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Open AccessHIV-1 diversity and pre-treatment drug resistance in the era of integrase inhibitor among newly diagnosed ART-naïve adult patients in Luanda, Angola
The surveillance of drug resistance in the HIV-1 naïve population remains critical to optimizing the effectiveness of antiretroviral therapy (ART), mainly in the era of integrase strand transfer inhibitor (INS...
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Open AccessShifting patterns of dengue three years after Zika virus emergence in Brazil
In 2015, the Zika virus (ZIKV) emerged in Brazil, leading to widespread outbreaks in Latin America. Following this, many countries in these regions reported a significant drop in the circulation of dengue viru...
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Open AccessIncreased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil
The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow fever, zika, chikungunya, and dengue have had serious impacts on public health. Concerns have been raised due to the rapid diss...
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Article
Open AccessGlobal transmission suitability maps for dengue virus transmitted by Aedes aegypti from 1981 to 2019
Mosquito-borne viruses increasingly threaten human populations due to accelerating changes in climate, human and mosquito migration, and land use practices. Over the last three decades, the global distribution...
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Article
Open AccessA traveling SARS-CoV-2 laboratory as part of a pandemic response among vulnerable Brazilian populations
Brazil has been dramatically hit by the SARS-CoV-2 pandemic and is a world leader in COVID-19 morbidity and mortality. Additionally, the largest country of Latin America has been a continuous source of SARS-Co...
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Article
Open AccessEmergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19)...
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Open AccessGenomic epidemiology of the SARS-CoV-2 epidemic in Brazil
The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps r...
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Open AccessRapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (...
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Article
Open AccessWest Nile virus transmission potential in Portugal
It is unclear whether West Nile virus (WNV) circulates endemically in Portugal. Despite the country’s adequate climate for transmission, Portugal has only reported four human WNV infections so far. We performe...
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Open AccessSARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulatio...
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Open AccessField and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil
Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and cla...
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Article
Detection of a SARS-CoV-2 variant of concern in South Africa
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (des...
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Open AccessReal-time seroprevalence and exposure levels of emerging pathogens in infection-naive host populations
For endemic pathogens, seroprevalence mimics overall exposure and is minimally influenced by the time that recent infections take to seroconvert. Simulating spatially-explicit and stochastic outbreaks, we set ...
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Article
Sixteen novel lineages of SARS-CoV-2 in South Africa
The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. ...
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Open AccessPotential impact of individual exposure histories to endemic human coronaviruses on age-dependent severity of COVID-19
Cross-reactivity to SARS-CoV-2 from exposure to endemic human coronaviruses (eHCoV) is gaining increasing attention as a possible driver of both protection against infection and COVID-19 severity. Here we expl...
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Open AccessA persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual
Since the first outbreak of SARS-CoV-2, the clinical characteristics of the Coronavirus Disease 2019 (COVID-19) have been progressively changed. Data reporting a viral intra-host and inter-host evolution favou...
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Open AccessEmerging of a SARS-CoV-2 viral strain with a deletion in nsp1
The new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first detected in Wuhan (China) in December of 2019 is responsible for the current global pandemic. Phylogenetic analysis reveale...
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Open AccessHIV rapid testing in community and outreach sites: results of a nationwide demonstration project in Italy
Globally the access to HIV testing has greatly increased over the past 30 years. Nonetheless, a high proportion of people living with HIV remains undiagnosed, even in resource rich countries. To increase the p...
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Article
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
This multiplex PCR enrichment protocol enables sequencing of Zika and other viral genomes of low abundance from clinical samples using the Illumina platform, or the portable MinION sequencer, facilitating dire...
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Article
Open AccessMISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification
Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires h...
