Infectious disease dynamics and restrictions on social gathering size

Social gatherings can be an important locus of transmission for many pathogens including SARS-CoV-2. During an outbreak, restricting the size of these gatherings is one of several non-pharmaceutical interventions available to policy-makers to reduce transmission. Often these restrictions take the form of prohibitions on gatherings above a certain size. While it is generally agreed that such restrictions reduce contacts, the specific size threshold separating "allowed" from "prohibited" gatherings often does not have a clear scientific basis, which leads to dramatic differences in guidance across location and time. Building on the observation that gathering size distributions are often heavy-tailed, we develop a theoretical model of transmission during gatherings and their contribution to general disease dynamics. We find that a key, but often overlooked, determinant of the optimal threshold is the distribution of gathering sizes. Using data on pre-pandemic contact patterns from several sources as well as empirical estimates of transmission parameters for SARS-CoV-2, we apply our model to better understand relationship between restriction threshold and reduction in cases. We find that, under reasonable transmission parameter ranges, restrictions may have to be set quite low to have any demonstrable effect on cases due to relative frequency of smaller gatherings. We compare our conceptual model with observed changes in reported contacts during lockdown in March of 2020.

Genomic surveillance reveals the emergence of SARS-CoV-2 Lineage A from Islamabad Pakistan

The lineage A of SARS-CoV-2 has been around the world since the start of the pandemic. In Pakistan the last case of lineage A was reported in April, 2021 since then no case has been reported. In November, 2021 during routine genomic surveillance at National Institute of Health we have found 07 cases of lineage A from Islamabad, Pakistan. The study reports two novel deletions in the spike glycoprotein. One 09 amino acid deletion (68-76 a.a) is found in the S1 subunit while another 10 amino acid deletion (679-688 a.a) observed at the junction of S1/S2 referred as furin cleavage site. The removal of furin cleavage site may result in impaired virus replication thus decreasing its pathogenesis. The actual impact of these two deletions on the virus replication and disease dynamics needs to be studied in detail. Moreover, the enhanced genomic surveillance will be required to track the spread of this lineage in other parts of the country.

Impact of Population Mixing Between a Vaccinated Majority and Unvaccinated Minority on Disease Dynamics. Implications for SARS-CoV-2

Background: The speed of vaccine development has been a singular achievement during the SARS-CoV-2 pandemic. However, anti-vaccination movements and disinformation efforts have resulted in suboptimal uptake of available vaccines. Vaccine opponents often frame their opposition in terms of the rights of the unvaccinated. Our objective was to explore the impact of mixing of vaccinated and unvaccinated populations on risk among vaccinated individuals. Methods: We constructed a simple Susceptible-Infectious-Recovered (SIR) compartmental model of a respiratory infectious disease with two connected sub-populations: vaccinated individuals and unvaccinated individuals (Figure 1). We modeled the non-random mixing of these two groups using a matrix approach with a mixing constant varied to simulate a spectrum of patterns ranging from random mixing to complete assortativity. We evaluated the dynamics of an epidemic within each subgroup, and in the population as a whole, and also evaluated the contact-frequency-adjusted contribution of unvaccinated individuals to risk among the vaccinated. Results: As expected, the relative risk of infection was markedly higher among unvaccinated individuals than among vaccinated individuals. However, the contact-adjusted contribution of unvaccinated individuals to infection risk during the epidemic was disproportionate with unvaccinated individuals contributing to infection risk among the vaccinated at a rate up to 6.4 times higher than would have been expected based on contact numbers alone in the base case. As assortativity increased the final attack rate decreased among vaccinated individuals, but the contact-adjusted contribution to risk among vaccinated individuals derived from contact with unvaccinated individuals increased. Interpretation: While risk associated with avoiding vaccination during a virulent pandemic accrues chiefly to the unvaccinated, the choices of these individuals are likely to impact the health and safety of vaccinated individuals in a manner disproportionate to the fraction of unvaccinated individuals in the population.

COEVOLUTION WITH SPATIALLY STRUCTURED RICE LANDRACES MAINTAINS MULTIPLE GENERALIST LINEAGES IN THE RICE BLAST PATHOGEN

Traditional agrosystems, where humans, crops and microbes have coevolved over long periods, can serve as models to understand the eco-evolutionary determinants of disease dynamics and help the engineering of durably resistant agrosystems. Here, we investigated the genetic and phenotypic relationship between rice (Oryza sativa) landraces and their rice blast pathogen (Magnaporthe oryzae) in the traditional Yuanyang terraces of flooded rice paddies in China, where rice landraces have been grown and bred over centuries without significant disease outbreaks. Analyses of genetic subdivision revealed that indica rice plants clustered according to landrace names. Three new diverse lineages of rice blast specific to the Yuanyang terraces coexisted with lineages previously detected at the worldwide scale. Population subdivision in the pathogen population did not mirror pattern of population subdivision in the host. Measuring the pathogenicity of rice blast isolates on landraces revealed generalist life histories. Our results suggest that the implementation of disease control strategies based on the emergence or maintenance of a generalist lifestyle in pathogens may sustainably reduce the burden of disease in crops.

Prevention of COVID-19 Through Optimization of Tabi’at: A Unani Medicine’s Perspective

Background: Unani System of Medicine (USM) is one of the traditional systems of medicine practiced in India and the Indian subcontinent. It is a holistic system of health care based on inceptive principles applied by Hippocrates, Galen, and Ibn-e-Sina, the founders of present-day medicine. USM encompasses a distinct way of looking at the human body and it considers health to be the result of natural dynamic harmonious balance within the body. USM also recognizes the presence of inherent wisdom which is responsible for controlling all physiological functions, maintenance of health, restoration of health, and self-healing. This intrinsic ability of the body to restore health and the mechanism that activates the body’s healing process is called Tabi’at/ physis. The ultimate goal of prevention of disease can be obtained by optimization of tabi’at/physis, increasing the host defense. It can be achieved through the implication of asbab-e-sitta zarooriyah which includes some Unani Regimenal Therapies also, fostering change in lifestyle habits resulting in good health. Aims: In this raging pandemic all the therapeutic strategies are based on destroying the agent, breaking the means of transmission and immunization. Although we are leaving behind a huge gap in maintaining the host defense even though it has a crucial role in disease dynamics. In this paper, we have attempted to highlight the concept of tabi’at/Physis and its optimization to prevent this disease and its transmission. Methods: The authors had gone through classical Unani medical textbooks books related to the concept of tabi’at, asbab-e-sitta zarooriyah, and various modalities that help in health promotion and host defense. Important Unani medicine textbooks like Al Qanoon, Kamilus Sana’at, Kitab-al- Hawi, Al-asbab wa Alamat, Moalijat Buqratiya, Firdausul Hikmat and Kitabul Mansuri in addition to other published literature on the concerned subject was also reviewed for further clarification on the topic. Keywords: Unani System of Medicine, Tabi’at (physis), Host defense & Asbab-e- Sitta zarooriyah

Disaster displacement and zoonotic disease dynamics: The impact of structural and chronic drivers in Sindh, Pakistan

Projected increases in human and animal displacement driven by climate change, disasters and related environmental degradation will have significant implications to global health. Pathways for infectious disease transmission including zoonoses, diseases transmitted between animals and humans, are complex and non-linear. While forced migration is considered an important driver for the spread of zoonoses, actual disease dynamics remain under researched. This paper presents the findings of a case study investigating how disaster displacement affected zoonotic disease transmission risk following the 2010 ‘superfloods’ in Sindh province, Pakistan. We interviewed 30 key informants and 17 household members across 6 rural communities between March and November 2019, supported by observational studies and a review of secondary data. Results were analysed using the ecosocial theoretical framework. Buffalo, cattle and goats were often the only moveable asset, therefore livestock was an important consideration in determining displacement modality and destination location, and crowded locations were avoided to protect human and animal health. Meanwhile however, livestock was rarely included in the humanitarian response, resulting in communities and households fragmenting according to the availability of livestock provisions. We found that rather than a driver for disease, displacement acted as a process affecting community, household and individual zoonotic disease risk dynamics, based on available resources and social networks before, during and after displacement, rooted in the historical, political and socio-economic context. We conclude that in rural Sindh, disaster displaced populations’ risk of zoonoses is the result of changes in dynamics rooted in pre-existing structural and chronic inequalities, making people more or less vulnerable to disease through multiple interlinked pathways. Our findings have implications for policy makers and humanitarian responders assisting displaced populations dependent on livestock, with a call to integrate livestock support in humanitarian policies and responses for health, survival and recovery.

The dark side of shade: How microclimates drive the epidemiological mechanisms of coffee berry disease

Coffee berry disease (CBD) can cause significant coffee yield losses along with major income losses for African smallholders. Although these farmers cannot afford to purchase pesticides to control the disease, agroecological solutions have rarely been investigated, and how epidemiological mechanisms are linked to the environment of the coffee tree and the plot remains unclear. Agroforestry systems are a promising agroecological option, but the effect of shade on CBD regulation is the subject of debate, and the use of plant species diversity remains uncertain. Here, we address how shade affects epidemiological mechanisms by modifying the microclimate. For this purpose, we developed a mechanistic susceptible-exposed-infectious-removed (SEIR) model, and used a Bayesian framework to infer the epidemiological parameters against microclimatic covariates. We show that shade has opposing effects on different epidemiological mechanisms. Specifically, shade can limit disease dynamics by reducing disease transmission while simultaneously promoting disease dynamics by reducing the latent period of the pathogen. However, in full sun, efficient disease transmission compensates for long latent periods. As a result, the balances between microclimatic variables can counterbalance the epidemiological rates, which can dramatically alter the fate of epidemics in shade versus full sun conditions. We propose research avenues to help design cost- and environmentally effective management strategies for CBD that are notably based on the functional traits of shade trees that could hamper CBD dispersal.

Comparing human and model-based forecasts of COVID-19 in Germany and Poland

1AbstractForecasts based on epidemiological modelling have played an important role in shaping public policy throughout the COVID-19 pandemic. This modelling combines knowledge about infectious disease dynamics with the subjective opinion of the researcher who develops and refines the model and often also adjusts model outputs. Developing a forecast model is difficult, resource- and time-consuming. It is therefore worth asking what modelling is able to add beyond the subjective opinion of the researcher alone. To investigate this, we analysed different real-time forecasts of cases of and deaths from COVID-19 in Germany and Poland over a 1-4 week horizon submitted to the German and Polish Forecast Hub. We compared crowd forecasts elicited from researchers and volunteers, against a) forecasts from two semi-mechanistic models based on common epidemiological assumptions and b) the ensemble of all other models submitted to the Forecast Hub. We found crowd forecasts, despite being overconfident, to outperform all other methods across all forecast horizons when forecasting cases (weighted interval score relative to the Hub ensemble 2 weeks ahead: 0.89). Forecasts based on computational models performed comparably better when predicting deaths (rel. WIS 1.26), suggesting that epidemiological modelling and human judgement can complement each other in important ways.