Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde

Abstract

Z ika virus (ZIKV), first discovered in Uganda in 1947 and sporadically found in Africa and Asia, was long believed to only cause mild disease in humans (1). ZIKV isolates are classified into 1 of 2 lineages, representing the African and Asian genotypes. ZIKVs of the African lineage have been isolated from many regions of Africa (2), mostly through entomologic investigations, and serologic evidence suggests that ZIKV infections in humans are frequent (3). However, until the 2000s, the virus had seldom been detected in humans. The Asian lineage has spread throughout the Pacific, causing outbreaks in humans in Yap, Federated States of Micronesia, in 2007 and in French Polynesia during 2013-2014, where an association with neurologic afflictions was first detected (4). Zika cases were first reported in Brazil in May 2015, and from there, the virus quickly spread to most of the Americas (5). The high number of cases led to the discovery of an association between congenital ZIKV infection and neonatal neurologic complications, particularly microcephaly (6,7). In October 2015, an epidemic of rash, conjunctivitis, and arthralgia was noted by physicians in Praia, the capital of Cape Verde, an archipelago nation located in the Atlantic Ocean, west of the coast of Senegal. Blood samples sent to the regional reference laboratory of the Institut Pasteur de Dakar (Dakar, Senegal) confirmed the epidemic involved ZIKV infection. By the end of the outbreak in May 2016, a total of 7,580 suspected Zika cases and 18 microcephaly cases were

Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains

“…Genome sequencing of ZIKV strains. The consensus genome sequences of the seven ZIKV strains of the panel were obtained by high-throughput sequencing 24,92 . Briefly, RNA was extracted from virus stock using QIAamp Viral RNA Mini Kit (Qiagen) and treated with TURBO DNase (Ambion).…”

“…Autochthonous ZIKV transmission was also detected in Angola during the same time period with four confirmed acute Zika cases and several suspected cases of microcephaly. Phylogenetic analyses revealed that the ZIKV strains detected in Cape Verde and Angola belonged to the Asian lineage and were probably independently imported from Brazil 24 , 25 . So far, the African ZIKV lineage has never been detected outside the African continent and never been associated with epidemic transmission, birth defects or neurological disorders 9 , 13 .…”

Enhanced Zika virus susceptibility of globally invasive Aedes aegypti populations

“…aegypti population from Luanda, Angola consisted of a genetic mixture of Aaa and Aaf(6). Possibly, a similar situation could have facilitated the large ZIKV outbreak that occurred in Cape Verde during 2015-2016(42), based on the untested assumption that the local Ae. aegypti population there harbors a large proportion of 'domestic' ancestry similar to the nearby populations of Western Senegal.…”

High transmissibility and fetal pathogenicity of recent Zika virus strains from the African lineage

“…Briefly, RNA was extracted from virus stock using QIAamp Viral RNA Mini Kit (Qiagen) and treated with TURBO DNase (Ambion). The Senegal_2011 and Senegal_2015 strains also underwent depletion of host ribosomal RNA following a homemade protocol 25 . cDNA was produced with random hexameric primers (Roche) using M-MLV (Invitrogen) or Superscript IV (Thermo Fisher Scientific) reverse transcriptase.…”

“…Autochthonous ZIKV transmission was also detected in Angola during the same time period with four confirmed acute Zika cases and several suspected cases of microcephaly. Phylogenetic analyses revealed that the ZIKV strains detected in Cape Verde and Angola belonged to the Asian lineage and were probably independently imported from Brazil 25,26 . So far, the African ZIKV lineage has never been detected outside the African continent and never been associated with epidemic transmission, birth defects or neurological disorders 27 .…”