Overview
Influenza: molecular epidemiology of seasonal influenza in South Africa
Both influenza A and B viruses cause influenza epidemics almost annually in many parts of the world with high mortality and morbidity. The epidemics are the result of frequently occurring point mutations that occur in the viral surface haemagglutinin (HA) and neuraminidase (NA) proteins, which allow these viruses to escape existing immunity to previously circulating influenza viruses in an individual and in the population. Through this process of antigenic drift, new variants evolve in humans throughout the world, causing epidemics almost every year. The subtypes of influenza A that have been circulating globally in humans in recent years are the H1N1 and H3N2 viruses, while two distinct lineages of influenza B virus have also circulated since the late 1980s.
The influenza laboratories at NICD are one of the WHO National Influenza centres and as such are tasked with monitoring the drift of influenza viruses circulating in South Africa during each season relative to the vaccine strains. This is determined by sequencing the HA1 subunit of the haemagglutinin gene of representative virus isolates. Changes in the neuraminidase gene of a number of the influenza A viruses are also monitored. Phylogenetic analysis is performed to examine the evolutionary relationships between the South African strains and influenza viruses isolated in recent years in this country as well as in other parts of the world.
Pandemic influenza
In addition to the annual outbreaks of disease, influenza A viruses have been responsible for several human pandemics in recent history. Pandemics occur due to an abrupt major change in the viruses, resulting in new HA and/or new HA and NA proteins not present in the previously circulating human influenza viruses. This antigenic shift results in a novel influenza A subtype with most people having little or no protection, and subsequent high morbidity in millions of individuals and a high level of mortality worldwide.
The recent outbreaks of highly pathogenic H5N1 avian influenza in South East Asia and other countries pose a pandemic threat should the H5N1 virus mutate to transmit easily from human to human. As a result of this increased pandemic threat, the role of the NICD influenza laboratories has now expanded to include pandemic planning for laboratory diagnosis of avian influenza infections in humans.
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