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The assessment of data sources for influenza virologic surveillance in New York State

View Article: PubMed Central - PubMed

ABSTRACT

Background: Following the 2013 USA release of the Influenza Virologic Surveillance Right Size Roadmap, the New York State Department of Health (NYSDOH) embarked on an evaluation of data sources for influenza virologic surveillance.

Objective: To assess NYS data sources, additional to data generated by the state public health laboratory (PHL), which could enhance influenza surveillance at the state and national level.

Methods: Potential sources of laboratory test data for influenza were analyzed for quantity and quality. Computer models, designed to assess sample sizes and the confidence of data for statistical representation of influenza activity, were used to compare PHL test data to results from clinical and commercial laboratories, reported between June 8, 2013 and May 31, 2014.

Results: Sample sizes tested for influenza at the state PHL were sufficient for situational awareness surveillance with optimal confidence levels, only during peak weeks of the influenza season. Influenza data pooled from NYS PHLs and clinical laboratories generated optimal confidence levels for situational awareness throughout the influenza season. For novel influenza virus detection in NYS, combined real‐time (rt) RT‐PCR data from state and regional PHLs achieved ≥85% confidence during peak influenza activity, and ≥95% confidence for most of low season and all of off‐season.

Conclusions: In NYS, combined data from clinical, commercial, and public health laboratories generated optimal influenza surveillance for situational awareness throughout the season. Statistical confidence for novel virus detection, which is reliant on only PHL data, was achieved for most of the year.

No MeSH data available.


Related in: MedlinePlus

Influenza testing performed during 2013‐2014 by the Wadsworth Center, and NYS regional PHLs. Total number of positives are shown relative to the recommended Flu+ sample sizes determined from the Right Size Roadmap Calculator B for detection of a rare/novel event with 95% confidence and expected prevalence of 30% for high season (1/700 detection threshold), 10% for low season (1/200 detection threshold), and 1% for off‐season (1/4 detection threshold). (The elevated specimen numbers for Wadsworth for weeks ending June 29, April 19, and May 10, are due to one EIP submitter sending backlogged specimens)
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irv12433-fig-0005: Influenza testing performed during 2013‐2014 by the Wadsworth Center, and NYS regional PHLs. Total number of positives are shown relative to the recommended Flu+ sample sizes determined from the Right Size Roadmap Calculator B for detection of a rare/novel event with 95% confidence and expected prevalence of 30% for high season (1/700 detection threshold), 10% for low season (1/200 detection threshold), and 1% for off‐season (1/4 detection threshold). (The elevated specimen numbers for Wadsworth for weeks ending June 29, April 19, and May 10, are due to one EIP submitter sending backlogged specimens)

Mentions: For the detection of a rare/novel influenza virus, Wadsworth test data were compared to recommended sample sizes for NYS, aggregated on a national scale, determined from Calculator B (Figure 5). The total number of Flu+ specimens tested at the Wadsworth Center was insufficient to detect a rare/novel event for influenza surveillance at the recommended confidence levels. To augment detection of a rare/novel influenza virus, NYS regional PHL influenza rtRT‐PCR data supplemented the Wadsworth Center rtRT‐PCR data (Figure 5). From the last week of December 2013 through January 2014 with peak influenza activity, Flu+ data provided 86% to 94% confidence in the likelihood of detecting a novel virus present at 1/700 of cases. During low season, the recommended threshold for detection of a novel virus outside of peak season is 1/200 with a minimum Flu+ sample size of 37; sample sizes with 95% confidence were obtained for 4 of those 6 weeks (Table 2). During off‐season, the recommended threshold drops to ¼ with a minimum Flu+ sample size of 1. In fact, just 1 Flu+ sample is needed every 5 weeks per state, as 11 Flu+ samples are needed per week for 52 states nationally (personal communication, Lynette Brammer, CDC). Sample sizes with 95% confidence were obtained for 40 of 40 off‐season weeks when counting 1 Flu+ every 5 weeks. Thus, to contribute to national surveillance in detecting a rare/novel influenza virus, combined sample sizes from Wadsworth and the regional PHLs were sufficient to reach minimum confidence levels (≥85%) for recommended detection thresholds during peak weeks of influenza activity, and optimal (≥95%) confidence for the majority of low season and all of off‐season, yet not throughout the year.


The assessment of data sources for influenza virologic surveillance in New York State
Influenza testing performed during 2013‐2014 by the Wadsworth Center, and NYS regional PHLs. Total number of positives are shown relative to the recommended Flu+ sample sizes determined from the Right Size Roadmap Calculator B for detection of a rare/novel event with 95% confidence and expected prevalence of 30% for high season (1/700 detection threshold), 10% for low season (1/200 detection threshold), and 1% for off‐season (1/4 detection threshold). (The elevated specimen numbers for Wadsworth for weeks ending June 29, April 19, and May 10, are due to one EIP submitter sending backlogged specimens)
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irv12433-fig-0005: Influenza testing performed during 2013‐2014 by the Wadsworth Center, and NYS regional PHLs. Total number of positives are shown relative to the recommended Flu+ sample sizes determined from the Right Size Roadmap Calculator B for detection of a rare/novel event with 95% confidence and expected prevalence of 30% for high season (1/700 detection threshold), 10% for low season (1/200 detection threshold), and 1% for off‐season (1/4 detection threshold). (The elevated specimen numbers for Wadsworth for weeks ending June 29, April 19, and May 10, are due to one EIP submitter sending backlogged specimens)
Mentions: For the detection of a rare/novel influenza virus, Wadsworth test data were compared to recommended sample sizes for NYS, aggregated on a national scale, determined from Calculator B (Figure 5). The total number of Flu+ specimens tested at the Wadsworth Center was insufficient to detect a rare/novel event for influenza surveillance at the recommended confidence levels. To augment detection of a rare/novel influenza virus, NYS regional PHL influenza rtRT‐PCR data supplemented the Wadsworth Center rtRT‐PCR data (Figure 5). From the last week of December 2013 through January 2014 with peak influenza activity, Flu+ data provided 86% to 94% confidence in the likelihood of detecting a novel virus present at 1/700 of cases. During low season, the recommended threshold for detection of a novel virus outside of peak season is 1/200 with a minimum Flu+ sample size of 37; sample sizes with 95% confidence were obtained for 4 of those 6 weeks (Table 2). During off‐season, the recommended threshold drops to ¼ with a minimum Flu+ sample size of 1. In fact, just 1 Flu+ sample is needed every 5 weeks per state, as 11 Flu+ samples are needed per week for 52 states nationally (personal communication, Lynette Brammer, CDC). Sample sizes with 95% confidence were obtained for 40 of 40 off‐season weeks when counting 1 Flu+ every 5 weeks. Thus, to contribute to national surveillance in detecting a rare/novel influenza virus, combined sample sizes from Wadsworth and the regional PHLs were sufficient to reach minimum confidence levels (≥85%) for recommended detection thresholds during peak weeks of influenza activity, and optimal (≥95%) confidence for the majority of low season and all of off‐season, yet not throughout the year.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Following the 2013 USA release of the Influenza Virologic Surveillance Right Size Roadmap, the New York State Department of Health (NYSDOH) embarked on an evaluation of data sources for influenza virologic surveillance.

Objective: To assess NYS data sources, additional to data generated by the state public health laboratory (PHL), which could enhance influenza surveillance at the state and national level.

Methods: Potential sources of laboratory test data for influenza were analyzed for quantity and quality. Computer models, designed to assess sample sizes and the confidence of data for statistical representation of influenza activity, were used to compare PHL test data to results from clinical and commercial laboratories, reported between June 8, 2013 and May 31, 2014.

Results: Sample sizes tested for influenza at the state PHL were sufficient for situational awareness surveillance with optimal confidence levels, only during peak weeks of the influenza season. Influenza data pooled from NYS PHLs and clinical laboratories generated optimal confidence levels for situational awareness throughout the influenza season. For novel influenza virus detection in NYS, combined real‐time (rt) RT‐PCR data from state and regional PHLs achieved ≥85% confidence during peak influenza activity, and ≥95% confidence for most of low season and all of off‐season.

Conclusions: In NYS, combined data from clinical, commercial, and public health laboratories generated optimal influenza surveillance for situational awareness throughout the season. Statistical confidence for novel virus detection, which is reliant on only PHL data, was achieved for most of the year.

No MeSH data available.


Related in: MedlinePlus