Primary care influenza‐like illness surveillance in Ho Chi Minh City, Vietnam 2013‐2015

Todd, Stacy; Hường, Nguyễn Thị Cẩm; Thanh, Nguyen Thi Le; Vy, Nguyen Ha Thao; Hưng, Nguyễn Thành; Thao, Tran Thi Nhu; Phuong, Huynh Thi; Doorn, H. Rogier van; Hang, Vu Thi Ty; Châu, Nguyễn Văn Vĩnh; Read, Jonathan M.; Lalloo, David G.; Boni, Maciej F.

doi:10.1111/irv.12574

Cited by 10 publications

(10 citation statements)

References 33 publications

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“…To validate that PC1 is an appropriate surrogate for seroprevalence, an individual-based epidemic simulation was developed in C++ (Supplementary Methods). The simulation mimics the non-seasonal patterns of influenza A/ H3N2 cases in Vietnam over a 10-year period 30,77 and uses influenza susceptibility data, antibody response data, and antibody waning data (measured with the same protein microarray) from a concurrently run clinical study run in Ho Chi Minh City from 2013 to 2015 78,79 . Simulations of 500,000 individuals are run with fixed attack rates ranging from 5 to 30%, and 6700 samples are taken at the exact sampling times (from 2010 to 2015) as in the serum collections for Ho Chi Minh City.…”

Section: Methodsmentioning

confidence: 99%

Age-seroprevalence curves for the multi-strain structure of influenza A virus

et al. 2021

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The relationship between age and seroprevalence can be used to estimate the annual attack rate of an infectious disease. For pathogens with multiple serologically distinct strains, there is a need to describe composite exposure to an antigenically variable group of pathogens. In this study, we assay 24,402 general-population serum samples, collected in Vietnam between 2009 to 2015, for antibodies to eleven human influenza A strains. We report that a principal components decomposition of antibody titer data gives the first principal component as an appropriate surrogate for seroprevalence; this results in annual attack rate estimates of 25.6% (95% CI: 24.1% – 27.1%) for subtype H3 and 16.0% (95% CI: 14.7% – 17.3%) for subtype H1. The remaining principal components separate the strains by serological similarity and associate birth cohorts with their particular influenza histories. Our work shows that dimensionality reduction can be used on human antibody profiles to construct an age-seroprevalence relationship for antigenically variable pathogens.

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Section: Methodsmentioning

confidence: 99%

Age-seroprevalence curves for the multi-strain structure of influenza A virus

et al. 2021

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“…To validate that PC1 is an appropriate surrogate for seroprevalence, an individual-based epidemic simulation was developed in C++ (Supplementary Materials Section 1). The simulation mimics the non-seasonal patterns of influenza A/H3N2 cases in Vietnam over a 10-year period 30,45 , and uses influenza susceptibility data, antibody response data, and antibody waning data (measured with the same protein microarray) from a concurrently run clinical study run in Ho Chi Minh City from 2013 to 2015 46,47 . Simulations of 500,000 individuals are run with fixed attack rates ranging from 5% to 30%, and 6700 samples are taken at the exact sampling times (from 2010 to 2015) as in the serum collections for Ho Chi Minh City.…”

Section: Methodsmentioning

confidence: 99%

“…Clustering. Clustering of serological profiles was performed with a principal components analysis 46,47 . Simulations of 500,000 individuals are run with fixed attack rates ranging from 5% to 30%, and 6700 samples are taken at the exact sampling times (from 2010 to 2015) as in the serum collections for Ho Chi Minh City.…”

Section: Methodsmentioning

confidence: 99%

Age-seroprevalence curves for the multi-strain structure of influenza A virus

Vinh

Nhat

Bruin

et al. 2021

Preprint

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The relationship between age and seroprevalence provides the simplest and least expensive approach to computing the annual attack rate of an infectious disease. However, many pathogens circulate as multiple serologically distinct strains, with no single assay able to determine seropositivity or seronegativity to an entire clade or family of co-circulating pathogens. An approach is needed to describe population exposure to an antigenically variable group of pathogens without focusing on any particular strain or serotype in the group. In this study, we focus on the two-subtype multi-strain taxonomy of human influenza A virus. We describe a data set of 24,402 general-population serum samples collected in central and southern Vietnam between 2009 to 2015, and assayed for influenza HA1 antibodies to eleven different strains of human influenza A (both H3 and H1 subtypes). We find that a principal components decomposition of the data results in the first principal component PC1 being an appropriate surrogate for seroprevalence (or composite antibody titer) which can be further decomposed for H1 and H3 contribution to the serological profile. Using this approach, we are able to provide the first ELISA-based standardized measurements of serology to reconstruct population exposure history, which correlates well with known influenza epidemiology. Annual attack rates in Vietnam are estimated at 25.6% (95% CI: 24.1% – 27.1%) for H3 and 16.0% (95% CI: 14.7% – 17.3%) for H1, with some variation in location-specific attack rates. The remaining principal components act as descriptors of influenza history and sort the population by birth year. The novel contributions of this analysis are (1) the introduction of dimensionality reduction on human antibody profiles to construct an age-seroprevalence relationship for an antigenically variable pathogen, (2) an analysis of >24,000 individuals, using >260,000 serological data points in total, allowing us to construct age-seroprevalence relationships with the precision of modern big data studies, and (3) a description of long-term attack rates in a non-vaccinated setting showing the natural history of influenza A virus in a densely-populated tropical country.

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“…The low prevalence or absence of respiratory viruses like PIVs, PEV, RSVA, and RSVB in the present study may be attributed to the age structure of the present cohort. Indeed, while, these viral species are well-established agents of (respiratory) infections in children, and to some extent in elderly people (eg, in case of PIVs), 3,10,14,15,[36][37][38] over 92% of the respiratory disease episodes reported in this study were among cohort members aging ≥16 years. In terms of seasonal distribution of the predominant viruses as EVs, influenza A virus, HRV and ADV, our report supports previous findings.…”

Section: Animal Exposurementioning

confidence: 99%

“…(PIV)1-4, human CoV (including subtypes OC43 and NL63), human bocavirus (BoV) and parechovirus (PEV) are the most common viruses detected in respiratory samples worldwide. [3][4][5][6][7][8][9] Of these, influenza A virus, influenza B virus, and CoV have been reported as the most common viruses detected in people over 5 years old, [10][11][12][13] while RSV and PIVs have been regarded as the leading causes of respiratory infections in children under 5 years old in South East Asia. 3,14,15 Zoonotic infections are of global concern, and approximately 60% of known infectious diseases in humans are of zoonotic origin.…”

mentioning

confidence: 99%

Respiratory viruses in individuals with a high frequency of animal exposure in southern and highland Vietnam

Nguyen

Ngo

Tran

et al. 2019

Journal of Medical Virology

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Active surveillance for zoonotic respiratory viruses is essential to inform the development of appropriate interventions and outbreak responses. Here we target individuals with a high frequency of animal exposure in Vietnam. Three-year community-based surveillance was conducted in Vietnam during 2013-2016. We enrolled a total of 581 individuals (animal-raising farmers, slaughterers, animal-health workers, and rat traders), and utilized reverse transcription-polymerase chain reaction to detect 15 common respiratory viruses in pooled nasal-throat swabs collected at baseline or acute respiratory disease episodes. A respiratory virus was detected in 7.9% (58 of 732) of baseline samples, and 17.7% (136 of 770) of disease episode samples (P < .001), with enteroviruses (EVs), rhinoviruses and influenza A virus being the predominant viruses detected. There were temporal and spatial fluctuations in the frequencies of the detected viruses over the study period, for example, EVs and influenza A viruses were more often detected during rainy seasons. We reported the detection of common respiratory viruses in individuals with a high frequency of animal exposure in Vietnam, an emerging infectious disease hotspot. The results show the value of baseline/control sampling in delineating the causative relationships and have revealed important insights into the ecological aspects of EVs, rhinoviruses and influenza A and their contributions to the burden posed by respiratory infections in Vietnam.

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Primary care influenza‐like illness surveillance in Ho Chi Minh City, Vietnam 2013‐2015

Cited by 10 publications

References 33 publications

Age-seroprevalence curves for the multi-strain structure of influenza A virus

Age-seroprevalence curves for the multi-strain structure of influenza A virus

Age-seroprevalence curves for the multi-strain structure of influenza A virus

Respiratory viruses in individuals with a high frequency of animal exposure in southern and highland Vietnam

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