Investigation of cross-regional spread and evolution of equine influenza H3N8 at US and global scales using Bayesian phylogeography based on balanced subsampling.

Equine influenza virus (EIV) is a highly contagious pathogen of equids, and a well-known burden in global equine health. EIV H3N8 variants seasonally emerged and resulted in EIV outbreaks in the United States and worldwide. The present study evaluated the pattern of cross-regional EIV H3N8 spread and evolutionary characteristics at US and global scales using Bayesian phylogeography with balanced subsampling based on regional horse population size. A total of 297 haemagglutinin (HA) sequences of global EIV H3N8 were collected from 1963 to 2019 and subsampled to global subset (n = 67), raw US sequences (n = 100) and US subset (n = 44) datasets. Discrete trait phylogeography analysis was used to estimate the transmission history of EIV using four global and US genome datasets. The North American lineage was the major source of globally dominant EIV variants and spread to other global regions. The US EIV strains generally spread from the southern and midwestern regions to other regions. The EIV H3N8 accumulated approximately three nucleotide substitutions per year in the HA gene under heterogeneous local positive selection. Our findings will guide better decision making of target intervention strategies of EIV H3N8 infection and provide the better scheme of genomic surveillance in the United States and global equine health.

Testing and vaccination to reduce the impact of COVID-19 in nursing homes: an agent-based approach.

BACKGROUND: Efforts to protect residents in nursing homes involve non-pharmaceutical interventions, testing, and vaccine. We sought to quantify the effect of testing and vaccine strategies on the attack rate, length of the epidemic, and hospitalization. METHODS: We developed an agent-based model to simulate the dynamics of SARS-CoV-2 transmission among resident and staff agents in a nursing home. Interactions between 172 residents and 170 staff based on data from a nursing home in Los Angeles, CA. Scenarios were simulated assuming different levels of non-pharmaceutical interventions, testing frequencies, and vaccine efficacy to reduce transmission. RESULTS: Under the hypothetical scenario of widespread SARS-CoV-2 in the community, 3-day testing frequency minimized the attack rate and the time to eradicate an outbreak. Prioritization of vaccine among staff or staff and residents minimized the cumulative number of infections and hospitalization, particularly in the scenario of high probability of an introduction. Reducing the probability of a viral introduction eased the demand on testing and vaccination rate to decrease infections and hospitalizations. CONCLUSIONS: Improving frequency of testing from 7-days to 3-days minimized the number of infections and hospitalizations, despite widespread community transmission. Vaccine prioritization of staff provides the best protection strategy when the risk of viral introduction is high.

Impact of social distancing on early SARS-CoV-2 transmission in the United States.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a viral pathogen that quickly became a global pandemic in the winter of 2020-2021. In response, governments issued social distancing orders to minimize transmission by reducing community contacts. We tested the efficacy of this social distancing at the state level during the first 2 months of the pandemic in the United States. We utilized data on daily SARS-CoV-2 case numbers and human community mobility (anonymized, aggregated cell phone location data stratified into six categories used as an index of social distancing), the date of government-issued social distancing orders, demographics, urbanization and public transportation. We implemented cross-correlation to identify lag times between declines in mobility and SARS-CoV-2 cases. Incorporating state-specific lag times, we tested for associations between case counts and mobility metrics using Bayesian multilevel models. Decreased mobility around grocery stores/pharmacies, retail/recreation locations, transit stations and workplaces was correlated with decreases in SARS-CoV-2 cases with significant lag times of ≥21 days. Social distancing orders were associated with fewer cumulative SARS-CoV-2 cases when they were put in place earlier. Community mobility had already started declining prior to most social distancing orders, especially the more restrictive orders implemented later in the pandemic. Social distancing is an important tool that has been implemented throughout the pandemic to decrease SARS-CoV-2 transmission, although with significant social and economic impacts. Our results suggest that declines in cases were observed several weeks subsequent to implementation of social distancing measures, and that implementing social distancing earlier could potentially minimize the duration of time these policies need to be in effect. Our findings can inform ongoing management of this pandemic and other emerging infectious disease outbreaks by identifying areas where reductions in mobility are associated with reduced disease transmission, and the expected time frame between behavioural changes and measurable population outcomes.

Global subtype diversity, spatial distribution patterns, and phylogenetic analysis of avian influenza virus in water.

The current COVID-19 pandemic highlights the need for zoonotic infectious disease surveillance. Avian influenza virus (AIV) poses a significant threat to animal and public health due to its pandemic potential. Virus-contaminated water has been suggested as an important AIV spread mechanism among multiple species. Nevertheless, few studies have characterized the global AIV subtype diversity and distribution in environmental water. Therefore, this study aims to provide an updated descriptive and phylogenetic analysis of AIVs isolated in water samples from high risk-sites for influenza outbreaks (i.e. live bird markets, poultry farms, and wild bird habitats) on a global scale. The descriptive analysis evidenced that 21 subtypes were reported from nine countries between 2003 and 2020. Fourteen AIV subtypes were solely reported from Asian countries. Most of the viral sequences were obtained in China and Bangladesh with 47.44% and 23.93%, respectively. Likewise, the greatest global AIV subtype diversity was observed in China with 12 subtypes. Live bird markets represented the main sampling site for AIV detection in water samples (64.1%), mostly from poultry cage water. Nevertheless, the highest subtype diversity was observed in water samples from wild bird habitats, especially from the Izumi plain and the Dongting Lake located in Japan and China, respectively. Water from drinking poultry troughs evidenced the greatest subtype diversity in live bird markets; meanwhile, environmental water used by ducks had the highest number of different subtypes in poultry farms. Maximum-likelihood phylogenetic trees of hemagglutinin (HA) and neuraminidase (NA) genes showed that some sequences were closely related among different poultry/wild bird-related environments from different geographic origins. Therefore, the results suggest that even though the availability of gene sequences in public-access databases varies greatly among countries, environmental AIV surveillance represents a useful tool to elucidate potential viral diversity in wild and domestic bird populations.