Epidemiology and Global Health

Evaluation Summary:

This paper presents a modeling framework that can be used to track the complex behavioral and immunological landscape of the COVID-19 pandemic over multiple surges and variants in South Africa, which has been validated previously for other regions and time periods. This work may be useful for infectious disease modelers, epidemiologists, and public health officials as they navigate the next phase of the pandemic or seek to understand the history of the epidemic in South Africa.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This study uses social media data (namely twitter) to analyse factors of covid-vaccine acceptance. It first trains a classifier to detect whether a tweets pro-vaccine, neutral, or against. Using then a large corpus of accounts, it investigates multiple factors explaining this position in a light counterfactual analysis. The central finding is that the most socioeconomically disadvantaged groups are more likely to hold polarized opinions on COVID-19 vaccines; other findings inclduing that personal pandemic experience has an important impact on acceptance, or that interest in politics modulates acceptance. This study a good example of what machine learning can do with social media data; however it is also a good example of the high data-demands and limitations of a machine learning approach. The correlations found are plausible but the causal implications are not evidenced strongly enough to guide public policy.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

A pathogen's generation interval directly affects estimates of its transmissibility (R), and the period of self-isolation or quarantine needed to prevent transmission. This study shows that the unmitigated generation interval of the original variant of SARS-CoV-2 is several days longer than previously estimated and that interventions have substantially decreased the effective generation interval. These findings improve our ability to model counterfactual intervention-free scenarios. Overall technically sound analyses support the conclusions, and extensive sensitivity analyses show that the findings are robust. However, sampling or ascertainment bias in this relatively small pre-intervention dataset or biased inputs could affect the accuracy of the reported estimates.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This is a systematic review by meta-analysis about the effect of calcium supplementation on bone health in people under 35 years old. The authors found that calcium supplementation can significantly improve BMD and BMC in young people. Moreover, a better effect of calcium supplementation was shown in people who are at the plateau of their PBM. A unique feature of this study is that it focused on people at the age before achieving PBM or age at the plateau of PBM, which is different from previous studies that mainly focused on the elderly or children.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper presents an integrated algorithm, based on several standard techniques in infectious disease epidemiology, to estimate the real-time reproductive number and show how it has evolved in different countries during COVID-19. However, the analyses should be modelled in a more integrated fashion. Uncertainty estimation requires more work. And additional data streams should be incorporated to more reliably capture infection dynamics.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This work presents in-depth epidemiologic and phylogenetic analyses of tuberculosis cases across Valencia, Spain and comparator low-burden (Oxfordshire, UK) and high-burden (Karonga, Malawi) regions. Findings reveal that the "low burden" observed in Valencia is not in fact reflective of low transmission in this setting, with detected lineages likely to have circulated locally over the course of decades and to have been transmitted in the community.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

In this paper, the authors presented the joint efforts from nine modeling teams to provide six-month projection of the COVID-19 pandemic across the US, in view of the circulation of the more transmissible Delta variant. All of the nine models projected substantial Fall resurgences based on data as of 3 July 2021, but the actual resurgence scale as of 31 July 2021 had exceeded the projections of all of the nine models. This suggests that transmission may be even higher than expected given model assumptions, and that forecasts beyond more than a few weeks are likely to be highly uncertain. This paper will be of high interest to public health specialists, forecast modelers, and members of the general public interested in the evolution of the COVID-19 pandemic and the impact of public health interventions in the USA.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Basic epidemiological parameters such as the force of infection (rate at which susceptible individuals acquire the infection) remain undetermined for human infection with the neglected food-borne zoonotic cestode Taenia solium, which may cause taeniasis and cysticercosis. Dixon and colleagues address this major gap by fitting simple mathematical models to datasets that describe the prevalence of taeniasis and cysticercosis in several countries. Importantly, they found that infection acquisition rates per year vary widely (up to two orders of magnitude) across endemic settings and provide an approach for mapping the global public health impact of taeniasis and cysticercosis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The authors analyzed a national database to gain insights on deficits in cervical and colorectal cancer screening in the United States. Their work may provide a set of predictors to enhance health promotion messaging to women who are underscreened and thus eliminate disparities in cancer control.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper will be of interest to public health specialists and cancer scientists working in cancer prevention. The work presents valuable data on how the COVID-19 pandemic has impacted breast cancer screening indicators compared with previous years. Overall, the results support the assertion that while many key indicators have not been substantially impacted, the screening participation rate declined and fewer cancers were screen-detected in 2020-21.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This paper extends a previous analytical method that the authors developed to evaluate the time to infectiousness of COVID-19, in order to evaluate differences in the generation interval across different time periods during the course of the pandemic in England in 2020. This study will be of interest to policymakers and modellers. While the results appear technically robust for the data analysed, its usefulness is limited by difficulty in extending the results to other contexts.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This manuscript will be of broad interest to readers interested in understanding characteristics of variants in ongoing epidemics that lead to faster (or slower) growth rates, and will be of particular interest to those wishing to understand the factors leading to selection of SARS-CoV-2 variants. The transmission advantage of a novel strain of a pathogen depends not only on its relative transmissibility, but also on its generation time relative to other strains; the relation between transmissibility, transmission advantage and generation time changes across different phases of the epidemic, enabling statistical inferences to be made about both the transmissibility advantage and generation time of an emerging variant. The method is supported by simulation studies and applied to the Alpha and Delta SARS-CoV-2 variants to show that selection was likely driven by changes in transmissibility rather than changes in the generation time.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper is the first to characterize overdispersion of COVID-19 spread in schools using crowdsourcing . It has the potential to serve as a useful platform for assessing preventative measures in schools but needs more clarity regarding the sensitivity of the approach to the completeness of input data, as evidence by different model conclusions when sparse data from the US is used as an input as opposed to the more detailed Canadian data.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript will be of interest to oncologists, cardiologists, cardio-oncologists, and primary care providers who treat patients with breast cancer and adds to the growing body of literature that identifies the increased risk for cardiotoxicity associated with breast cancer treatment and does so at the general population level. The results of this study are interesting and supported by the data provided, however they must be interpreted with caution as the database utilized includes intended treatment regimens (chemotherapy, radiotherapy) rather than the confirmed treatments patients received.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper describes a two-sample randomization study of the impact of several measures of epigenetic aging acceleration (four different DNA methylation clocks) on risk for various common cancers (prostate, colon, lung, ovary, and breast). Data from large case-control cancer GWAS results are leveraged, as well as large cohort GWAS (UK Biobank and FinnGen) and GWAS of epigenetic aging. The most convincing finding is an an estimated effect of GrimAge on colon cancer risk (while results for other cancers are null or suggestive). This analysis is an important contribution as it addresses a question of substantial interest in cancer epidemiology.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Leptospirosis is an important zoonotic disease with a major global health impact. Although the role of rats as hosts is well known, it is less clear how important the fine-scale local and simultaneous presence of infected rats is relative to contact with water that could have been contaminated by rats elsewhere, or some time in the past. This study leverages a fine-scaled spatial dataset on human infection data and rat abundance to address this question, using a carefully developed statistical model that incorporates key variables and takes into account spatial variation. The models show that 'rattiness', a proxy for local rat abundance, might be an important driver of human infection risk, suggesting that rodent control measures might be an avenue for lowering the risk of infection with Leptospira bacteria.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Public Evaluation Summary:

This manuscript is of interest to readers in the field of metabolomics, particularly lipidomics. It measures hundreds of cord and plasma lipid species in mother-child pairs in a longitudinal fashion starting in gestation up to four years after birth. The authors perform regression analyses of cord lipid species with clinical characteristics at birth and 4 years old to support the key claims of the paper.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper will be of interest to a broad audience of epidemiologists and early childhood researchers as it provides data on the relationship between infection burden in infancy and metabolomic/lipidomic profiles at 12 months of age from a unique cohort of 555 mother-infant dyads. The paper also examines potential biologic pathways that may inform prevention of cardiovascular disease. The series of analyses presented support the preliminary associations outlined and require validation and interventional studies to support the causal relationship between infection, cumulative inflammation burden, and atherosclerosis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript which links early markers of inflammation with residual abnormalities on chest CT following SARS-CoV-2 infection. Surprisingly, early surveyed symptoms do not predict long term radiologic outcomes (6 months after infection) while inflammatory markers have stronger predictive value. Residual symptoms are common at the 6 month time point.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Nowicka et al., evaluated radiation dose and time dependent changes in the levels of selected serum miRNAs in human patients who received partial or complete myeloablative total body irradiation (TBI) and propose a panel of circulating miRNAs as potential radiation biodoismeters. The team employed next generation sequencing approach for discovery (or rediscovery) and quantification of selected responders by qRT-PCR using non-responsive miRNAs purified from exosomes in serum for evaluation of relative changes. Excellent bioinformatics and bio statistical methods are employed. However, critical biomarkers they propose as radiation biodosimeters have already been identified and published earlier. There is little novelty here and the translational significance of the study is moderate.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)