Predicting hosts based on early SARS-CoV-2 samples and analyzing the 2020 pandemic

The SARS-CoV-2 pandemic has raised concerns in the identification of the hosts of the virus since the early stages of the outbreak. To address this problem, we proposed a deep learning method, DeepHoF, based on extracting viral genomic features automatically, to predict the host likelihood scores on five host types, including plant, germ, invertebrate, non-human vertebrate and human, for novel viruses. DeepHoF made up for the lack of an accurate tool, reaching a satisfactory AUC of 0.975 in the five-classification, and could make a reliable prediction for the novel viruses without close neighbors in phylogeny. Additionally, to fill the gap in the efficient inference of host species for SARS-CoV-2 using existing tools, we conducted a deep analysis on the host likelihood profile calculated by DeepHoF. Using the isolates sequenced in the earliest stage of the COVID-19 pandemic, we inferred that minks, bats, dogs and cats were potential hosts of SARS-CoV-2, while minks might be one of the most noteworthy hosts. Several genes of SARS-CoV-2 demonstrated their significance in determining the host range. Furthermore, a large-scale genome analysis, based on DeepHoF’s computation for the later pandemic in 2020, disclosed the uniformity of host range among SARS-CoV-2 samples and the strong association of SARS-CoV-2 between humans and minks.

Predicting Hosts Based on Early SARS-CoV-2 Samples and Analyzing Later World-wide Pandemic in 2020

The SARS-CoV-2 pandemic has raised the concern for identifying hosts of the virus since the early-stage outbreak. To address this problem, we proposed a deep learning method, DeepHoF, based on extracting the viral genomic features automatically, to predict host likelihood scores on five host types, including plant, germ, invertebrate, non-human vertebrate and human, for novel viruses. DeepHoF made up for the lack of an accurate tool applicable to any novel virus and overcame the limitation of the sequence similarity-based methods, reaching a satisfactory AUC of 0.987 on the five-classification. Additionally, to fill the gap in the efficient inference of host species for SARS-CoV-2 using existed tools, we conducted a deep analysis on the host likelihood profile calculated by DeepHoF. Using the isolates sequenced in the earliest stage of COVID-19, we inferred minks, bats, dogs and cats were potential hosts of SARS-CoV-2, while minks might be one of the most noteworthy hosts. Several genes of SARS-CoV-2 demonstrated their significance in determining the host range. Furthermore, the large-scale genome analysis, based on DeepHoF’s computation for the later world-wide pandemic in 2020, disclosed the uniformity of host range among SARS-CoV-2 samples and the strong association of SARS-CoV-2 between humans and minks.

Predicting hosts based on early SARS-CoV-2 samples and analyzing later world-wide pandemic in 2020

The SARS-CoV-2 pandemic has raised the concern for identifying hosts of the virus since the early-stage outbreak. To address this problem, we proposed a deep learning method, DeepHoF, based on extracting the viral genomic features automatically, to predict host likelihood scores on five host types, including plant, germ, invertebrate, non-human vertebrate and human, for novel viruses. DeepHoF made up for the lack of an accurate tool applicable to any novel virus and overcame the limitation of the sequence similarity-based methods, reaching a satisfactory AUC of 0.987 on the five-classification. Additionally, to fill the gap in the efficient inference of host species for SARS-CoV-2 using existed tools, we conducted a deep analysis on the host likelihood profile calculated by DeepHoF. Using the isolates sequenced in the earliest stage of COVID-19, we inferred minks, bats, dogs and cats were potential hosts of SARS-CoV-2, while minks might be one of the most noteworthy hosts. Several genes of SARS-CoV-2 demonstrated their significance in determining the host range. Furthermore, the large-scale genome analysis, based on DeepHoF's computation for the later world-wide pandemic in 2020, disclosed the uniformity of host range among SARS-CoV-2 samples and the strong association of SARS-CoV-2 between humans and minks.

Pairwise meta-analysis of aggregate data using metaan in Stata

A few years ago, we developed metaan, a package to perform fixedor random-effects meta-analysis. In terms of random-effects meta-analysis, it offered a wide choice of models, including maximum likelihood, profile likelihood, or restricted maximum-likelihood, in addition to the established DerSimonian–Laird method available in metan or Cochrane’s RevMan software. Other unique features included a wide range of reported heterogeneity measures and a plot of the maximum likelihood function. Since then, metaan has been continuously updated to offer improved graphics, more options, and more meta-analysis models. In this necessary update, we describe these additions and discuss the new models and the evidence behind them.

Probability Density Functions

This chapter builds on probability distributions. Its focus is on general concepts associated with probability density functions (pdf’s), which are distributions associated with continuous random variables. The continuous uniform and normal distributions are highlighted as examples of pdf’s. These and other pdf’s can be used to specify prior distributions, likelihoods, and/or posterior distributions in Bayesian inference. Although this chapter specifically focuses on the continuous uniform and normal distributions, the concepts discussed in this chapter will apply to other continuous probability distributions. By the end of the chapter, the reader should be able to define and use the following terms for a continuous random variable: random variable, probability distribution, parameter, probability density, likelihood, and likelihood profile.

Nonidentifiability in Model Calibration and Implications for Medical Decision Making

Background. Calibration is the process of estimating parameters of a mathematical model by matching model outputs to calibration targets. In the presence of nonidentifiability, multiple parameter sets solve the calibration problem, which may have important implications for decision making. We evaluate the implications of nonidentifiability on the optimal strategy and provide methods to check for nonidentifiability. Methods. We illustrate nonidentifiability by calibrating a 3-state Markov model of cancer relative survival (RS). We performed 2 different calibration exercises: 1) only including RS as a calibration target and 2) adding the ratio between the 2 nondeath states over time as an additional target. We used the Nelder-Mead (NM) algorithm to identify parameter sets that best matched the calibration targets. We used collinearity and likelihood profile analyses to check for nonidentifiability. We then estimated the benefit of a hypothetical treatment in terms of life expectancy gains using different, but equally good-fitting, parameter sets. We also applied collinearity analysis to a realistic model of the natural history of colorectal cancer. Results. When only RS is used as the calibration target, 2 different parameter sets yield similar maximum likelihood values. The high collinearity index and the bimodal likelihood profile on both parameters demonstrated the presence of nonidentifiability. These different, equally good-fitting parameter sets produce different estimates of the treatment effectiveness (0.67 v. 0.31 years), which could influence the optimal decision. By incorporating the additional target, the model becomes identifiable with a collinearity index of 3.5 and a unimodal likelihood profile. Conclusions. In the presence of nonidentifiability, equally likely parameter estimates might yield different conclusions. Checking for the existence of nonidentifiability and its implications should be incorporated into standard model calibration procedures.

Richards growth model and viability indicators for populations subject to interventions

In this work we study the problem of modeling identification of a population employing a discrete dynamic model based on the Richards growth model. The population is subjected to interventions due to consumption, such as hunting or farming animals. The model identification allows us to estimate the probability or the average time for a population number to reach a certain level. The parameter inference for these models are obtained with the use of the likelihood profile technique as developed in this paper. The identification method here developed can be applied to evaluate the productivity of animal husbandry or to evaluate the risk of extinction of autochthon populations. It is applied to data of the Brazilian beef cattle herd population, and the the population number to reach a certain goal level is investigated.