Epidemiology and viral etiology of the influenza-like illness in corsica during the 2012-2013 Winter: an analysis of several sentinel surveillance systems

Abstract

Influenza-like illness (ILI) surveillance is important to identify circulating and emerging/reemerging strains and unusual epidemiological trends. The present study aimed to give an accurate picture of the 2012-2013 ILI outbreak in Corsica by combining data from several surveillance systems: general practice, emergency general practice, hospital emergency units, intensive care units, and nursing homes. Twenty-eight respiratory viruses were retrospectively investigated from patients in general practice with ILI. Sequence analysis of the genetic changes in the hemagglutinin gene of influenza viruses (A(H1N1)pdm2009, A(H3N2) and B) was performed. The trends in ILI/influenza consultation rates and the relative illness ratios (RIRs) of having an ILI consultation were estimated by age group for the different surveillance systems analyzed. Of the 182 ILI patients enrolled by general practitioners, 57.7% tested positive for influenza viruses. Phylogenetic analyses suggested a genetic drift for influenza B and A(H3N2) viruses. The ILI/influenza surveillance systems showed similar trends and were well correlated. In accordance with virological data, the RIRs of having an ILI consultation were highest among the young (<15 years old) and decreased with age. No clusters of acute respiratory illness were declared by the sentinel nursing homes. This study is noteworthy in that it is the first extensive description of the 2012-2013 ILI outbreak in Corsica as monitored through several surveillance systems. To improve ILI surveillance in Corsica, a consortium that links together the complementary regional surveillance ILI systems described here is being implemented.

Figure 1. Distribution of influenza-like illness surveillance networks in Corsica.

Figure 2. Temporal distribution of influenza-like illness (ILI) consultation rates from November 2012 (week 46) to April 2013 (week 14) by surveillance networks in Corsica.

From top to bottom, (1) Weekly rates (black line) of J09 to J11 diagnostics estimated over the totality of number of visits coded per week at hospital emergencies (OSCOUR network), (2) Weekly rates (black line) of R80 Influenza/R80 ILI diagnostics estimated over the totality of number of visits coded per week by GPs of the emergency general practice network (SOS Médecins). (3) ILI incidence rates (grey line) per 100 000 inhabitants and weekly distribution of ILI samples positives (histogram bars) to at least one respiratory viruses analyzed (GPs of the Corsican Sentinelles network). (4) ILI incidence rates (black line) per 100 000 inhabitants (GPs of the French Sentinelles network) and epidemic threshold (red dotted line) calculated by a periodic regression on model applied to the former observed data (Serfling'method) .

Figure 3. Relative Illness Ratio (RIR) by age-group for the 2012–2013 epidemic (black line) and 95% confidence intervals (CIs) (dotted line) by surveillance ILI network: (a) Corsican Sentinelles network; (b) SOS Médecins and (c) OSCOUR network.

Figure 4. Evolutionary relationship of A(H1N1)pdm2009 influenza viruses sampled in Corsica during the 2012–2013 influenza like-illness outbreak.

The evolutionary history was inferred using the Neighbor-Joining method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The analysis involved 79 sequences.

Figure 5. Evolutionary relationship of A(H3N2) influenza viruses sampled in Corsica during the 2012–2013 influenza like-illness outbreak.

The evolutionary history was inferred using the Neighbor-Joining method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The analysis involved 50 sequences.

Figure 6. Evolutionary relationship of B influenza viruses sampled in Corsica during the 2012–2013 influenza like-illness outbreak.

The evolutionary history was inferred using the Neighbor-Joining method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The analysis involved 75 sequences.