Since the late 1800s, the discovery of new viruses was a gradual process. Viruses were described one by one using a suite of techniques such as (electron) microscopy and viral culture. Investigators were usually interested in a disease state within an organism, and expeditions in viral ecology were rare. The advent of metagenomics using high-throughput sequencing has revolutionized not only the rate of virus discovery, but also the nature of the discoveries. For example, the viral ecology and etiology of many human diseases are being characterized, non-pathogenic viral commensals are ubiquitous, and the description of environmental viromes is making progress. This Frontiers in Virology Research Topic showcases how metagenomic and bioinformatic approaches have been combined to discover, classify and characterize novel viruses.

Virology is the branch of microbiology that deals with viruses and viral infections. The overall goal of virus research is understand the action of various viruses and develop vaccines or techniques that are effective at preventing or treating the diseases caused by them. Viruses that affect humans range in severity from the rhinoviruses that cause the "common cold" to the human immune deficiency (HIV) virus that causes AIDS.By their very nature, viruses are highly contagious and therefore affect millions of people, plants, and animals. This field continues to have new discoveries that are important to researchers and clinicians in the field.

Zika virus (ZIKV) is a mosquito-borne member of the Flaviviridae family that historically has been associated with mild febrile illness. However, the recent outbreaks in Brazil in 2015 and its rapid spread throughout South and Central America and the Caribbean, together with its association with severe neurological disorders—including fetal microcephaly and Guillain-Barré syndrome in adults—have changed the historic perspective of ZIKV. Currently, ZIKV is considered an important public health concern that has the potential to affect millions of people worldwide. The significance of ZIKV in human health and the lack of approved vaccines and/or antiviral drugs to combat ZIKV infection have triggered a global effort to develop effective countermeasures to prevent and/or treat ZIKV infection. In this Special Issue of Viruses, we have assembled a collection of 32 research and review articles that cover the more recent advances on ZIKV molecular biology, replication and transmission, virus–host interactions, pathogenesis, epidemiology, vaccine development, antivirals, and viral diagnosis.

The pestiviruses encompass some of the most economically important viral infections in the cattle, swine, and sheep industries worldwide. Discovered more than 70 years ago, bovine viral diarrhea virus (BVDV) and classical swine fever virus (CSFV) were long the main concern, but many new pestiviruses have emerged in recent years, which may also present additional threats to biosecurity and food safety. This issue brings together contributions from multiple disciplines – virology, immunology, veterinary clinical medicine, epidemiology, and pathology – on the subject of BVDV and related pestiviruses, and cover host–virus interactions, virus–cell interactions, cross-species transmission as well as the role of wildlife species as reservoirs of some of the pestiviruses.