Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation

Abstract

Background: Zika virus infections and suspected microcephaly cases have been reported in Angola since late 2016, but no data are available about the origins, epidemiology, and diversity of the virus. We aimed to investigate the emergence and circulation of Zika virus in Angola.

Methods: Diagnostic samples collected by the Angolan Ministry of Health as part of routine arboviral surveillance were tested by real-time reverse transcription PCR by the Instituto Nacional de Investigação em Saúde (Ministry of Health, Luanda, Angola). To identify further samples positive for Zika virus and appropriate for genomic sequencing, we also tested samples from a 2017 study of people with HIV in Luanda. Portable sequencing was used to generate Angolan Zika virus genome sequences from three people positive for Zika virus infection by real-time reverse transcription PCR, including one neonate with microcephaly. Genetic and mobility data were analysed to investigate the date of introduction and geographical origin of Zika virus in Angola. Brain CT and MRI, and serological assays were done on a child with microcephaly to confirm microcephaly and assess previous Zika virus infection.

Findings: Serum samples from 54 people with suspected acute Zika virus infection, 76 infants with suspected microcephaly, 24 mothers of infants with suspected microcephaly, 336 patients with suspected dengue virus or chikungunya virus infection, and 349 samples from the HIV study were tested by real-time reverse transcription PCR. Four cases identified between December, 2016, and June, 2017, tested positive for Zika virus. Analyses of viral genomic and human mobility data suggest that Zika virus was probably introduced to Angola from Brazil between July, 2015, and June, 2016. This introduction probably initiated local circulation of Zika virus in Angola that continued until at least June, 2017. The infant with microcephaly in whom CT and MRI were done had brain abnormalities consistent with congenital Zika syndrome and serological evidence for Zika virus infection.

Interpretation: Our analyses show that autochthonous transmission of the Asian lineage of Zika virus has taken place in Africa. Zika virus surveillance and surveillance of associated cases of microcephaly throughout the continent is crucial.

Funding: Royal Society, Wellcome Trust, Global Challenges Research Fund (UK Research and Innovation), Africa Oxford, John Fell Fund, Oxford Martin School, European Research Council, Departamento de Ciência e Tecnologia/Ministério da Saúde/National Council for Scientific and Technological Development, and Ministério da Educação/Coordenação de Aperfeicoamento de Pessoal de Nível Superior.

Figure 1

Confirmed Angola-associated cases of Zika virus infection Cases in travellers from Angola identified elsewhere are shown above the line,, , whereas locally identified cases are shown below the line. Dates and locations in bold are the data and place of birth for the girls with microcephaly, and the date and location of sampling for other cases. Cycle threshold values for cases confirmed by real-time RT-PCR are also shown. RT-PCR=reverse transcription PCR.

Figure 2

Spatial distribution of suspected cases of acute Zika virus infection and microcephaly (A) and dates of suspected cases of microcephaly (B) in Angola (B) Dates of birth, rather than report dates, are shown, so only infants for whom the date of birth was recorded were included (73 [96%] of 76 cases). Arrows mark the month of birth of the two cases of microcephaly independently identified and confirmed in Brazil (August, 2017), and Portugal (October, 2017). Orange dots on the horizontal axis show the sampling dates of the four cases of Zika virus infection that were confirmed by real-time RT-PCR in patients who did not have microcephaly. RT-PCR=reverse transcription PCR.

Figure 3

Phylogenetic analysis of the introduction of Zika virus to Angola (A) Maximum clade credibility phylogeny, estimated from complete and near-complete Zika virus genomes with a molecular clock phylogenetic approach. Branch colours indicate the most parsimonious locations of ancestral lineages. Triangular clades represent larger groups of sequences that have been collapsed for visual clarity. (B) Expansion of the clade containing the Angolan Zika virus (red) and closely related sequences from the Americas (blue and yellow). Clade posterior probabilities are shown at well supported nodes.

Figure 4

Factors affecting the likelihood of introduction of Asian lineage Zika virus to Angola The 11 countries shown are those with the seven highest median passenger numbers and number of cases of Zika virus per person. Error bars show the IQRs.

Figure 5

Brain CT and MRI scans of an Angolan child with microcephaly (A) Compensatory ventriculomegaly and calcification areas in the subcortical region are shown by green arrows. In (B) and (C), calcification in the basal ganglia is shown by the green arrows. (D) Brainstem hypoplasia. (E) Dysgenesis of the cerebellum. (F) Pachygyria.