A systematic review of using population-level human mobility data to understand SARS-CoV-2 transmission.

The emergence of SARS-CoV-2 into a highly susceptible global population was primarily driven by human mobility-induced introduction events. Especially in the early stages, understanding mobility was vital to mitigating the pandemic prior to widespread vaccine availability. We conducted a systematic review of studies published from January 1, 2020, to May 9, 2021, that used population-level human mobility data to understand SARS-CoV-2 transmission.

Disentangling the seasonality effects of malaria transmission in the Brazilian Amazon basin.

The evidence of seasonal patterns in malaria epidemiology in the Brazilian Amazon basin indicates the need for a thorough investigation of seasonality in this last and heterogeneous region. Additionally, since these patterns are linked to climate variables, malaria models should also incorporate them. This study applies wavelet analysis to incidence data from 2003 to 2020 in the Epidemiological Surveillance System for Malaria (SIVEP-Malaria) database.

Assessing the impact of preventative measures to limit the spread of Toxoplasma gondii in wild carnivores of Madagascar.

Novel multihost pathogens can threaten endangered wildlife species, as well as humans and domestic animals. The zoonotic protozoan parasite Toxoplasma gondii is transmitted by members of Felidae and can infect a large number of animal species, including humans. This parasite can have significant health consequences for infected intermediate hosts and could further endanger wild carnivore populations of Madagascar.

Why do some coronaviruses become pandemic threats when others do not?

Despite multiple spillover events and short chains of transmission on at least 4 continents, Middle East Respiratory Syndrome Coronavirus (MERS-CoV) has never triggered a pandemic. By contrast, its relative, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has, despite apparently little, if any, previous circulation in humans. Resolving the unsolved mystery of the failure of MERS-CoV to trigger a pandemic could help inform how we understand the pandemic potential of pathogens, and probing it underscores a need for a more holistic understanding of the ways in which viral genetic changes scale up to population-level transmission.

Infectious disease in an era of global change.

The twenty-first century has witnessed a wave of severe infectious disease outbreaks, not least the COVID-19 pandemic, which has had a devastating impact on lives and livelihoods around the globe. The 2003 severe acute respiratory syndrome coronavirus outbreak, the 2009 swine flu pandemic, the 2012 Middle East respiratory syndrome coronavirus outbreak, the 2013-2016 Ebola virus disease epidemic in West Africa and the 2015 Zika virus disease epidemic all resulted in substantial morbidity and mortality while spreading across borders to infect people in multiple countries. At the same time, the past few decades have ushered in an unprecedented era of technological, demographic and climatic change: airline flights have doubled since 2000, since 2007 more people live in urban areas than rural areas, population numbers continue to climb and climate change presents an escalating threat to society.

Existing human mobility data sources poorly predicted the spatial spread of SARS-CoV-2 in Madagascar.

For emerging epidemics such as the COVID-19 pandemic, quantifying travel is a key component of developing accurate predictive models of disease spread to inform public health planning. However, in many LMICs, traditional data sets on travel such as commuting surveys as well as non-traditional sources such as mobile phone data are lacking, or, where available, have only rarely been leveraged by the public health community. Evaluating the accuracy of available data to measure transmission-relevant travel may be further hampered by limited reporting of suspected and laboratory confirmed infections.

Why are there so few (or so many) circulating coronaviruses?

Despite vast diversity in non-human hosts and conspicuous recent spillover events, only a small number of coronaviruses have been observed to persist in human populations. This puzzling mismatch suggests substantial barriers to establishment. We detail hypotheses that might contribute to explain the low numbers of endemic coronaviruses, despite their considerable evolutionary and emergence potential.

Variation in SARS-CoV-2 outbreaks across sub-Saharan Africa.

A surprising feature of the SARS-CoV-2 pandemic to date is the low burdens reported in sub-Saharan Africa (SSA) countries relative to other global regions. Potential explanations (for example, warmer environments, younger populations) have yet to be framed within a comprehensive analysis. We synthesized factors hypothesized to drive the pace and burden of this pandemic in SSA during the period from 25 February to 20 December 2020, encompassing demographic, comorbidity, climatic, healthcare capacity, intervention efforts and human mobility dimensions.

Monitoring for outbreak-associated excess mortality in an African city: Detection limits in Antananarivo, Madagascar.

Objectives: Quantitative estimates of the impact of infectious disease outbreaks are required to develop measured policy responses. In many low- and middle-income countries, inadequate surveillance and incompleteness of death registration are important barriers.

Design: Here, we characterize how large an impact on mortality would have to be for being detectable using the uniquely detailed mortality notification data from the city of Antananarivo, Madagascar, with application to a recent measles outbreak.

Cohort Description of the Madagascar Health and Environmental Research-Antongil (MAHERY-Antongil) Study in Madagascar.

The Madagascar Health and Environmental Research-Antongil (MAHERY-Antongil) study cohort was set up in September 2015 to assess the nutritional value of seafood for the coastal Malagasy population living along Antongil Bay in northeastern Madagascar. Over 28 months of surveillance, we aimed to understand the relationships among different marine resource governance models, local people's fish catch, the consumption of seafood, and nutritional status. In the Antongil Bay, fisheries governance takes three general forms: traditional management, marine national parks, and co-management.

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]).

Predicting nutrient content of ray-finned fishes using phylogenetic information.

Human food and nutrition security is dependent on marine ecosystems threatened by overfishing, climate change, and other processes. The consequences on human nutritional status are uncertain, in part because current methods of analyzing fish nutrient content are expensive. Here, we evaluate the possibility of predicting nutrient content of ray-finned fishes using existing phylogenetic and life history information.

The utility of genomic data for Plasmodium vivax population surveillance.

Genetic polymorphisms identified from genomic sequencing can be used to track changes in parasite populations through time. Such tracking is particularly informative when applying control strategies and evaluating their effectiveness. Using genomic approaches may also enable improved ability to categorise populations and to stratify them according to the likely effectiveness of intervention.

The origin and diversification of the merozoite surface protein 3 (msp3) multi-gene family in Plasmodium vivax and related parasites.

The genus Plasmodium is a diversified group of parasites with more than 200 known species that includes those causing malaria in humans. These parasites use numerous proteins in a complex process that allows them to invade the red blood cells of their vertebrate hosts. Many of those proteins are part of multi-gene families; one of which is the merozoite surface protein-3 (msp3) family.

Merozoite surface protein-3 alpha as a genetic marker for epidemiologic studies in Plasmodium vivax: a cautionary note.

Background: Plasmodium vivax is the most widespread of the human malaria parasites in terms of geography, and is thought to present unique challenges to local efforts aimed at control and elimination. Parasite molecular markers can provide much needed data on P. vivax populations, but few such markers have been critically evaluated.