National Influenza Center – Pathology and Microbiology Department,
University Teaching Hospital, Virology Laboratory
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 follows: below epidemic threshold, low, moderate, high and very high. Transmissibility of influenza can be inferred from ILI data while SARI data gives an indication of severity.
Comments
The 2019 season started in between weeks 4- 18 (4th – 1st week of January/May), when the rates of Influenza-Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) attributable to influenza virus infection was within the low seasonal threshold. The epidemic threshold rose from low to within moderate transmissibility in week 13 -14 and maintained the low severity until week 18 (1th week of May). There appear to be experiencing the first cycle of activity which is currently in the below the threshold in week 21.
ILI Surveillance:
As at 31st May 2019, week 21. Specimens from 411 outpatients were received from two ILI surveillance sites. 378 were adequately sampled and tested. Influenza virus was detected in 32 of these samples; 24 were identified as Influenza B, 3 Influenza A H3N2, 3 Influenza A H1N1 and 2 as Influenza A Unsubtypable.
SARI Surveillance:
During this same period, specimens were received from 766 patients admitted to four SARI surveillance sites. 512 were adequately sampled and tested. Influenza was detected in 20 specimens; 16 of which were identified as Influenza B, 1 as Influenza A H3N2, 1 as Influenza A H1N1 and 2 as Influenza A Unsubtypable.
31st May 2019: Influenza Transmissibility
Fig 1: Out-Patient Clinic Visit Surveillance1 – (ILI Surveillance) for Influenza Detection and Epidemic Thresholds
1ILI Case / Total ILI Sampled *100
*Threshold based on 2013 – 2018
In April – May 2019, ILI outpatient visits attributable to influenza virus infection from weeks 14-19 fell within low to below epidemic levels of transmissibility throughout the month.
31st May 2019: Influenza Severity (Impact)
Fig 2: Hospital Admission Surveillance1 – (SARI Surveillance) for Influenza Detection and Epidemic Thresholds *
1 SARI Case / Total Admission Sampled *100
*Threshold based on 2013 – 2018
In April – May 2019, SARI admissions attributable to influenza virus infection from weeks 14 -21, fell from low to below the threshold for high severity.
Fig 3: Positives samples* by influenza types and detection rate by weeks in 2019.
*Specimens from patients with influenza-like illness at two (2) sentinel sites and three (3) sentinel sites for admitted patients from
week 1 -20. The 2019 influenza season is currently characterized by spread of seasonal influenza and random detection of flu A,
A H1N1 and subtypes A H3N2 in weeks, 1 – 13. A high number of seasonal influenza was detected between weeks 7-18 from all
sentinel sites.
A high number of seasonal and pandemic A influenza detections was in the age group between 1 – 4 years.
Fig: 4: Cumulative number of influenza types and subtypes and total number of samples tested by sentinel sites.
The total samples collected as at 31st May 2019, are 1177; 1069(91%) have been tested. 73 (7%), are positive for influenza virus and 996 (93%) negative. Two (2) samples were rejected.