Abstract
Emerging and re-emerging RNA viruses pose significant public health, economic, and societal burdens. Hantaviruses (genus Orthohantavirus, family Hantaviridae, order Bunyavirales) are enveloped, negative-sense, single-stranded, tripartite RNA viruses that are emerging zoonotic pathogens harbored by small mammals such as rodents, bats, moles, and shrews. Orthohantavirus infections cause hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome in humans (HCPS). Active targeted surveillance has elucidated high-resolution phylogeographic relationships between patient- and rodent-derived orthohantavirus genome sequences and identified the infection source by temporally and spatially tracking viral genomes. Active surveillance of patients with HFRS entails 1) recovering whole-genome sequences of Hantaan virus (HTNV) using amplicon (multiplex PCR-based) next-generation sequencing, 2) tracing the putative infection site of a patient by administering an epidemiological questionnaire, and 3) collecting HTNV-positive rodents using targeted rodent trapping. Moreover, viral genome tracking has been recently performed to rapidly and precisely characterize an outbreak from the emerging virus. Here, we reviewed genomic epidemiological and active surveillance data for determining the emergence of zoonotic RNA viruses based on viral genomic sequences obtained from patients and natural reservoirs. This review highlights the recent studies on tracking viral genomes for identifying and characterizing emerging viral outbreaks worldwide. We believe that active surveillance is an effective method for identifying rodent-borne orthohantavirus infection sites, and this report provides insights into disease mitigation and preparedness for managing emerging viral outbreaks.
Highlights
Hantaviruses are enveloped, negativesense, single-stranded RNA viruses belonging to the family Hantaviridae and order Bunyavirales (Abudurexiti et al, 2019)
In 2016, genomic surveillance and phylodynamic analyses of Zika virus (ZIKV) genomes from infected patients and Aedes aegypti mosquitoes showed that the Caribbean Islands were the main source of the local ZIKV outbreak in Florida, whereas multiple ZIKV transmissions occurred throughout the Americas (Grubaugh et al, 2017)
We reviewed the active surveillance for emerging hantaviruses by focusing on concurrent genome sequencing, epidemiological data, and targeted rodent trapping (Figure 3 and Box 1)
Summary
Hantaviruses (genus Orthohantavirus) are enveloped, negativesense, single-stranded RNA viruses belonging to the family Hantaviridae and order Bunyavirales (Abudurexiti et al, 2019). We summarize active targeted surveillance developed for emerging hantaviruses by focusing on nextgeneration sequencing (NGS), epidemiological interviews, and targeted rodent trapping. This includes 1) genome tracking using whole-genome sequencing, 2) follow-up of suspected infection sites using patient interview data, and 3) rodent trapping to capture the natural reservoir host.
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