Data from: The persistence of multiple strains of avian influenza in live bird markets

Multiple subtypes of avian influenza (AI) and novel reassortants are frequently isolated from live bird markets (LBMs). However, our understanding of the drivers of persistence of multiple AI subtypes is limited. We propose a stochastic model of AI transmission within an LBM that incorporates market size, turnover rate and the balance of direct versus environmental transmissibility. We investigate the relationship between these factors and the critical community size (CCS) for the persistence of single and multiple AI strains within an LBM. We fit different models of seeding from farms to two-strain surveillance data collected from Shantou, China. For a single strain and plausible estimates for continuous turnover rates and transmissibility, the CCS was approximately 11 800 birds, only a 4.2% increase in this estimate was needed to ensure persistence of the co-infecting strains (two strains in a single host). Precise values of CCS estimates were sensitive to changes in market turnover rate and duration of the latent period. Assuming a gradual daily sell rate of birds the estimated CCS was higher than when an instantaneous selling rate was assumed. We were able to reproduce prevalence dynamics similar to observations from a single market in China with infection seeded every 5–15 days, and a maximum non-seeding duration of 80 days. Our findings suggest that persistence of co-infections is more likely to be owing to sequential infection of single strains rather than ongoing transmission of both strains concurrently. In any given system for a fixed set of ecological and epidemiological conditions, there is an LBM size below which the risk of sustained co-circulation is low and which may suggest a clear policy opportunity to reduce the frequency of influenza co-infection in poultry.

活禽市场（Live Bird Markets, LBMs）中常分离到禽流感（Avian Influenza, AI）的多种亚型及新型重配株。然而，目前学界对多种禽流感亚型持续传播的驱动因素认知仍较为有限。本研究构建了活禽市场内禽流感传播的随机模型，纳入了市场规模、禽只周转速率以及直接传播与环境传播的能力平衡三类核心因素。本研究分析了上述因素与活禽市场内单株及多株禽流感毒株持续传播所需的临界群落规模（critical community size, CCS）之间的关联，并将多种病毒引入模型拟合至中国汕头地区采集的双毒株监测数据。针对单毒株场景，结合合理的连续周转速率与传播能力估算值，临界群落规模约为11800只禽只；仅需将该估算值提升4.2%，即可确保共感染毒株（单个宿主内感染两株毒株）的持续传播。临界群落规模的精确估算值对市场周转速率及潜伏期时长的变化较为敏感。假设禽只按每日渐进式售出速率进行交易时，估算得到的临界群落规模高于采用瞬时售出速率假设的场景。本研究成功复现了中国某单一活禽市场的感染流行动态：该市场病毒引入周期为每5~15天一次，最长无病毒引入时长可达80天，与实际观测结果相符。本研究结果显示，共感染的持续维持更可能源于单毒株的先后感染，而非两株毒株同时开展持续传播。在生态与流行病学条件固定的特定系统中，存在一个临界活禽市场规模：当市场规模低于该值时，病毒持续共同循环的风险较低，这为降低家禽流感共感染发生频率提供了明确的政策干预方向。