Surveillance for zoonotic viruses in human population at the human-animal interface in North Sulawesi, Indonesia

For the past decades, novel, emerging and re-emerging zoonotic diseases have been identified with the potential to cause pandemics. Our study aims at detecting viruses that circulate in people who have close contact with animals including wildlife, poultry and companion animals in North Sulawesi, Indonesia to better characterize viruses and zoonotic disease transmission. This study was conducted at one hospital and one primary health center in the Minahasa Regency, North Sulawesi, Indonesia from November 2017 to December 2018. We enrolled syndromic patients exhibiting symptoms of respiratory illness (including severe acute respiratory illness), or fever of unknown origin. Questionnaires and biological specimens, including respiratory and blood-derived samples, were collected. Specimens were then tested using consensus PCR followed by sequencing for nine viral families/genera with pandemic potential or endemic significance. A total of 217 patients were enrolled, of whom 63 (29%) tested positive for at least one of the viral families screened. The detected viruses included Influenza virus (n = 21, 9.6%), Flavivirus (n = 15, 6.9%), Pneumovirus (n = 14, 6.4%), Enteroviruses (n = 10, 4.6%), Paramyxovirus (n = 2, 0.9%) and Coronavirus (n = 1, 0.5%). None of the filovirus, hantavirus, or henipavirus detected in this study. 32% and 22% of patients with positive viral detection had contact with rodents and bats, respectively, primarily through the preparation or cooking of wild meat. Our study provides proof-of-concept for integrating zoonotic virus screening among symptomatic patients with assessments of human-animal contact within a clinical setting.