New methods for analyzing serological data with applications to influenza surveillance.

Abstract:

BACKGROUND:Two important challenges to the use of serological assays for influenza surveillance include the substantial amount of experimental effort involved and the inherent noisiness of serological data. RESULTS:I show that log-transformed serological data exist in an effectively one-dimensional space. I use this result, together with new mechanistic insights into serological assays, to develop computational methods for accurately and efficiently recovering unmeasured serological data from a sample of measured data, for systematically minimizing noise and other types of non-antigenic variation found in the data, and for quantifying and visualizing antigenic variation. The methods can also be applied to data with effective dimensionality greater than one, under certain conditions. CONCLUSION:Careful application of the methods developed here would enable the collection of better-quality serological data on a greater number of circulating influenza viruses than is currently possible and improve the ability to identify potential epidemic and pandemic viruses before they become widespread. Although the focus here is on influenza surveillance, the described methods are more widely applicable.

authors

Ndifon W

doi

10.1111/j.1750-2659.2010.00192.x

subject

Has Abstract

pub_date

2011-05-01 00:00:00

pages

206-12

issue

3

eissn

1750-2640

issn

1750-2659

journal_volume

5

pub_type

杂志文章
  • Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness.

    abstract:BACKGROUND:Although it is known that febrile respiratory illnesses (FRI) may be caused by multiple respiratory pathogens, there are no population-level studies describing its impact on clinical disease. METHODS:Between May 2009 and October 2012, 7733 FRI patients and controls in the Singapore military had clinical dat...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12312

    authors: Ho ZJ,Zhao X,Cook AR,Loh JP,Ng SH,Tan BH,Lee VJ

    更新日期:2015-07-01 00:00:00

  • Parental perceptions and predictors of consent for school-located influenza vaccination in urban elementary school children in the United States.

    abstract:BACKGROUND:School-located influenza vaccination (SLV) programs have the potential to mass-vaccinate all enrolled children, but parental consent is required. OBJECTIVE:To examine parental attitudes and determine predictors of parental consent for vaccination of schoolchildren through SLV programs. PATIENTS/METHODS:Sur...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12332

    authors: Cheung S,Wang HL,Mascola L,El Amin AN,Pannaraj PS

    更新日期:2015-09-01 00:00:00

  • The WHO global influenza surveillance and response system (GISRS)-A future perspective.

    abstract::In the centenary year of the devastating 1918-19 pandemic, it seems opportune to reflect on the success of the WHO Global Influenza Surveillance and Response System (GISRS) initiated 70 years ago to provide early warning of changes in influenza viruses circulating in the global population to help mitigate the conseque...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章,评审

    doi:10.1111/irv.12565

    authors: Hay AJ,McCauley JW

    更新日期:2018-09-01 00:00:00

  • Influenza antivirals currently in late-phase clinical trial.

    abstract::Influenza antiviral drugs are important for the control of influenza, most specifically for the treatment of influenza patients with severe disease following infection with a seasonal influenza virus, a newly emerging influenza strain, or in the event of a pandemic. Many influenza antivirals that are currently under i...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章,评审

    doi:10.1111/irv.12446

    authors: Koszalka P,Tilmanis D,Hurt AC

    更新日期:2017-05-01 00:00:00

  • Evaluation of obesity as an independent risk factor for medically attended laboratory-confirmed influenza.

    abstract:BACKGROUND:The relationship between obesity and susceptibility to influenza infection in humans is unclear. Morbidly obese people were at an increased risk of complications from 2009 pandemic H1N1 influenza [A(H1N1)pdm09]. OBJECTIVE:The goal of this study was to determine whether medically attended, laboratory-confirm...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/j.1750-2659.2012.00377.x

    authors: Coleman LA,Waring SC,Irving SA,Vandermause M,Shay DK,Belongia EA

    更新日期:2013-03-01 00:00:00

  • Inter-seasonality of influenza in Australia.

    abstract:BACKGROUND:It appears inter-seasonal influenza notifications have been increasing in summer months in Australia. This study aims to determine changes in inter-seasonal influenza activity in Australia over time. METHODS:Routine influenza surveillance data and hospitalisations data were analysed to study the epidemiolog...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12642

    authors: Moa AM,Adam DC,MacIntyre CR

    更新日期:2019-09-01 00:00:00

  • Assessment of the benefits of seasonal influenza vaccination: Elements of a framework to interpret estimates of vaccine effectiveness and support robust decision-making and communication.

    abstract::Systematic reviews and meta-analyses confirm that influenza vaccination reduces the risk of influenza illness by between about 40% and 60% in seasons when circulating influenza stains are well matched to vaccine strains. Influenza vaccine effectiveness (IVE) estimates, however, are often discordant and a source of con...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章,评审

    doi:10.1111/irv.12786

    authors: Hollingsworth R,El Guerche-Séblain C,Tsai T,Vasiliev Y,Lee S,Bright H,Barbosa P

    更新日期:2021-01-01 00:00:00

  • Advances in antivirals for non-influenza respiratory virus infections.

    abstract::Progress in the development of antivirals for non-influenza respiratory viruses has been slow with the result that many unmet medical needs and few approved agents currently exist. This commentary selectively reviews examples of where specific agents have provided promising clinical benefits in selected target populat...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章,评审

    doi:10.1111/irv.12173

    authors: Hayden FG

    更新日期:2013-11-01 00:00:00

  • Antigenic drift of H1N1 influenza A virus in pigs with and without passive immunity.

    abstract:BACKGROUND:The genetic and antigenic characteristics of influenza A viruses (IAV) within and between species change over time due to antigenic shift and drift. Although pigs are known to play a key role in the epidemiology of IAV between species, little is known about the molecular evolution of IAV hemagglutinin (HA) i...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12190

    authors: Diaz A,Allerson M,Culhane M,Sreevatsan S,Torremorell M

    更新日期:2013-12-01 00:00:00

  • Influenza-associated severe acute respiratory infections in 2 sentinel sites in Lebanon-September 2015 to August 2016.

    abstract:BACKGROUND:Given the sparse information on the burden of influenza in Lebanon, the Ministry of Public Health established a sentinel surveillance for severe acute respiratory infections (SARI) to identify the attribution of influenza to reported cases. We aim to highlight the proportion of influenza-associated SARI from...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12527

    authors: Saleh M,Bazzi L,Ismail E,Mroueh L,Jammal N,Elkholy A,Mrad P,Samadi AA,Hijazi A,Abiad F,Nsouli G,Rady A,Khan W,Malik M,Zalloua P,Ammar W,Ghosn N

    更新日期:2018-05-01 00:00:00

  • A comparative antibody study of the potential susceptibility of Thoroughbred and non-Thoroughbred horse populations in Ireland to equine influenza virus.

    abstract:BACKGROUND:In Ireland, horses may be protected against equine influenza virus (EIV) as a result of natural exposure or vaccination. Current mandatory vaccination programmes are targeted at highly mobile horses. A correlation between antibody levels as measured by single radial haemolysis (SRH) and protective immunity a...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/j.1750-2659.2010.00163.x

    authors: Gildea S,Arkins S,Cullinane A

    更新日期:2010-11-01 00:00:00

  • Influenza surveillance capacity improvements in Africa during 2011-2017.

    abstract:BACKGROUND:Influenza surveillance helps time prevention and control interventions especially where complex seasonal patterns exist. We assessed influenza surveillance sustainability in Africa where influenza activity varies and external funds for surveillance have decreased. METHODS:We surveyed African Network for Inf...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12818

    authors: Igboh LS,McMorrow M,Tempia S,Emukule GO,Talla Nzussouo N,McCarron M,Williams T,Weatherspoon V,Moen A,Fawzi D,Njouom R,Nakoune E,Dauoda C,Kavunga-Membo H,Okeyo M,Heraud JM,Mambule IK,Sow SO,Tivane A,Lagare A,Adebay

    更新日期:2020-11-04 00:00:00

  • Influenza vaccination coverage and effectiveness in young children in Thailand, 2011-2013.

    abstract:BACKGROUND:Since 2009, Thailand has recommended influenza vaccine for children aged 6 months through 2 years, but no estimates of influenza vaccine coverage or effectiveness are available for this target group. METHODS:During August 2011-May 2013, high-risk and healthy children aged ≤36 months were enrolled in a 2-yea...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12302

    authors: Kittikraisak W,Suntarattiwong P,Levy J,Fernandez S,Dawood FS,Olsen SJ,Chotpitayasunondh T

    更新日期:2015-03-01 00:00:00

  • Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA.

    abstract:BACKGROUND:Wild birds are the natural hosts for influenza A viruses (IAVs) and provide a niche for the maintenance of this virus. OBJECTIVES:This study was undertaken to analyze nucleotide sequences of the matrix (M) gene of AIVs isolated from wild birds and live bird markets (LBMs) to index the changes occurring in t...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12003

    authors: Chander Y,Jindal N,Sreevatsan S,Stallknecht DE,Goyal SM

    更新日期:2013-07-01 00:00:00

  • Estimates of US influenza-associated deaths made using four different methods.

    abstract:BACKGROUND:A wide range of methods have been used for estimating influenza-associated deaths in temperate countries. Direct comparisons of estimates produced by using different models with US mortality data have not been published. OBJECTIVE:Compare estimates of US influenza-associated deaths made by using four models...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/j.1750-2659.2009.00073.x

    authors: Thompson WW,Weintraub E,Dhankhar P,Cheng PY,Brammer L,Meltzer MI,Bresee JS,Shay DK

    更新日期:2009-01-01 00:00:00

  • Confronting the next influenza pandemic with anti-inflammatory and immunomodulatory agents: why they are needed and how they might work.

    abstract::Despite the best efforts of influenza scientists, companies and health officials to prepare for the next pandemic, most of the world's people will not have access to affordable supplies of vaccines and antiviral agents. They will have to rely on 19th century public health 'technologies' to see them through. In the 21s...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章,评审

    doi:10.1111/j.1750-2659.2009.00090.x

    authors: Fedson DS

    更新日期:2009-07-01 00:00:00

  • Safety and immunogenicity of Sinovac's prototype pandemic influenza H5N1 vaccines: a review on clinical trials.

    abstract::Sinovac Biotech started to develop prototype pandemic influenza H5N1 vaccines in March 2004. On 2 April 2008, Sinovac's inactivated, aluminium-adjuvanted, whole-virion prototype pandemic influenza A (H5N1) vaccine (PanFlu) was granted production licensure by the China regulatory authority State Food and Drug Administr...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章,随机对照试验,评审

    doi:10.1111/j.1750-2659.2008.00067.x

    authors: Qiu YZ,Yin WD

    更新日期:2008-11-01 00:00:00

  • The 1918 influenza pandemic in New York City: age-specific timing, mortality, and transmission dynamics.

    abstract:BACKGROUND:The 1918 influenza pandemic caused disproportionately high mortality among certain age groups. The mechanisms underlying these differences are not fully understood. OBJECTIVES:To explore the dynamics of the 1918 pandemic and to identify potential age-specific transmission patterns. METHODS:We examined 1915...

    journal_title:Influenza and other respiratory viruses

    pub_type: 历史文章,杂志文章

    doi:10.1111/irv.12217

    authors: Yang W,Petkova E,Shaman J

    更新日期:2014-03-01 00:00:00

  • Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea.

    abstract:BACKGROUND:The influenza virus is reportedly associated with 3-5 million cases of severe illness and 250 000-500 000 deaths annually worldwide. OBJECTIVES:We investigated the variation of influenza A virus in Korea and examined the association with death. METHODS:A total of 13 620 cases were enrolled in the Hospital-...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12549

    authors: Lee HS,Noh JY,Song JY,Cheong HJ,Choi WS,Jeong HW,Wie SH,Kim WJ

    更新日期:2018-07-01 00:00:00

  • Whole-genome analysis of influenza A(H1N1)pdm09 viruses isolated in Uganda from 2009 to 2011.

    abstract::We report a whole-genome analysis of 19 influenza A(H1N1)pdm09 isolates from four Ugandan hospitals between 2009 and 2011. The isolates differed from the vaccine strain A/California/07/2009 by three amino acid substitutions P100S, S220T, and I338V in the hemagglutinin and by two amino acid substitutions V106I and N248...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12401

    authors: Byarugaba DK,Erima B,Millard M,Kibuuka H,Lkwago L,Bwogi J,Mimbe D,Kiconco JB,Tugume T,Mworozi EA,Turner J,Mckenzie PP,Webby RR,Webster RG,Foret C,Ducatez MF,Coldren R,Wabwire-Mangen F,Krauss S

    更新日期:2016-11-01 00:00:00

  • Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China.

    abstract:BACKGROUND:Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES:Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two impo...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12535

    authors: Zhou JY,Peng Y,Peng XY,Gao HC,Sun YP,Xie LY,Zhong LL,Duan ZJ,Xie ZP,Cao YD

    更新日期:2018-03-01 00:00:00

  • A systematic review of factors affecting intended and actual adherence with antiviral medication as treatment or prophylaxis in seasonal and pandemic flu.

    abstract::The aim of this review was to identify factors predicting actual or intended adherence to antivirals as treatment or prophylaxis for influenza. Literature from inception to March 2015 was systematically reviewed to find studies reporting predictors of adherence to antivirals and self-reported reasons for non-adherence...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章,评审

    doi:10.1111/irv.12406

    authors: Smith LE,D'Antoni D,Jain V,Pearce JM,Weinman J,Rubin GJ

    更新日期:2016-11-01 00:00:00

  • Estimating influenza incidence and rates of influenza-like illness in the outpatient setting.

    abstract:BACKGROUND:Estimating influenza incidence in outpatient settings is challenging. We used outpatient healthcare practice populations as a proxy to estimate community incidence of influenza-like illness (ILI) and laboratory-confirmed influenza-associated ILI. METHODS:From October 2009 to July 2010, 38 outpatient practic...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12014

    authors: Fowlkes A,Dasgupta S,Chao E,Lemmings J,Goodin K,Harris M,Martin K,Feist M,Wu W,Boulton R,Temte J,Brammer L,Finelli L

    更新日期:2013-09-01 00:00:00

  • Extremely low risk for acquisition of a respiratory viral infection in the emergency room of a large pediatric hospital during the winter season.

    abstract::The aim of this study was to investigate the rate of transmission of respiratory viral infections to children visiting the emergency room of a large pediatric hospital during winter. A total of 615 children were prospectively studied. Twenty-two (3·6%) children developed at least one symptom compatible with a respirat...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/j.1750-2659.2012.00355.x

    authors: Maltezou HC,Mougkou K,Asimaki H,Koniaraki K,Katerelos P,Giannaki M,Theodoridou M

    更新日期:2013-01-01 00:00:00

  • Antibody levels in a cohort of pregnant women after the 2009 influenza A(H1N1) pandemic: Waning and association with self-reported severity and duration of illness.

    abstract:BACKGROUND:A population-based pregnancy cohort was established in Norway to study potential effects of exposure to the 2009 influenza pandemic or pandemic vaccination during pregnancy. OBJECTIVES:We studied maternal A(H1N1)pdm09-specific hemagglutination inhibition (HI)-titer levels and waning in women with influenza-...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12623

    authors: Tunheim G,Laake I,Robertson AH,Waalen K,Hungnes O,Naess LM,Cox RJ,Mjaaland S,Trogstad L

    更新日期:2019-03-01 00:00:00

  • Surveillance of influenza in Indonesia, 2003–2007.

    abstract:BACKGROUND:Longitudinal data are limited about the circulating strains of influenza viruses and their public health impact in Indonesia. We conducted influenza surveillance among outpatients and hospitalized patients with influenza-like illness (ILI) across the Indonesian archipelago from 2003 through 2007. METHODOLOG...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/j.1750-2659.2012.00403.x

    authors: Kosasih H,Roselinda,Nurhayati,Klimov A,Xiyan X,Lindstrom S,Mahoney F,Beckett C,Burgess TH,Blair PJ,Uyeki TM,Sedyaningsih ER

    更新日期:2013-05-01 00:00:00

  • 1918 pandemic morbidity: The first wave hits the poor, the second wave hits the rich.

    abstract:BACKGROUND:Whether morbidity from the 1918-19 influenza pandemic discriminated by socioeconomic status has remained a subject of debate for 100 years. In lack of data to study this issue, the recent literature has hypothesized that morbidity was "socially neutral." OBJECTIVES:To study the associations between influenz...

    journal_title:Influenza and other respiratory viruses

    pub_type: 历史文章,杂志文章

    doi:10.1111/irv.12541

    authors: Mamelund SE

    更新日期:2018-05-01 00:00:00

  • Evidence of reassortment of pandemic H1N1 influenza virus in swine in Argentina: are we facing the expansion of potential epicenters of influenza emergence?

    abstract::In this report, we describe the occurrence of two novel swine influenza viruses (SIVs) in pigs in Argentina. These viruses are the result of two independent reassortment events between the H1N1 pandemic influenza virus (H1N1pdm) and human-like SIVs, showing the constant evolution of influenza viruses at the human-swin...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/j.1750-2659.2011.00246.x

    authors: Pereda A,Rimondi A,Cappuccio J,Sanguinetti R,Angel M,Ye J,Sutton T,Dibárbora M,Olivera V,Craig MI,Quiroga M,Machuca M,Ferrero A,Perfumo C,Perez DR

    更新日期:2011-11-01 00:00:00

  • Transmission parameters of the A/H1N1 (2009) influenza virus pandemic: a review.

    abstract:BACKGROUND:The new influenza virus A/H1N1 (2009), identified in mid-2009, rapidly spread over the world. Estimating the transmissibility of this new virus was a public health priority. METHODS:We reviewed all studies presenting estimates of the serial interval or generation time and the reproduction number of the A/H1...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章,评审

    doi:10.1111/j.1750-2659.2011.00234.x

    authors: Boëlle PY,Ansart S,Cori A,Valleron AJ

    更新日期:2011-09-01 00:00:00

  • Estimates and determinants of economic impacts from influenza-like illnesses caused by respiratory viruses in Australian children attending childcare: a cohort study.

    abstract:BACKGROUND:Influenza and other respiratory infections cause excess winter morbidity in children. This study assessed the economic impact of influenza-like illness (ILI) on families with children attending childcare using a societal perspective. METHODS:We conducted a prospective cohort study in 90 childcare centres an...

    journal_title:Influenza and other respiratory viruses

    pub_type: 杂志文章

    doi:10.1111/irv.12138

    authors: Yin JK,Salkeld G,Lambert SB,Dierig A,Heron L,Leask J,Yui Kwan Chow M,Booy R

    更新日期:2013-11-01 00:00:00