| Domain | Specific phenotype (suggested HPO term) | Quantitative estimate(s) | Population / study type | Notes | Supporting citation IDs |
|---|---|---:|---|---|---|
| CNS | Microcephaly (HP:0000252) | ~4% absolute risk of microcephaly after confirmed maternal ZIKV infection; baseline pre-epidemic microcephaly ~2.0/10,000 newborns | Brazil meta-analysis/review summarized in 2024 update | Signature phenotype; risk estimate refers to infected pregnancies/offspring follow-up | (pqac-00000002, pqac-00000014) |
| CNS | Severe microcephaly (HP:0011451) | 384/601 (63.9%) among children with microcephaly at birth; moderate 217/601 (36.1%) | IPD meta-analysis of 12 Brazilian cohorts, n=843 children with Zika-related microcephaly | Captures severity distribution among those already affected | (pqac-00000006) |
| CNS | Postnatal microcephaly (HP:0000252) | 172/843 (20.4%) | IPD meta-analysis of 12 Brazilian cohorts | Highlights progression after birth in some exposed infants | (pqac-00000006) |
| Neuroimaging | Intracranial calcifications (HP:0002514) | ~80% across pooled Brazilian cohorts; 94% in systematic clinicopathologic review | IPD meta-analysis; systematic review of Brazilian outbreak cohorts | One of the most consistent structural markers of severe CZS | (pqac-00000006, pqac-00000001, pqac-00000023) |
| Neuroimaging | Ventriculomegaly (HP:0002119) | ~80% across pooled cohorts; 89% in systematic clinicopathologic review | IPD meta-analysis; systematic review | Often co-occurs with calcifications and cortical atrophy | (pqac-00000006, pqac-00000001, pqac-00000023) |
| Neuroimaging | Cortical atrophy / reduced cerebral parenchyma (HP:0007373, HP:0002059) | ~50% cortical atrophy/developmental disorders across pooled cohorts; reduced cerebral parenchyma 86%; malformation of cortical development/lack of gyri 78% | IPD meta-analysis; systematic review | Marks severe prenatal brain disruption | (pqac-00000006, pqac-00000001, pqac-00000023) |
| CNS | Neurological alteration of any type | 18.7% | Zika Brazilian Cohorts pooled pregnancy/child follow-up | Broader than microcephaly alone | (pqac-00000020) |
| CNS | Any abnormality after antenatal exposure | 24.7% had ≥1 alteration | Zika Brazilian Cohorts pooled pregnancy/child follow-up | Includes isolated abnormalities; not restricted to classic CZS | (pqac-00000020) |
| CNS | Epilepsy / seizures (HP:0001250) | 37.7%–71.4% in reviewed cohorts; 71.4% cumulative incidence within 2 years in one microcephaly cohort; 30%–80% across 12-cohort IPD; 91% in clinicopathologic review | Brazil cohorts, systematic reviews, IPD meta-analysis | Often early-onset; epileptic spasms may begin after 3 months | (pqac-00000003, pqac-00000006, pqac-00000023) |
| Ocular | Ocular abnormalities overall (HP:0000478) | 21.4%–70%; about one-third in one multisite Brazilian study | Brazil cohorts/review | Some affected infants had ocular findings without microcephaly | (pqac-00000003) |
| Ocular | Fundus abnormalities (HP:0000580) | 0%–67.1% | IPD meta-analysis of 12 Brazilian cohorts | Wide heterogeneity across sites | (pqac-00000006) |
| Ocular | Optic nerve abnormalities (HP:0001138) | 0%–36.5% across cohorts; 67% in systematic clinicopathologic review | IPD meta-analysis; systematic review | Includes optic nerve pallor/atrophy | (pqac-00000006, pqac-00000023) |
| Ocular | Retinal lesions / chorioretinal atrophy/scarring (HP:0000556, HP:0007703) | 79% retinal lesions in systematic review; examples: chorioretinal atrophy 11/17 eyes (64.7%), macular chorioretinal atrophy/scarring 45.8% | Systematic review; outbreak case series summarized in review | Major cause of visual impairment | (pqac-00000023, pqac-00000007) |
| Auditory | Hearing abnormality (HP:0000365) | 0%–50% across cohorts; ~20% in systematic clinicopathologic review | IPD meta-analysis; systematic review | Conductive or sensorineural deficits reported | (pqac-00000006, pqac-00000005, pqac-00000023) |
| Musculoskeletal | Arthrogryposis / congenital contractures (HP:0002804, HP:0001371) | ~15% in systematic review; 19.0% (n=4) in one summarized series | Systematic review; case series summarized in review | Commonly associated with severe CNS disease and hypertonia | (pqac-00000023, pqac-00000007) |
| Musculoskeletal | Hypertonia / spasticity (HP:0001276, HP:0001257) | Hypertonia up to 92%; spasms/spasticity 97%; appendicular hypertonia 94.8% in one series | Systematic review; summarized cohorts | Major contributor to cerebral palsy phenotype | (pqac-00000023, pqac-00000007) |
| Musculoskeletal | Quadriparesis / severe motor impairment (HP:0002510, HP:0001270) | Quadriparesis 92%; one cohort reported 81% severe motor function impairment | Systematic review; Brazil cohort review | Usually evident in infancy/early childhood | (pqac-00000001, pqac-00000020, pqac-00000023) |
| Feeding-Growth | Dysphagia / swallowing dysfunction (HP:0002015) | 17.9%–70% across reviews; 22.2%–67.7% across 12-cohort IPD; oropharyngeal dysphagia 79.3% in microcephaly vs 8.5% in normocephalic peers | Brazil cohorts, review, IPD meta-analysis | Major driver of malnutrition and aspiration risk; ~20% required alternative feeding by age 2 | (pqac-00000000, pqac-00000003, pqac-00000006, pqac-00000020) |
| Feeding-Growth | Low birth weight (HP:0001518) | 10%–43.8% across cohorts; 23.9% in one infant cohort up to 12 months | IPD meta-analysis; observational cohort | Reflects prenatal growth effects and heterogeneity | (pqac-00000006) |
| Feeding-Growth | Linear growth deficit / short stature (HP:0004322) | 39.1% of length-for-age measurements below deficit threshold in one cohort; stunting in literature 14.3%–57.1% | Infant cohort; systematic review of malnutrition studies | Often linked to dysphagia and feeding difficulty | (pqac-00000006) |
| Feeding-Growth | Underweight / wasting (HP:0004325) | Underweight 14.3%–54.4%; wasting 4.3%–48.0% | Systematic review of observational studies in children with CZS | Reflects chronic nutritional vulnerability | (pqac-00000006) |
| Other | Urological impairment | Frequency not pooled; repeatedly reported as common comorbidity | Brazil cohort review | Included as part of broader multisystem CZS spectrum | (pqac-00000002, pqac-00000049) |
| Other | Hospitalization burden | 41.4% in children with microcephaly vs 16.2% in normocephalic peers | Brazil cohorts summarized in review | Likely reflects feeding, neurologic, and respiratory complications | (pqac-00000020) |
| Other | Mortality | 11.3-fold higher mortality up to 36 months in children with CZS / Zika-related microcephaly vs unexposed peers | Systematic review summary | Severe disease substantially increases early-childhood mortality | (pqac-00000001, pqac-00000023) |

| Epidemiology statistic | Estimate | Population / timeframe | Notes | Supporting citation IDs |
|---|---:|---|---|---|
| CZS proportion among ZIKV-infected pregnancies | 4.65% (95% CI 3.38–6.67%) | Systematic review/meta-analysis of ZIKV epidemiology | Pooled estimate for CZS among infected pregnancies | (pqac-00000008, pqac-00000013) |
| Countries/territories with documented autochthonous mosquito-borne ZIKV transmission | 92 | Global status as of Dec 2023 | Transmission likely underrecognized because many infections are asymptomatic/mild | (pqac-00000009, pqac-00000012) |
| Brazil confirmed CZS cases | 1,858 confirmed; 2,960 suspected under investigation | 2015 to epidemiological week 31 of 2023 | National surveillance; cases fell sharply after 2017 | (pqac-00000002, pqac-00000014) |
| Brazil 2023 reported Zika cases | 54,116 cases; incidence 25/100,000; 6,201 laboratory confirmed | Brazil, 2023 | Brazil accounted for 97% of reported Americas cases in preliminary 2023 surveillance | (pqac-00000010) |
| Preliminary Americas Zika cases in 2023 | 55,813 cases from 14 countries; 4 deaths | Americas, 2023 preliminary surveillance | 11% laboratory confirmed | (pqac-00000010) |


*Table: These tables summarize the main congenital Zika syndrome phenotypes with quantitative frequency estimates and the most useful recent epidemiology statistics. They are designed for rapid knowledge-base extraction and link each major claim to supporting context IDs.*