National Influenza Center – Pathology and Microbiology Department, University Teaching Hospital, Virology Laboratory

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Methodology for Establishment of Epidemic Thresholds
Thresholds are calculated using Moving Epidemic Methods (MEM), a sequential analysis using R language available from: http// =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 third quarter of 2019 between epi-weeks 27 and 34. Rates of Influenza-Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) attributable to influenza virus infection were within the moderate – high threshold and remained within the low seasonal threshold in week 39. This second cycle of activity was of a moderate transmissibility and high severity. Children below five years of age were most affected.

ILI Surveillance:
Specimens from 749 outpatients were received from two ILI surveillance sites. 637 (85%) were adequately sampled and tested. Influenza virus was detected in 89 (14%) of these samples of which, 58 (65%) were identified as Influenza B, 6 (7%) Influenza A H3N2, 11(12%) Influenza A H1N1 (pandemic), 7 (8%) influenza A Untyped and 4(4%) as Influenza A unsubtypeable.

SARI Surveillance:
During this same period, specimens were received from 1390 patients admitted to four SARI surveillance sites. 854 (61%) were adequately sampled and tested. Influenza was detected in 114 (13%) specimens; 80 (70%) of which were identified as Influenza B, 1 as Influenza A H3N2 (1%), 5 (4%) as Influenza A H1N1 (pandemic), 25(22%) influenza A Untyped and 3(3%) as Influenza A unsubtypeable.

Influenza Transmissibility
Fig 1: Percentage of Influenza Positive ILI Cases1 (Out-Patient Visit Surveillance) per Epi-Week Against Epidemic Thresholds Set Using 2013 – 2018 Data

1ILI Case / Total ILI Sampled *100
In September 2019, ILI outpatient visits attributable to influenza virus infection were below epidemic threshold between weeks 35 and 39.

Influenza Severity (Impact)
Fig 2: Percentage of Influenza Positive SARI Cases1 (Hospital Admission Surveillance) per Epi-Week against Epidemic Thresh

SARI Influenza Positive Cases / Total Admissions Sampled *100
In September 2019, all SARI admission attributable to influenza virus infection declined to below epidemic threshold in week 35 but has remained in low epidemic threshold from week 35 to week 30

Fig 3: Positives samples* by influenza type and detection rate** by epi-week in 2019.

Influenza viruses circulating in the 3rd quarter of 2019 were predominantly influenza B. There was also random detection of influenza A. Among the influenza A viruses that have been subtyped, H1N1 (Pandemic) and H3N2 were seen in weeks 26 -32. Most viruses were detected between weeks 5 and 33.

The virus circulation was greater at either end of the age spectrum but the most affected age groups were the under-fives.

Fig: 5: Cumulative number of influenza types and subtypes and total number of samples tested by sentinel sites.

The total number of samples collected as at 30th September 2019, is 2139; 1822(85%) were tested. 203 (11%), were positive for influenza virus and 1619 (89%) were negative.