Center for Research on Influenza Pathogenesis and Transmission (CRIPT)

Surveillance

The CRIPT 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 better understand interspecies transmission of influenza viruses, rapidly isolate and characterize genotypically, antigenically and phenotypically influenza viruses with increased risk for zoonotic transmission and/or for severe disease, and increase our knowledge on seasonal influenza transmission and disease in humans. Al viruses, reagents, including reverse genetics viruses and plasmids that might serve as the basis of human vaccines, and data generated by the four CRIPT Influenza Surveillance, Risk Assessment and Response Research projects will be made available to the scientific community. Genotypic, phenotypic and meta-data information will be deposited in publicly available databases, such as IRB, though collaboration with the designated iDPCC.

CRIPT Surveillance Sites

CRIPT 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)
  • Poultry in Indonesia and Vietnam (Kawaoka)
  • Wild birds in Argentina and Guatemala (Perez)

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)

Marine mammals

  • Harbor seals/grey seals in Maine (Runstadler)

Human

  • GOTHAM - Genomics of Organisms that Target Health and Affect Medicine at ISMMS, NY Metropolitan area (van Bakel, Simon)
  • H5N1 in Indonesia and Vietnam (Kawaoka, Fouchier)

Environmental

  • Potential environmental reservoirs (Runstadler)

Below are some highlights from our surveillance programs:

World map graphic

  • 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

Image of large group of pigs

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. 

Seals on the beach

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.