Tracking progress towards malaria elimination in China: estimates of reproduction numbers and their spatiotemporal variation

Isobel Routledge; Shengjie Lai; Katherine E Battle; Azra C Ghani; Manuel Gomez-Rodriguez; Kyle B Gustafson; Swapnil Mishra; Joshua L Proctor; Andrew J Tatem; Zhongjie Li; Samir Bhatt

Yunnan province, has seen a notable downward trend since 2011 and is expected to remain low 209 with maintained interventions into 2020. This decline coincides with 1-3-7 strategy in improved 210 Assuming all cases reaching health workers or health facilities are recorded, missing cases may be 326 generated by two processes. Symptomatic cases may be missed by not seeking care or not being 327 found through active case detection, or cases may be asymptomatic and therefore unlikely to seek 328 care or be detected. The latter may have densities of parasites in their blood which are too low to be 329 detectable by microscopy if active case detection occurs. These processes apply to both imported 330 cases or locally acquired cases. We assume the pool of asymptomatic cases in the country is low and 331 has a small contribution to ongoing transmission. To account for unobserved infectors within our 332 framework we include a time-independent edge that can infect any individual. The survival and 333 hazard functions for this edge are defined as ( ) = and = . As we will see below, as a 334 consequence of our optimisation problem these edges are encouraged to be sparse and only 335 invoked if no other infectors can continue the transmission chain. 336