Virus genomes reveal the establishment of Zika virus in Brazil and the Americas, and provide an appropriate timeframe for baseline (pre-Zika) microcephaly in different regions. Three papers in this issue present a wealth of new Zika virus (ZIKV) genome sequences and further insights into the genetic epidemiology of ZIKV. Nathan Grubaugh et al. provide 39 new ZIKV genome sequences from infected patients and Aedes aegypti mosquitoes in Florida. Phylogenetic analysis suggests that the virus has been introduced on multiple separate occasions, probably linked to travel from the Caribbean. They find a low probability of long-term persistence of ZIKV transmission chains within Florida, suggesting that the potential for future ZIKV outbreaks there will depend on transmission dynamics in the Americas. Nuno Faria et al. and Hayden Metsky et al. reconstruct the spread of ZIKV in Brazil and the Americas. Faria et al. provide 54 new ZIKV genomes, several sequenced in real time in a mobile genomics laboratory. They trace the spatial origins and spread of ZIKV in Brazil and the Americas and date the timing of the international spread of ZIKV from Brazil. They find that northeast Brazil had a crucial role in the establishment of the epidemic and the spread of the virus within Brazil and the Americas. Metsky et al. generate 110 ZIKV genomes from clinical and mosquito samples from ten regions. They also see rapid expansion of the epidemic within Brazil and multiple introductions to other geographic areas. In agreement with Faria et al., they find that ZIKV circulated unobserved for many months before transmission was detected. Metsky et al. additionally describe ZIKV evolution and discuss how the accumulation of mutations might affect the performance of diagnostic tests in the future. Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil1. Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 20162) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 20162). Since the initial detection of ZIKV in Brazil, more than 45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting severe ZIKV-associated disease3. However, the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly. Here we address this issue by generating 54 complete or partial ZIKV genomes, mostly from Brazil, and reporting data generated by a mobile genomics laboratory that travelled across northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Analyses of viral genomes with ecological and epidemiological data yield an estimate that ZIKV was present in northeast Brazil by February 2014 and is likely to have disseminated from there, nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates for the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. The role of northeast Brazil in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the basic reproduction number of the virus.

Summary: Proteins with bacterial immunoglobulin‐like (Big) domains, such as the Yersinia pseudotuberculosis invasin and Escherichia coli intimin, are surface‐expressed proteins that mediate host mammalian cell invasion or attachment. Here, we report the identification and characterization of a new family of Big domain proteins, referred to as Lig (leptospiral Ig‐like) proteins, in pathogenic Leptospira. Screening of L. interrogans and L. kirschneri expression libraries with sera from leptospirosis patients identified 13 lambda phage clones that encode tandem repeats of the 90 amino acid Big domain. Two lig genes, designated ligA and ligB, and one pseudogene, ligC, were identified. The ligA and ligB genes encode amino‐terminal lipoprotein signal peptides followed by 10 or 11 Big domain repeats and, in the case of ligB, a unique carboxy‐terminal non‐repeat domain. The organization of ligC is similar to that of ligB but contains mutations that disrupt the reading frame. The lig sequences are present in pathogenic but not saprophytic Leptospira species. LigA and LigB are expressed by a variety of virulent leptospiral strains. Loss of Lig protein and RNA transcript expression is correlated with the observed loss of virulence during culture attenuation of pathogenic strains. High‐pressure freeze substitution followed by immunocytochemical electron microscopy confirmed that the Lig proteins were localized to the bacterial surface. Immunoblot studies with patient sera found that the Lig proteins are a major antigen recognized during the acute host infection. These observations demonstrate that the Lig proteins are a newly identified surface protein of pathogenic Leptospira, which by analogy to other bacterial immunoglobulin superfamily virulence factors, may play a role in host cell attachment and invasion during leptospiral pathogenesis.

Zika virus (ZIKV) is an emerging flavivirus, which has caused a widespread outbreak in the Americas. Shortly after its introduction in 2015, a cluster of cases with Guillain–Barré syndrome was detected in Brazil. Herein, we describe two cases from the city of Salvador, who developed ascending paresis after an acute exanthematous illness. The patients were admitted to the intensive care unit with tetraparesis and cranial nerve palsy, which resolved after intravenous administration of human immunoglobulin. Serological evaluation detected IgM-specific ZIKV antibodies. In regions of Zika virus transmission, health-care workers must be aware of the potential severe neurological complications associated with ZIKV infection and be prepared to provide prompt diagnosis, treatment, and supportive care.

In recent years, an increasing number of outbreaks of Dengue, Chikungunya and Zika viruses have been reported in Asia and the Americas. Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks, both aspects that are vital to develop effective prevention and treatment strategies. Hence, we developed an efficient method to classify virus sequences with respect to their species and sub-species (i.e. serotype and/or genotype). This ArboTyping tool provides an easy-to-use software implementation of this new method and was validated on a large dataset assessing the classification performance with respect to whole-genome sequences and partial-genome sequences. Available online: http://krisp.ukzn.ac.za/app/. Dengue (DENV), Chikungunya (CHIKV) and Zika (ZIKV) are considered major public health challenges. In addition to the epidemic caused by DENV, which has been described in many tropical countries, the introduction of CHIKV and ZIKV in these countries is a major public health concern. These arboviruses are primarily transmitted by mosquitoes of the species Ae. Aegypti and its related diseases result in increased financial costs associated with diagnosis and treatment. To support the design of efficient diagnosis, prevention and treatment strategies, a bioinformatics tool has been developed for the genotyping of these viruses based on appropriate evolutionary models in an automatic, accurate and rapid manner. A set of virus reference sequences was obtained from GenBank and used for the development of the tools. This process involved the alignment of the reference sequences followed by phylogenetic tree reconstructions. To assign the genotypes uploaded by the user, the tool analyses the sequences one by one, genotypes through identification, alignment and phylogenetic reconstruction. This computational method allows the high-throughput classification of these virus species and genotypes in seconds. As shown experimentally, genotypes are classified most confidently using the envelope gene or complete genome sequences.

Several months after the introduction of Zika virus into northeastern Brazil, obstetricians noticed an increased number of fetuses with congenital malformations during ultrasound screening. Microce...

Neurodevelopment in 29 normocephalic children with in utero exposure to Zika virus (ZIKV) was evaluated by the Bayley Scales of Infant and Toddler Development-Third Edition. Ten (35%) infants presented neurodevelopment delay. Language, cognitive and motor delays were identified in 9 (31%), 4 (14%) and 1 (3%) infants, respectively. Children exposed to ZIKV in utero must undergo careful evaluations for the early detection of any neurodevelopment delays in order to implement prompt intervention.