National Influenza Center – Pathology and Microbiology Department,
University Teaching Hospital, Virology Laboratory
Methodology for Establishment of Epidemic Thresholds
Thresholds are calculated using Moving Epidemic Methods (MEM), a sequential analysis using R language available from: http//CRAN.R-project.org/web/package =mem) designed to calculate the duration, start and end of the annual influenza epidemic. MEM uses the 40th, 90th and 97.5th percentile established from available years of historical data to calculate threshold activities. Threshold activity for influenza is categorized as: below epidemic threshold, low, moderate, high or very high. Transmissibility of influenza can be inferred from ILI data while SARI data gives an indication of severity.
There was increased influenza activity in the first half of 2019 between epi-weeks 4 and 22. Rates of Influenza-Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) attributable to influenza virus infection remained within the low seasonal threshold. This first cycle of activity was of low transmissibility and low severity. Children below five years of age were most affected.
Specimens from 553 outpatients were received from two ILI surveillance sites. 455 (82%) were adequately sampled and tested. Influenza virus was detected in 37 of these samples of which, 27 were identified as Influenza B, 3 Influenza A H3N2, 3 Influenza A H1N1 (pandemic) and 4 as Influenza A unsubtypeable.
During this same period, specimens were received from 1055 patients admitted to four SARI surveillance sites. 651 (62%) were adequately sampled and tested. Influenza was detected in 29 specimens; 24 of which were identified as Influenza B, 1 as Influenza A H3N2, 1 as Influenza A H1N1 (pandemic) and 3 as Influenza A unsubtypeable.
Fig 1: Percentage of Influenza Positive ILI Cases1 (Out-Patient Visit Surveillance) per Epi-Week Against Epidemic Thresholds Set Using 2013 – 2018 Data
30th June 2019: Influenza Severity (Impact)
Fig 2: Hospital Admission Surveillance1 – (SARI Surveillance) for Influenza Detection and Epidemic Thresholds *
Fig 3: Positives samples* by influenza types and detection rate by weeks in 2019.
Fig: 5: Cumulative number of influenza types and subtypes and total number of samples tested by sentinel sites.