[Paper Review] Cellular reproduction number, generation time and growth rate differ between human- and avian-adapted influenza strains

Ada W. C. Yan, Jie Zhou+4 more|arXiv (Cornell University)|Mar 19, 2019

Influenza Virus Research StudiesMedicine51 references3 citations

TL;DR

This study proposes that the cellular basic reproduction number (R₀), mean generation time (τG), and initial growth rate (r) are key predictors of influenza virus adaptation to humans. Using a mechanistic model fitted to in vitro data from human and avian influenza strains, the authors show that human-adapted strains exhibit lower R₀, shorter τG, and slower r than avian-adapted strains—differences driven by internal viral genes. These parameters can inform pandemic risk assessment by quantifying host adaptation in high-throughput assays.

ABSTRACT

When analysing in vitro data, growth kinetics of influenza strains are often compared by computing their growth rates, which are sometimes used as proxies for fitness. However, analogous to mechanistic epidemic models, the growth rate can be defined as a function of two parameters: the basic reproduction number (the average number of cells each infected cell infects) and the mean generation time (the average length of a replication cycle). Using a mechanistic model, previously published data from experiments in human lung cells, and newly generated data, we compared estimates of all three parameters for six influenza A strains. Using previously published data, we found that the two human-adapted strains (pre-2009 seasonal H1N1, and pandemic H1N1) had a lower basic reproduction number, shorter mean generation time and slower growth rate than the two avian-adapted strains (H5N1 and H7N9). These same differences were then observed in data from new experiments where two strains were engineered to have different internal proteins (pandemic H1N1 and H5N1), but the same surface proteins (PR8), confirming our initial findings and implying that differences between strains were driven by internal genes. Also, the model predicted that the human-adapted strains underwent more replication cycles than the avian-adapted strains by the time of peak viral load, potentially accumulating mutations more quickly. These results suggest that the in vitro reproduction number, generation time and growth rate differ between human-adapted and avian-adapted influenza strains, and thus could be used to assess host adaptation of internal proteins to inform pandemic risk assessment.

Motivation & Objective

• To identify quantitative in vitro parameters that predict host adaptation of influenza strains, addressing limitations in current animal-based pandemic risk assessment.
• To evaluate whether the cellular basic reproduction number (R₀), mean generation time (τG), and initial growth rate (r) differ between human- and avian-adapted influenza strains.
• To determine whether these parameters can serve as high-throughput, quantitative predictors of pandemic potential for surveillance and public health decision-making.
• To investigate the role of internal viral genes in driving differences in infection dynamics between human- and avian-adapted strains.

Proposed method

• A mechanistic ordinary differential equation (ODE) model of influenza infection in human lung cells was developed, tracking target cells (T), latently infected (L), actively infected (I), and infectious virus (Vinf).
• The model estimates R₀ as R₀ = (β_inf * T₀ * p_inf * τ_I) / (c + β_inf * T₀), where β_inf is infection rate, p_inf is virus production rate, τ_I is infected cell lifespan, and c is clearance rate.
• Mean generation time τG is calculated as τL + [(n_I + 1)/(2n_I)] * τ_I + 1/(c + β_inf * T₀), incorporating latent and infectious periods and viral clearance.
• Initial growth rate r is derived by linearising the model around the disease-free equilibrium (T₀, 0, 0, 0).
• Parameter estimation used an adaptive Metropolis-Hastings algorithm on combined multi-cycle, single-cycle, and mock-yield experimental data, with lognormal observation error and a threshold for low titres.
• A generation-tracking extension was implemented to compute the proportion of virions from each generation at a given time, enabling analysis of replication cycles.

Experimental results

Research questions

• RQ1 Do human-adapted and avian-adapted influenza strains differ in their cellular basic reproduction number (R₀), mean generation time (τG), and initial growth rate (r)?
• RQ2 Are differences in these parameters driven by internal viral genes or surface glycoproteins?
• RQ3 Can R₀, τG, and r serve as quantitative, high-throughput predictors of host adaptation and pandemic potential?
• RQ4 How do the number of replication cycles and mutation accumulation differ between human- and avian-adapted strains by peak viral load?

Key findings

• Human-adapted strains (pre-2009 seasonal H1N1 and pandemic H1N1) had significantly lower basic reproduction numbers (R₀) than avian-adapted strains (H5N1 and H7N9).
• Human-adapted strains exhibited shorter mean generation times (τG) compared to avian-adapted strains, indicating faster replication cycles.
• The initial growth rate (r) was slower in human-adapted strains than in avian-adapted strains, consistent with lower R₀ and shorter τG.
• Strains engineered with the same surface proteins (PR8 HA/NA) but different internal proteins (pandemic H1N1 vs. H5N1) showed the same R₀, τG, and r differences, confirming that internal genes drive the observed dynamics.
• The model predicted that human-adapted strains underwent more replication cycles than avian-adapted strains by the time of peak viral load, potentially accelerating mutation accumulation.
• These three parameters—R₀, τG, and r—differ systematically between human- and avian-adapted influenza strains, suggesting their utility in quantifying host adaptation and informing pandemic risk assessment.