case management; and (iv) vaccine development. These axes should be cross-cutting, translational, and focused on delivering context-specific strategies. Results of this research should feed a global control and prevention strategy within a "One Health" approach. |
Corrigendum: Updated classification of norovirus genogroups and genotypes.
Chhabra P , Graaf M , Parra GI , Chan MC , Green K , Martella V , Wang Q , White PA , Katayama K , Vennema H , Koopmans MPG , Vinjé J . J Gen Virol 2020 101 (8) 893 The genotypes referred to in this article were stated incorrectly. The genotype number 49 should have been stated as 48 and the number 27 should have been stated as 26. These errors occurred in the 'Abstract' section on page 1, in the ‘Discussion’ section on page 11, and within Fig. 5 on page 12. | | The sentence in the 'Abstract' should have read: | | ‘Using previously described 2× standard deviation (sd) criteria to group sequences into separate clusters, we expanded the number of genogroups to 10 (GI-GX) and the number of genotypes to 48 (9 GI, 26 GII, 3 GIII, 2 GIV, 2 GV, 2 GVI and 1 genotype each for GVII, GVIII, GIX [formerly GII.15] and GX).’ | | The sentence in the 'Discussion' section on page 11 should have read: | | ‘Viruses in these ten genogroups can be further divided into 48 confirmed capsid genotypes based on amino acids of the complete VP1 and 60 confirmed P-types based on partial nucleotide sequences of RdRp regions.’ | | Fig. 5 on page 12 erroneously stated ‘27+2T’. This should have been stated as ‘26+2T’. |
Cryptic transmission of SARS-CoV-2 in Washington State.
Bedford T , Greninger AL , Roychoudhury P , Starita LM , Famulare M , Huang ML , Nalla A , Pepper G , Reinhardt A , Xie H , Shrestha L , Nguyen TN , Adler A , Brandstetter E , Cho S , Giroux D , Han PD , Fay K , Frazar CD , Ilcisin M , Lacombe K , Lee J , Kiavand A , Richardson M , Sibley TR , Truong M , Wolf CR , Nickerson DA , Rieder MJ , Englund JA , Hadfield J , Hodcroft EB , Huddleston J , Moncla LH , Müller NF , Neher RA , Deng X , Gu W , Federman S , Chiu C , Duchin J , Gautom R , Melly G , Hiatt B , Dykema P , Lindquist S , Queen K , Tao Y , Uehara A , Tong S , MacCannell D , Armstrong GL , Baird GS , Chu HY , Shendure J , Jerome KR . medRxiv 2020 Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding. |
Potential indirect effects of the COVID-19 pandemic on use of emergency departments for acute life-threatening conditions - United States, January-May 2020.
Lange SJ , Ritchey MD , Goodman AB , Dias T , Twentyman E , Fuld J , Schieve LA , Imperatore G , Benoit SR , Kite-Powell A , Stein Z , Peacock G , Dowling NF , Briss PA , Hacker K , Gundlapalli AV , Yang Q . Am J Transplant 2020 20 (9) 2612-2617 This article describes a significant decline in emergency department visits for acute life-threatening conditions during the COVID-19 pandemic, suggesting that patients may be delaying or avoiding care or unable to access care during the pandemic. |
Trends in the Use of Telehealth During the Emergence of the COVID-19 Pandemic - United States, January-March 2020.
Koonin LM , Hoots B , Tsang CA , Leroy Z , Farris K , Jolly T , Antall P , McCabe B , Zelis CBR , Tong I , Harris AM . MMWR Morb Mortal Wkly Rep 2020 69 (43) 1595-1599 In February 2020, CDC issued guidance advising persons and health care providers in areas affected by the coronavirus disease 2019 (COVID-19) pandemic to adopt social distancing practices, specifically recommending that health care facilities and providers offer clinical services through virtual means such as telehealth.* Telehealth is the use of two-way telecommunications technologies to provide clinical health care through a variety of remote methods.(†) To examine changes in the frequency of use of telehealth services during the early pandemic period, CDC analyzed deidentified encounter (i.e., visit) data from four of the largest U.S. telehealth providers that offer services in all states.(§) Trends in telehealth encounters during January-March 2020 (surveillance weeks 1-13) were compared with encounters occurring during the same weeks in 2019. During the first quarter of 2020, the number of telehealth visits increased by 50%, compared with the same period in 2019, with a 154% increase in visits noted in surveillance week 13 in 2020, compared with the same period in 2019. During January-March 2020, most encounters were from patients seeking care for conditions other than COVID-19. However, the proportion of COVID-19-related encounters significantly increased (from 5.5% to 16.2%; p<0.05) during the last 3 weeks of March 2020 (surveillance weeks 11-13). This marked shift in practice patterns has implications for immediate response efforts and longer-term population health. Continuing telehealth policy changes and regulatory waivers might provide increased access to acute, chronic, primary, and specialty care during and after the pandemic. |
Corrigendum: Whole Genome Sequencing: Bridging One-Health Surveillance of Foodborne Diseases.
Gerner-Smidt P , Besser J , Concepción-Acevedo J , Folster JP , Huffman J , Joseph LA , Kucerova Z , Nichols MC , Schwensohn CA , Tolar B . Front Public Health 2019 7 365 In the original article, there was a mistake in Figure 1 and Figure 2 as published. The graphics used are different than those originally submitted. |
New Lineage of Lassa Virus, Togo, 2016.
Whitmer SLM , Strecker T , Cadar D , Dienes HP , Faber K , Patel K , Brown SM , Davis WG , Klena JD , Rollin PE , Schmidt-Chanasit J , Fichet-Calvet E , Noack B , Emmerich P , Rieger T , Wolff S , Fehling SK , Eickmann M , Mengel JP , Schultze T , Hain T , Ampofo W , Bonney K , Aryeequaye JND , Ribner B , Varkey JB , Mehta AK , Lyon GM 3rd , Kann G , De Leuw P , Schuettfort G , Stephan C , Wieland U , Fries JWU , Kochanek M , Kraft CS , Wolf T , Nichol ST , Becker S , Ströher U , Günther S . Emerg Infect Dis 2018 24 (3) 599-602 We describe a strain of Lassa virus representing a putative new lineage that was isolated from a cluster of human infections with an epidemiologic link to Togo. This finding extends the known range of Lassa virus to Togo. |
Building integrated testing programs for infectious diseases
Alemnji G , Mosha F , Maggiore P , Alexander H , Ndlovu N , Kebede Y , Tiam A , Albert H , Edgil D , de Lussigny S , Peter T . J Infect Dis 2023 228 (10) 1314-1317 In the past two decades, testing services for diseases such as HIV, TB and malaria have expanded dramatically. Investments in testing capacity and supportive health systems have often been disease specific, resulting in siloed testing programs with suboptimal capacity, reduced efficiency, and limited ability to introduce additional tests or respond to new outbreaks. Emergency demand for SARS-CoV2 testing overcame these silos and demonstrated the feasibility of integrated testing. Moving forward, an integrated public laboratory infrastructure that services multiple diseases, including SARS-CoV-2, influenza, HIV, TB, hepatitis, malaria, sexually transmitted diseases, and other infections will help improve universal healthcare delivery and pandemic preparedness. However, integrated testing faces many barriers including poorly aligned health systems, funding and policies. Strategies to overcome these include greater implementation of policies that support multi-disease testing and treatment systems, diagnostic network optimization, bundled test procurement, and more rapid spread of innovation and best practices across disease programs. |
The performance of using dried blood spot specimens for HIV-1 viral load testing: A systematic review and meta-analysis.
Vojnov L , Carmona S , Zeh C , Markby J , Boeras D , Prescott MR , Mayne ALH , Sawadogo S , Adje-Toure C , Zhang G , Perez Gonzalez M , Stevens WS , Doherty M , Yang C , Alexander H , Peter TF , Nkengasong J . PLoS Med 2022 19 (8) e1004076 BACKGROUND: Accurate routine HIV viral load testing is essential for assessing the efficacy of antiretroviral treatment (ART) regimens and the emergence of drug resistance. While the use of plasma specimens is the standard for viral load testing, its use is restricted by the limited ambient temperature stability of viral load biomarkers in whole blood and plasma during storage and transportation and the limited cold chain available between many health care facilities in resource-limited settings. Alternative specimen types and technologies, such as dried blood spots, may address these issues and increase access to viral load testing; however, their technical performance is unclear. To address this, we conducted a meta-analysis comparing viral load results from paired dried blood spot and plasma specimens analyzed with commonly used viral load testing technologies. METHODS AND FINDINGS: Standard databases, conferences, and gray literature were searched in 2013 and 2018. Nearly all studies identified (60) were conducted between 2007 and 2018. Data from 40 of the 60 studies were included in the meta-analysis, which accounted for a total of 10,871 paired dried blood spot:plasma data points. We used random effects models to determine the bias, accuracy, precision, and misclassification for each viral load technology and to account for between-study variation. Dried blood spot specimens produced consistently higher mean viral loads across all technologies when compared to plasma specimens. However, when used to identify virological failure, each technology compared best to plasma at a threshold of 1,000 copies/ml, the present World Health Organization recommended virological failure threshold. Some heterogeneity existed between technologies; however, 5 technologies had a sensitivity greater than 95%. Furthermore, 5 technologies had a specificity greater than 85% yet 2 technologies had a specificity less than 60% using a treatment failure threshold of 1,000 copies/ml. The study's main limitation was the direct applicability of findings as nearly all studies to date used dried blood spot samples prepared in laboratories using precision pipetting that resulted in consistent input volumes. CONCLUSIONS: This analysis provides evidence to support the implementation and scale-up of dried blood spot specimens for viral load testing using the same 1,000 copies/ml virological failure threshold as used with plasma specimens. This may support improved access to viral load testing in resource-limited settings lacking the required infrastructure and cold chain storage for testing with plasma specimens. |
Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021).
Walker PJ , Siddell SG , Lefkowitz EJ , Mushegian AR , Adriaenssens EM , Alfenas-Zerbini P , Davison AJ , Dempsey DM , Dutilh BE , García ML , Harrach B , Harrison RL , Hendrickson RC , Junglen S , Knowles NJ , Krupovic M , Kuhn JH , Lambert AJ , Łobocka M , Nibert ML , Oksanen HM , Orton RJ , Robertson DL , Rubino L , Sabanadzovic S , Simmonds P , Smith DB , Suzuki N , Van Dooerslaer K , Vandamme AM , Varsani A , Zerbini FM . Arch Virol 2021 166 (9) 2633-2648 This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of 'virus' and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes. |
Comparison of Symptoms and RNA Levels in Children and Adults With SARS-CoV-2 Infection in the Community Setting.
Chung E , Chow EJ , Wilcox NC , Burstein R , Brandstetter E , Han PD , Fay K , Pfau B , Adler A , Lacombe K , Lockwood CM , Uyeki TM , Shendure J , Duchin JS , Rieder MJ , Nickerson DA , Boeckh M , Famulare M , Hughes JP , Starita LM , Bedford T , Englund JA , Chu HY . JAMA Pediatr 2021 175 (10) e212025 IMPORTANCE: The association between COVID-19 symptoms and SARS-CoV-2 viral levels in children living in the community is not well understood. OBJECTIVE: To characterize symptoms of pediatric COVID-19 in the community and analyze the association between symptoms and SARS-CoV-2 RNA levels, as approximated by cycle threshold (Ct) values, in children and adults. DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used a respiratory virus surveillance platform in persons of all ages to detect community COVID-19 cases from March 23 to November 9, 2020. A population-based convenience sample of children younger than 18 years and adults in King County, Washington, who enrolled online for home self-collection of upper respiratory samples for SARS-CoV-2 testing were included. EXPOSURES: Detection of SARS-CoV-2 RNA by reverse transcription-polymerase chain reaction (RT-PCR) from participant-collected samples. MAIN OUTCOMES AND MEASURES: RT-PCR-confirmed SARS-CoV-2 infection, with Ct values stratified by age and symptoms. RESULTS: Among 555 SARS-CoV-2-positive participants (mean [SD] age, 33.7 [20.1] years; 320 were female [57.7%]), 47 of 123 children (38.2%) were asymptomatic compared with 31 of 432 adults (7.2%). When symptomatic, fewer symptoms were reported in children compared with adults (mean [SD], 1.6 [2.0] vs 4.5 [3.1]). Symptomatic individuals had lower Ct values (which corresponded to higher viral RNA levels) than asymptomatic individuals (adjusted estimate for children, -3.0; 95% CI, -5.5 to -0.6; P = .02; adjusted estimate for adults, -2.9; 95% CI, -5.2 to -0.6; P = .01). The difference in mean Ct values was neither statistically significant between symptomatic children and symptomatic adults (adjusted estimate, -0.7; 95% CI, -2.2 to 0.9; P = .41) nor between asymptomatic children and asymptomatic adults (adjusted estimate, -0.6; 95% CI, -4.0 to 2.8; P = .74). CONCLUSIONS AND RELEVANCE: In this community-based cross-sectional study, SARS-CoV-2 RNA levels, as determined by Ct values, were significantly higher in symptomatic individuals than in asymptomatic individuals and no significant age-related differences were found. Further research is needed to understand the role of SARS-CoV-2 RNA levels and viral transmission. |
COVID-19 and Chronic Disease: The Impact Now and in the Future.
Hacker KA , Briss PA , Richardson L , Wright J , Petersen R . Prev Chronic Dis 2021 18 E62 Chronic diseases represent 7 of the top 10 causes of death in the United States (1). Six in 10 Americans live with at least 1 chronic condition, such as heart disease, stroke, cancer, or diabetes (2). Chronic diseases are also the leading causes of disability in the US and the leading drivers of the nation’s $3.8 trillion annual health care costs (2,3). | | The COVID-19 pandemic has resulted in enormous personal and societal losses, with more than half a million lives lost (4). COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can result in respiratory distress. In addition to the physical toll, the emotional impact has yet to be fully understood. For those with chronic disease, the impact has been particularly profound (5,6). Heart disease, diabetes, cancer, chronic obstructive pulmonary disease, chronic kidney disease, and obesity are all conditions that increase the risk for severe illness from COVID-19 (7). Other factors, including smoking and pregnancy, also increase the risk (7). Finally, in addition to COVID-19–related deaths since February 1, 2020, an increase in deaths has been observed among people with dementia, circulatory diseases, and diabetes among other causes (8). This increase could reflect undercounting COVID-19 deaths or indirect effects of the virus, such as underutilization of, or stresses on, the health care system (8). |
Evaluation of post-introduction COVID-19 vaccine effectiveness: Summary of interim guidance of the World Health Organization.
Patel MK , Bergeri I , Bresee JS , Cowling BJ , Crowcroft NS , Fahmy K , Hirve S , Kang G , Katz MA , Lanata CF , L'Azou Jackson M , Joshi S , Lipsitch M , Mwenda JM , Nogareda F , Orenstein WA , Ortiz JR , Pebody R , Schrag SJ , Smith PG , Srikantiah P , Subissi L , Valenciano M , Vaughn DW , Verani JR , Wilder-Smith A , Feikin DR . Vaccine 2021 39 (30) 4013-4024 Phase 3 randomized-controlled trials have provided promising results of COVID-19 vaccine efficacy, ranging from 50 to 95% against symptomatic disease as the primary endpoints, resulting in emergency use authorization/listing for several vaccines. However, given the short duration of follow-up during the clinical trials, strict eligibility criteria, emerging variants of concern, and the changing epidemiology of the pandemic, many questions still remain unanswered regarding vaccine performance. Post-introduction vaccine effectiveness evaluations can help us to understand the vaccine's effect on reducing infection and disease when used in real-world conditions. They can also address important questions that were either not studied or were incompletely studied in the trials and that will inform evolving vaccine policy, including assessment of the duration of effectiveness; effectiveness in key subpopulations, such as the very old or immunocompromised; against severe disease and death due to COVID-19; against emerging SARS-CoV-2 variants of concern; and with different vaccination schedules, such as number of doses and varying dosing intervals. WHO convened an expert panel to develop interim best practice guidance for COVID-19 vaccine effectiveness evaluations. We present a summary of the interim guidance, including discussion of different study designs, priority outcomes to evaluate, potential biases, existing surveillance platforms that can be used, and recommendations for reporting results. |
Interim Estimates of Vaccine Effectiveness of Pfizer-BioNTech and Moderna COVID-19 Vaccines Among Health Care Personnel - 33 U.S. Sites, January-March 2021.
Pilishvili T , Fleming-Dutra KE , Farrar JL , Gierke R , Mohr NM , Talan DA , Krishnadasan A , Harland KK , Smithline HA , Hou PC , Lee LC , Lim SC , Moran GJ , Krebs E , Steele M , Beiser DG , Faine B , Haran JP , Nandi U , Schrading WA , Chinnock B , Henning DJ , LoVecchio F , Nadle J , Barter D , Brackney M , Britton A , Marceaux-Galli K , Lim S , Phipps EC , Dumyati G , Pierce R , Markus TM , Anderson DJ , Debes AK , Lin M , Mayer J , Babcock HM , Safdar N , Fischer M , Singleton R , Chea N , Magill SS , Verani J , Schrag S . MMWR Morb Mortal Wkly Rep 2021 70 (20) 753-758 Throughout the COVID-19 pandemic, health care personnel (HCP) have been at high risk for exposure to SARS-CoV-2, the virus that causes COVID-19, through patient interactions and community exposure (1). The Advisory Committee on Immunization Practices recommended prioritization of HCP for COVID-19 vaccination to maintain provision of critical services and reduce spread of infection in health care settings (2). Early distribution of two mRNA COVID-19 vaccines (Pfizer-BioNTech and Moderna) to HCP allowed assessment of the effectiveness of these vaccines in a real-world setting. A test-negative case-control study is underway to evaluate mRNA COVID-19 vaccine effectiveness (VE) against symptomatic illness among HCP at 33 U.S. sites across 25 U.S. states. Interim analyses indicated that the VE of a single dose (measured 14 days after the first dose through 6 days after the second dose) was 82% (95% confidence interval [CI] = 74%-87%), adjusted for age, race/ethnicity, and underlying medical conditions. The adjusted VE of 2 doses (measured ≥7 days after the second dose) was 94% (95% CI = 87%-97%). VE of partial (1-dose) and complete (2-dose) vaccination in this population is comparable to that reported from clinical trials and recent observational studies, supporting the effectiveness of mRNA COVID-19 vaccines against symptomatic disease in adults, with strong 2-dose protection. |
Acute Respiratory Illnesses in Children in the SARS-CoV-2 Pandemic: Prospective Multicenter Study.
Haddadin Z , Schuster JE , Spieker AJ , Rahman H , Blozinski A , Stewart L , Campbell AP , Lively JY , Michaels MG , Williams JV , Boom JA , Sahni LC , Staat M , McNeal M , Selvarangan R , Harrison CJ , Weinberg GA , Szilagyi PG , Englund JA , Klein EJ , Curns AT , Rha B , Langley GE , Hall AJ , Patel MM , Halasa NB . Pediatrics 2021 148 (2) OBJECTIVES: Nonpharmaceutical interventions against coronavirus disease 2019 likely have a role in decreasing viral acute respiratory illnesses (ARIs). We aimed to assess the frequency of respiratory syncytial virus (RSV) and influenza ARIs before and during the coronavirus disease 2019 pandemic. METHODS: This study was a prospective, multicenter, population-based ARI surveillance, including children seen in the emergency departments and inpatient settings in 7 US cities for ARI. Respiratory samples were collected and evaluated by molecular testing. Generalized linear mixed-effects models were used to evaluate the association between community mitigation and number of eligible and proportion of RSV and influenza cases. RESULTS: Overall, 45 759 children were eligible; 25 415 were enrolled and tested; 25% and 14% were RSV-positive and influenza-positive, respectively. In 2020, we noted a decrease in eligible and enrolled ARI subjects after community mitigation measures were introduced, with no RSV or influenza detection from April 5, 2020, to April 30, 2020. Compared with 2016-2019, there was an average of 10.6 fewer eligible ARI cases per week per site and 63.9% and 45.8% lower odds of patients testing positive for RSV and influenza, respectively, during the 2020 community mitigation period. In all sites except Seattle, the proportions of positive tests for RSV and influenza in the 2020 community mitigation period were lower than predicted. CONCLUSIONS: Between March and April 2020, rapid declines in ARI cases and the proportions of RSV and influenza in children were consistently noted across 7 US cities, which could be attributable to community mitigation measures against severe acute respiratory syndrome coronavirus 2. |
Addressing personal protective equipment (PPE) decontamination: Methylene blue and light inactivates severe acute respiratory coronavirus virus 2 (SARS-CoV-2) on N95 respirators and medical masks with maintenance of integrity and fit.
Lendvay TS , Chen J , Harcourt BH , Scholte FE , Lin YL , Kilinc-Balci FS , Lamb MM , Homdayjanakul K , Cui Y , Price A , Heyne B , Sahni J , Kabra KB , Lin YC , Evans D , Mores CN , Page K , Chu LF , Haubruge E , Thiry E , Ludwig-Begall LF , Wielick C , Clark T , Wagner T , Timm E , Gallagher T , Faris P , Macia N , Mackie CJ , Simmons SM , Reader S , Malott R , Hope K , Davies JM , Tritsch SR , Dams L , Nauwynck H , Willaert JF , De Jaeger S , Liao L , Zhao M , Laperre J , Jolois O , Smit SJ , Patel AN , Mayo M , Parker R , Molloy-Simard V , Lemyre JL , Chu S , Conly JM , Chu MC . Infect Control Hosp Epidemiol 2021 43 (7) 1-83 OBJECTIVE: The coronavirus disease 2019 (COVID-19) pandemic has resulted in shortages of personal protective equipment (PPE) underscoring the urgent need for simple, efficient, and inexpensive methods to decontaminate SARS-CoV-2-exposed masks and respirators. We hypothesized that methylene blue (MB) photochemical treatment, which has various clinical applications, could decontaminate PPE contaminated with coronavirus. DESIGN: The two arms of the study included: 1) PPE inoculation with coronaviruses followed by MB with light (MBL) decontamination treatment, and 2) PPE treatment with MBL for 5 cycles of decontamination (5CD) to determine maintenance of PPE performance. METHODS: MBL treatment was used to inactivate coronaviruses on three N95 filtering facepiece respirator (FFR) and two medical mask (MM) models. We inoculated FFR and MM materials with three coronaviruses, including SARS-CoV-2, and treated with 10 µM MB and exposed to 50,000 lux of white light or 12,500 lux of red light for 30 minutes. In parallel, integrity was assessed after 5CD using multiple US and international test methods and compared to the FDA-authorized vaporized hydrogen peroxide plus ozone (VHP+O3) decontamination method. RESULTS: Overall, MBL robustly and consistently inactivated all three coronaviruses with 99.8 - to >99.9% virus inactivation across all FFRs and MMs tested. FFR and MM integrity was maintained after 5 cycles of MBL treatment, whereas one FFR model failed after 5 cycles of VHP+O3. CONCLUSIONS: MBL treatment decontaminated respirators and masks by inactivating three tested coronaviruses without compromising integrity through 5CD. MBL decontamination is effective, low-cost and does not require specialized equipment, making it applicable in all-resource settings. |
COVID-19 Severity and COVID-19-Associated Deaths Among Hospitalized Patients with HIV Infection - Zambia, March-December 2020.
Chanda D , Minchella PA , Kampamba D , Itoh M , Hines JZ , Fwoloshi S , Boyd MA , Hamusonde K , Chirwa L , Nikoi K , Chirwa R , Siwingwa M , Sivile S , Zyambo KD , Mweemba A , Mbewe N , Mutengo KH , Malama K , Agolory S , Mulenga LB . MMWR Morb Mortal Wkly Rep 2021 70 (22) 807-810 The effect of HIV infection on COVID-19 outcomes is unclear. Studies in South Africa (1) and the United Kingdom (2) found an independent association between HIV infection and COVID-19 mortality; however, other studies have not found an association between poor COVID-19 outcomes and either HIV status among hospitalized patients (3-5) or HIV-associated factors such as CD4 count, viral load, or type of antiretroviral therapy (ART) (6). The effect of HIV infection on COVID-19 outcomes remains an urgent question in sub-Saharan Africa, where many countries are experiencing dual HIV and COVID-19 epidemics, and capacity to treat severe COVID-19 is limited. Using data from patients with probable or confirmed COVID-19 admitted to specialized treatment centers during March-December 2020 in Zambia, the Zambian Ministry of Health and CDC assessed the relationship between HIV infection and severe COVID-19 and COVID-19-associated death. Among 443 patients included in the study, 122 (28%) were HIV-positive, and of these, 91 (89%) were receiving ART at the time of hospitalization. HIV status alone was not significantly associated with severe COVID-19 at admission or during hospitalization or with COVID-19-associated death. However, among HIV-positive persons, those with severe HIV disease were more likely to develop severe COVID-19 and were at increased risk for COVID-19-associated death. Ensuring that persons maintain HIV disease control, including maintaining ART continuity and adherence, achieving viral suppression, and addressing and managing underlying medical conditions, could help reduce COVID-19-associated morbidity and mortality in sub-Saharan Africa. |
Genomic features of humoral immunity support tolerance model in Egyptian rousette bats.
Larson PA , Bartlett ML , Garcia K , Chitty J , Balkema-Buschmann A , Towner J , Kugelman J , Palacios G , Sanchez-Lockhart M . Cell Rep 2021 35 (7) 109140 Bats asymptomatically harbor many viruses that can cause severe human diseases. The Egyptian rousette bat (ERB) is the only known reservoir for Marburgviruses and Sosuga virus, making it an exceptional animal model to study antiviral mechanisms in an asymptomatic host. With this goal in mind, we constructed and annotated the immunoglobulin heavy chain locus, finding an expansion on immunoglobulin variable genes associated with protective human antibodies to different viruses. We also annotated two functional and distinct immunoglobulin epsilon genes and four distinctive functional immunoglobulin gamma genes. We described the Fc receptor repertoire in ERBs, including features that may affect activation potential, and discovered the lack of evolutionary conserved short pentraxins. These findings reinforce the hypothesis that a differential threshold of regulation and/or absence of key immune mediators may promote tolerance and decrease inflammation in ERBs. |
Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level.
Salimi V , Viegas M , Trento A , Agoti CN , Anderson LJ , Avadhanula V , Bahl J , Bont L , Brister JR , Cane PA , Galiano M , Graham BS , Hatcher EL , Hellferscee O , Henke DM , Hirve S , Jackson S , Keyaerts E , Kragten-Tabatabaie L , Lindstrom S , Nauwelaers I , Nokes DJ , Openshaw PJ , Peret TC , Piedra PA , Ramaekers K , Rector A , Trovão NS , von Gottberg A , Zambon M , Zhang W , Williams TC , Barr IG , Buchholz UJ . Emerg Infect Dis 2021 27 (6) 1-9 Human respiratory syncytial virus (HRSV) is the leading viral cause of serious pediatric respiratory disease, and lifelong reinfections are common. Its 2 major subgroups, A and B, exhibit some antigenic variability, enabling HRSV to circulate annually. Globally, research has increased the number of HRSV genomic sequences available. To ensure accurate molecular epidemiology analyses, we propose a uniform nomenclature for HRSV-positive samples and isolates, and HRSV sequences, namely: HRSV/subgroup identifier/geographic identifier/unique sequence identifier/year of sampling. We also propose a template for submitting associated metadata. Universal nomenclature would help researchers retrieve and analyze sequence data to better understand the evolution of this virus. |
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