Genetic Data Provide Evidence for Wind-Mediated Transmission of Highly Pathogenic Avian Influenza

Abstract

Outbreaks of highly pathogenic avian influenza in poultry can cause severe economic damage and represent a public health threat. Development of efficient containment measures requires an understanding of how these influenza viruses are transmitted between farms. However, the actual mechanisms of interfarm transmission are largely unknown. Dispersal of infectious material by wind has been suggested, but never demonstrated, as a possible cause of transmission between farms. Here we provide statistical evidence that the direction of spread of avian influenza A(H7N7) is correlated with the direction of wind at date of infection. Using detailed genetic and epidemiological data, we found the direction of spread by reconstructing the transmission tree for a large outbreak in the Netherlands in 2003. We conservatively estimate the contribution of a possible wind-mediated mechanism to the total amount of spread during this outbreak to be around 18%.

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

“…We finally applied the method to five published datasets on outbreaks of Mycobacterium tuberculosis (Mtb, [7]), Methicillin-resistant Staphylococcus aureus (MRSA, [25]), Foot-and-mouth disease (FMD2001 and FMD2007, [9, 11, 26, 27]), and H7N7 avian influenza (H7N7, [12, 28–30]).…”

The role of pathogen genomics in assessing disease transmission

“…Human influenza virus A H7/N9, [33][34][35] MERS-coronavirus, 36 Staphylococcus aureus, 37 38 Salmonella typhimurium, 39 Streptococcus pneumoniae, 28 40 Enterococcus spp 41 Pathogen risk assessment Identification of targets for assays differentiating highly virulent pathogen strains Influenza virus H5/N1, 22 23 Chlamydia trachomatis 42 43 Distinguishing recent from pre-existing (chronic) infection Mycobacterium tuberculosis 44 45 Redefining periods of transmissibility MRSA, 46 group A streptococcus 47 Detection, monitoring, and control of hospital acquired outbreaks Identification of new clones associated with hospital acquired pathogens Acinetobacter baumannii, 48 49 S aureus, 50 Escherichia coli, 51 52 Pseudomonas aeruginosa 53 Near real time identification of transmission events (patient to patient, healthcare staff to patient, environment to patient)* S aureus, [53][54][55][56][57][58][59] Clostridium difficile, 53-55 60 Klebsiella pneumoniae 61 Monitoring transmission and (antimicrobial resistance) gene flow between healthcare institutions C difficile, 56 S aureus, 62 HIV, 63 norovirus, 64 human influenza virus 65 Improved resolution of regional, national, and global public health laboratory surveillance Detection of outbreaks, covert clusters, and associated risk factors Neisseria meningitidis, 66 Salmonella enterica, 67 enterohaemorrhagic E coli, 51 68 M tuberculosis 4 69 70 Reconstruction of outbreak origins, transmission pathways and dating of transmission events within community outbreaks (person to person contact, water and food borne modes of direct transmission)* Ebola virus, 71 enterovirus, 72 Vibrio cholerae, 73 74 Mycobacterium tuberculosis, 4 46 75-78 g...…”

Transmission tree of the highly pathogenic avian influenza (H5N1) epidemic in Israel, 2015

“…For all infected farms, the location, the date when increased mortality was reported, the date when samples were taken for laboratory confirmation and the date when cleaning and disinfection ended were recorded. Actual dates of infection were unknown and were therefore treated as model parameters to be estimated [1]. In each infected farm, a single virus strain was isolated and its full hemagglutinin gene was sequenced [2].…”

“…It has already been used to model the spread of several animal pathogens, including highly pathogenic avian influenza virus [1, 3] and foot-and-mouth disease virus [4]. This approach assumes that all cases were reported and that there was only one virus introduction in the study area: except for the index case that had been infected by an unknown source, all successive cases were infected by one of the seven other infected farms through an unknown route.…”