Center for Research on Influenza Pathogenesis

Surveillance

The CRIP surveillance team uses sample collection from a variety of avian and mammalian species for the identification and characterization of emerging influenza viruses. This domestic and international network integrates data to answer research questions relating to the emergence and evolution of influenza viruses in nature.

Our surveillance has several goals, including improving our understanding of the evolution of influenza viruses in their natural reservoir, upon zoonotic transmission, and during epidemic circulation. We also seek to understand how host biology and ecology affects virus epidemiology and evolution. CRIP is also working to develop predictive models describing the epidemiology of influenza in wild birds and marine mammals. We aim to provide skills, expertise, and knowledge for risk assessment and to assist during outbreaks.

Crip Surveillance Sites

CRIP surveillance network is a worldwide effort by the following investigators to collect both environmental samples and those from species such as human, avian, swine, and marine mammals.

Avian

  • Poultry/wild birds in Georgia (Fouchier, Lewis)
  • Wild birds in Australia (Fouchier)
  • Poultry in Indonesia and Vietnam (Kawaoka)
  • Wild birds in Chile (Medina)
  • Wild birds in Argentina and Guatemala (Perez, Pereda, and Cordon-Rosales)
  • Gulls/shore birds in Alaska (Runstadler)

Swine

  • Pigs in Indonesia and Vietnam (Kawaoka)
  • Pigs in Chile (Medina)
  • Iberian pigs/wild boars in Spain (Real-Soldevilla)
  • Swine in Argentina and Guatemala (Perez, Pereda, and Cordon-Rosales)

Marine mammals

  • Elephant seals/harbor seals/sea lions in California (Boyce)
  • Harbor seals/grey seals in Maine (Runstadler)

Human

  • H5N1 in Indonesia and Vietnam (Kawaoka, Fouchier)

Environmental

  • Potential environmental reservoirs (Runstadler)

Below are some highlights from our surveillance programs:

  • We have collected 20,000 wild bird surveillance samples from the Netherlands and the Republic of Georgia. Whole genome sequences analyses from Georgia show a very strong host-specific pattern of virus tropism in wild birds despite co-mixing within the same ecosystem.

  • We detected:

    • H14 in Guatemala at a higher-than-expected frequency in recent years
    • IAV in flamingos and H13 in migratory gulls in Chile
    • LPAIV H5N5 subtype in an Antarctic penguin containing North American and Eurasian genes
    • Rare viruses including H8N4, H12N4, and H5N2 in a longitudinal study of wintering mallards in Alaska
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  • We intensidied surveillance for HPAI H5 in the Netherlands and Alaska, and identified precursors to the emergence of HPAI, H5N2, and H5N8

We have taken 24,000 surveillance samples of swine from North and South America, Europe, and Asia. In many of these sites, we detected new subtypes including H1N1, pdmH1N1, H3N2, and a novel H1N2 from Chile. Novel reassortants and new human seasonal influenza introductions have been detected at many sites. We have also characterized the antigenic diversity of swine influenza on a multi-continental scale. The substantial diversity of recently circulating viruses in different parts of the world adds complexity to the risk profiles for the movement of swine and the potential for swine-derived infections in humans. 

Sampling of Northwest Atlantic grey seals demonstrated they are both permissive to and tolerant of diverse IAV–possibly representing an endemically infected wild reservoir population. Opportunistic sampling identified IAV exposure in a number of other marine mammal species. Characterization of the European seal H10N7 virus revealed that it is airborne transmissible.