Next-Generation Sequencing of Infectious Pathogens Gwinn, Marta; MacCannell, Duncan; Armstrong, Gregory L
JAMA : the journal of the American Medical Association,
03/2019, Letnik:
321, Številka:
9
Journal Article
Recenzirano
Odprti dostop
The use and importance of next-generation sequencing for the diagnosis of pathogens is discussed. The next-generation sequencing techniques allow improvement in the clinical and public health ...microbiology. It helps in preventing transmission of communicable diseases, carrying out field investigations, surveillance of epidemics, and increases accuracy of diagnosis.
On December 14, 2020, the United Kingdom reported a SARS-CoV-2 variant of concern (VOC), lineage B.1.1.7, also referred to as VOC 202012/01 or 20I/501Y.V1.* The B.1.1.7 variant is estimated to have ...emerged in September 2020 and has quickly become the dominant circulating SARS-CoV-2 variant in England (1). B.1.1.7 has been detected in over 30 countries, including the United States. As of January 13, 2021, approximately 76 cases of B.1.1.7 have been detected in 12 U.S. states.
Multiple lines of evidence indicate that B.1.1.7 is more efficiently transmitted than are other SARS-CoV-2 variants (1-3). The modeled trajectory of this variant in the U.S. exhibits rapid growth in early 2021, becoming the predominant variant in March. Increased SARS-CoV-2 transmission might threaten strained health care resources, require extended and more rigorous implementation of public health strategies (4), and increase the percentage of population immunity required for pandemic control. Taking measures to reduce transmission now can lessen the potential impact of B.1.1.7 and allow critical time to increase vaccination coverage. Collectively, enhanced genomic surveillance combined with continued compliance with effective public health measures, including vaccination, physical distancing, use of masks, hand hygiene, and isolation and quarantine, will be essential to limiting the spread of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). Strategic testing of persons without symptoms but at higher risk of infection, such as those exposed to SARS-CoV-2 or who have frequent unavoidable contact with the public, provides another opportunity to limit ongoing spread.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, ODKLJ, OILJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK, VSZLJ
Pathogen Genomics in Public Health Armstrong, Gregory L; MacCannell, Duncan R; Taylor, Jill ...
The New England journal of medicine,
12/2019, Letnik:
381, Številka:
26
Journal Article
Recenzirano
Odprti dostop
The development of next-generation sequencing technology has had a major effect on a wide range of infectious diseases that affect public health. Next-generation sequencing promises to facilitate the ...diagnosis of outbreaks, the detection of drug resistance, and the selection of vaccine approaches and has many other applications.
Defining the primary characteristics of persons infected with hepatitis C virus (HCV) enables physicians to more easily identify persons who are most likely to benefit from testing for the disease.
...To describe the HCV-infected population in the United States.
Nationally representative household survey.
U.S. civilian, noninstitutionalized population.
15,079 participants in the National Health and Nutrition Examination Survey between 1999 and 2002.
All participants provided medical histories, and those who were 20 to 59 years of age provided histories of drug use and sexual practices. Participants were tested for antibodies to HCV (anti-HCV) and HCV RNA, and their serum alanine aminotransferase (ALT) levels were measured.
The prevalence of anti-HCV in the United States was 1.6% (95% CI, 1.3% to 1.9%), equating to an estimated 4.1 million (CI, 3.4 million to 4.9 million) anti-HCV-positive persons nationwide; 1.3% or 3.2 million (CI, 2.7 million to 3.9 million) persons had chronic HCV infection. Peak prevalence of anti-HCV (4.3%) was observed among persons 40 to 49 years of age. A total of 48.4% of anti-HCV-positive persons between 20 and 59 years of age reported a history of injection drug use, the strongest risk factor for HCV infection. Of all persons reporting such a history, 83.3% had not used injection drugs for at least 1 year before the survey. Other significant risk factors included 20 or more lifetime sex partners and blood transfusion before 1992. Abnormal serum ALT levels were found in 58.7% of HCV RNA-positive persons. Three characteristics (abnormal serum ALT level, any history of injection drug use, and history of blood transfusion before 1992) identified 85.1% of HCV RNA-positive participants between 20 and 59 years of age.
Incarcerated and homeless persons were not included in the survey.
Many Americans are infected with HCV. Most were born between 1945 and 1964 and can be identified with current screening criteria. History of injection drug use is the strongest risk factor for infection.
Without intervention, up to 25% of individuals chronically infected with hepatitis B virus (HBV) die of late complications, including cirrhosis and liver cancer. The United States, which in 1991 ...implemented a strategy to eliminate HBV transmission through universal immunization, is a country of low prevalence. Approximately 3,000-5,000 U.S.-acquired cases of chronic hepatitis B have occurred annually since 2001. Many more chronically infected persons migrate to the United States yearly from countries of higher prevalence. Although early identification of chronic HBV infection can reduce the likelihood of transmission and late complications, immigrants are not routinely screened for HBV infection during or after immigration.
To estimate the number of imported cases of chronic hepatitis B, we multiplied country-specific prevalence estimates by the yearly number of immigrants from each country during 1974-2008.
During 1974-2008, 27.9 million immigrants entered the U.S. Sixty-three percent were born in countries of intermediate or high chronic hepatitis B prevalence (range 2%-31%). On average, an estimated 53,800 chronic hepatitis B cases were imported to the U.S. yearly from 2004 through 2008. The Philippines, China, and Vietnam contributed the most imported cases (13.4%, 12.5%, and 11.0%, respectively). Imported cases increased from an estimated low of 105,750 during the period 1974-1977 to a high of 268,800 in 2004-2008.
Imported chronic hepatitis B cases account for approximately 95% of new U.S. cases. Earlier case identification and management of infected immigrants would strengthen the U.S. strategy to eliminate HBV transmission, and could delay disease progression and prevent some deaths among new Americans.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
End-stage liver disease accounts for one in forty deaths worldwide. Chronic infections with hepatitis B virus (HBV) and hepatitis C virus (HCV) are well-recognized risk factors for cirrhosis and ...liver cancer, but estimates of their contributions to worldwide disease burden have been lacking.
The prevalence of serologic markers of HBV and HCV infections among patients diagnosed with cirrhosis or hepatocellular carcinoma (HCC) was obtained from representative samples of published reports. Attributable fractions of cirrhosis and HCC due to these infections were estimated for 11 WHO-based regions.
Globally, 57% of cirrhosis was attributable to either HBV (30%) or HCV (27%) and 78% of HCC was attributable to HBV (53%) or HCV (25%). Regionally, these infections usually accounted for >50% of HCC and cirrhosis. Applied to 2002 worldwide mortality estimates, these fractions represent 929,000 deaths due to chronic HBV and HCV infections, including 446,000 cirrhosis deaths (HBV:
n
=
235,000; HCV:
n
=
211,000) and 483,000 liver cancer deaths (HBV:
n
=
328,000; HCV:
n
=
155,000).
HBV and HCV infections account for the majority of cirrhosis and primary liver cancer throughout most of the world, highlighting the need for programs to prevent new infections and provide medical management and treatment for those already infected.
Late in the twentieth century, interest intensified regarding the involvement of the circadian system in the aetiology and treatment of Parkinson’s disease (PD). It has been envisaged that this ...approach might provide relief beyond the limited benefits and severe side effects achieved by dopamine (DA) replacement. In the first clinical article, published in 1996, polychromatic light was used to shift the circadian clock as it is considered to be the most powerful zeitgeber (time keeper) that can be implemented to realign circadian phase. Since that time, 11 additional articles have implemented light treatment (LT) in various forms as an adjuvant to DA replacement. In spite of the growing interest in this area, the systematic exploration of LT in PD has been stymied by several methodological factors. Such factors include time of LT presentation, duration of studies undertaken, frequency of light employed, dose of light prescribed and relevance of experimental design to the prolonged course of the illness. On this basis, it is the purpose of this review to provide an in-depth examination of these papers, and the underlying preclinical work, to provide critique, thereby giving direction for future studies in therapeutic applications of LT for PD. Consideration of this collective work may serve to carve a path for future research and thereby improve the lives of those suffering from this debilitating disorder.
Understanding natural and anthropogenic climate change processes involves using computational models that represent the main components of the Earth system: the atmosphere, ocean, sea ice, and land ...surface. These models have become increasingly computationally expensive as resolution is increased and more complex process representations are included. However, to gain robust insight into how climate may respond to a given forcing, and to meaningfully quantify the associated uncertainty, it is often required to use either or both ensemble approaches and very long integrations. For this reason, more computationally efficient models can be very valuable tools. Here we provide a comprehensive overview of the suite of climate models based around the HadCM3 coupled general circulation model. This model was developed at the UK Met Office and has been heavily used during the last 15 years for a range of future (and past) climate change studies, but has now been largely superseded for many scientific studies by more recently developed models. However, it continues to be extensively used by various institutions, including the BRIDGE (Bristol Research Initiative for the Dynamic Global Environment) research group at the University of Bristol, who have made modest adaptations to the base HadCM3 model over time. These adaptations mean that the original documentation is not entirely representative, and several other relatively undocumented configurations are in use. We therefore describe the key features of a number of configurations of the HadCM3 climate model family, which together make up HadCM3@Bristol version 1.0. In order to differentiate variants that have undergone development at BRIDGE, we have introduced the letter B into the model nomenclature. We include descriptions of the atmosphere-only model (HadAM3B), the coupled model with a low-resolution ocean (HadCM3BL), the high-resolution atmosphere-only model (HadAM3BH), and the regional model (HadRM3B). These also include three versions of the land surface scheme. By comparing with observational datasets, we show that these models produce a good representation of many aspects of the climate system, including the land and sea surface temperatures, precipitation, ocean circulation, and vegetation. This evaluation, combined with the relatively fast computational speed (up to 1000 times faster than some CMIP6 models), motivates continued development and scientific use of the HadCM3B family of coupled climate models, predominantly for quantifying uncertainty and for long multi-millennial-scale simulations.
Human metapneumovirus (HMPV) infection causes respiratory illness, including bronchiolitis and pneumonia. However, national HMPV seasonality, as it compares with respiratory syncytial virus (RSV) and ...influenza seasonality patterns, has not been well described.
Hospital and clinical laboratories reported weekly aggregates of specimens tested and positive detections for HMPV, RSV, and influenza to the National Respiratory and Enteric Virus Surveillance System from 2008 to 2014. A season was defined as consecutive weeks with ≥3% positivity for HMPV and ≥10% positivity for RSV and influenza during a surveillance year (June through July). For each virus, the season, onset, offset, duration, peak, and 6-season medians were calculated.
Among consistently reporting laboratories, 33 583 (3.6%) specimens were positive for HMPV, 281 581 (15.3%) for RSV, and 401 342 (18.2%) for influenza. Annually, 6 distinct HMPV seasons occurred from 2008 to 2014, with onsets ranging from November to February and offsets from April to July. Based on the 6-season medians, RSV, influenza, and HMPV onsets occurred sequentially and season durations were similar at 21 to 22 weeks. HMPV demonstrated a unique biennial pattern of early and late seasonal onsets. RSV seasons (onset, offset, peak) were most consistent and occurred before HMPV seasons. There were no consistent patterns between HMPV and influenza circulations.
HMPV circulation begins in winter and lasts until spring and demonstrates distinct seasons each year, with the onset beginning after that of RSV. HMPV, RSV, and influenza can circulate simultaneously during the respiratory season.
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