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Background  The objectives of this study were to understand the differences in mortality rate, risk factors for mortality, and cause of death distribution in three neonatal age sub-groups (0–2, 3–7, and 8–27 days) and assess the change in mortality rate with previous assessments to inform programmatic decision-making in the Indian state of Bihar, a large state with a high burden of newborn deaths.    Methods  Detailed interviews were conducted in a representative sample of 23,602 live births between January and December 2016 (96.2% participation) in Bihar state. We estimated the neonatal mortality rate (NMR) for the three age sub-groups and explored the association of these deaths with a variety of risk factors using a hierarchical logistic regression model approach. Verbal autopsies were conducted using the PHMRC questionnaire and the cause of death assigned using the SmartVA automated algorithm. Change in NMR from 2011 to 2016 was estimated by comparing it with a previous assessment.    Results  The NMR 0–2-day, 3–7-day, and 8–27-day mortality estimates in 2016 were 24.7 (95% CI 21.8–28.0), 13.2 (11.1 to 15.7), 5.8 (4.4 to 7.5), and 5.8 (4.5 to 7.5) per 1000 live births, respectively. A statistically significant reduction of 23.3% (95% CI 9.2% to 37.3) was seen in NMR from 2011 to 2016, driven by a reduction of 35.3% (95% CI 18.4% to 52.2) in 0–2-day mortality. In the final regression model, the highest odds for mortality in 0–2 days were related to the gestation period of ≤ 8 months (OR 16.5, 95% CI 11.9–22.9) followed by obstetric complications, no antiseptic cord care, and delivery at a private health facility or home. The 3–7- and 8–27-day mortality was driven by illness in the neonatal period (OR 10.33, 95% CI 6.31–16.90, and OR 4.88, 95% CI 3.13–7.61, respectively) and pregnancy with multiple foetuses (OR 5.15, 95% CI 2.39–11.10, and OR 11.77, 95% CI 6.43–21.53, respectively). Birth asphyxia (61.1%) and preterm delivery (22.1%) accounted for most of 0–2-day deaths; pneumonia (34.5%), preterm delivery (33.7%), and meningitis/sepsis (20.1%) accounted for the majority of 3–7-day deaths; meningitis/sepsis (30.6%), pneumonia (29.1%), and preterm delivery (26.2%) were the leading causes of death at 8–27 days.    Conclusions  To our knowledge, this is the first study to report a detailed neonatal epidemiology by age sub-groups for a major Indian state, which has highlighted the distinctly different mortality rate, risk factors, and causes of death at 0–2 days versus the rest of the neonatal period. Monitoring mortality at 0–2 and 3–7 days separately in the traditional early neonatal period of 0–7 days would enable more effective programming to reduce neonatal mortality.    Electronic supplementary material  The online version of this article (10.1186/s12916-019-1372-z) contains supplementary material, which is available to authorized users.

Distinct mortality patterns at 0–2 days versus the remaining neonatal period: results from population-based assessment in the Indian state of Bihar