Tulio de Oliveira

• BSc, BSc(Honours), PhD
• Professor (Full) at University of KwaZulu-Natal

Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated intrahost recombination and single nuc...

Oropouche virus (OROV) is an emerging arbovirus with increasing outbreaks in South America, yet its environmental drivers and potential range remain poorly understood. Using ecological niche modeling (ENM) with random forests, we assessed the environmental suitability of OROV and its primary vector, Culicoides paraensis, across Brazil and the Ameri...

Oropouche virus (OROV), first detected in Trinidad and Tobago in 1955, was historically confined to the Brazilian Amazon Basin. However, since late 2022, an increasing number of OROV cases have been reported across various regions of Brazil as well as in urban centers in Bolivia, Ecuador, Guyana, Colombia, Cuba, Panama, and Peru. In collaboration w...

Priestia megaterium strain AB-S79 isolated from active gold mine soil previously expressed in vitro heavy metal resistance and has a 5.7 Mb genome useful for biotechnological exploitation. This study used web-based bioinformatic resources to analyze P. megaterium AB-S79 genomic relatedness, decipher its secondary metabolite biosynthetic gene cluste...

Motivation The dengue virus poses a major global health threat, with nearly 390 million infections annually. A recently proposed hierarchical dengue nomenclature system enhances spatial resolution by defining major and minor lineages within genotypes, aiding efforts to track viral evolution. While current subtyping tools – Genome Detective, GLUE, a...

Brazil, Russia, India, China, and South Africa (BRICS) are a group of developing countries with shared economic, healthcare, and scientific interests. These countries navigate multiple syndemics, and the COVID-19 pandemic placed severe strain on already burdened BRICS’ healthcare systems, hampering effective pandemic interventions. Genomic surveill...

Background In low- and middle-income countries (LMICs) such as South Africa, there is paucity of data on SARS-CoV-2 infections among children attending school, including seroprevalence and transmission dynamics. Objective This pilot study aims to assess (1) the prevalence of self-reported or confirmed SARS-CoV-2 prior infections, COVID-19 symptoms...

Background West Nile Virus (WNV) is a zoonotic flavivirus of significant One Health relevance and is classified as a priority pathogen with a high-risk of causing public health emergencies of global concern. WNV is endemic to Africa; however, the availability of genomic sequences from the continent remains limited. Methods We review the extent of p...

Background: The rapid increase in nucleotide sequence data generated by next-generation sequencing (NGS) technologies demands efficient computational tools for sequence comparison. Alignment-based methods, such as BLAST, are increasingly overwhelmed by the scale of contemporary datasets due to their high computational demands for classification. Th...

Background Dengue is a significant global public health concern that poses a threat in Africa. Particularly, African countries are at risk of viral introductions through air travel connectivity with areas of South America and Asia in which explosive dengue outbreaks frequently occur. Limited reporting and diagnostic capacity hinder a comprehensive...

Botswana, like the rest of the world, has been significantly impacted by SARS-CoV-2. In December 2022, we detected a monophyletic cluster of genomes comprising a sublineage of the Omicron variant of concern (VOC) designated as B.1.1.529.5.3.1.1.1.1.1.1.74.1 (alias FN.1, clade 22E). These genomes were sourced from both epidemiologically linked and u...

In March 2024, the Pan American Health Organization (PAHO) issued an alert in response to a rapid increase in Oropouche fever cases across South America. Brazil has been particularly affected, reporting a novel reassortant lineage of the Oropouche virus (OROV) and expansion to previously non-endemic areas beyond the Amazon Basin. Utilising phylogeo...

Background Dengue is a major mosquito-borne disease worldwide. The epidemiological trends of the disease in Africa over the past decade remain unclear. This review aims to provide insight into the epidemiological trends of dengue in Africa from 2013-2023. Methods We systematically searched PubMed/MEDLINE and Scopus for studies published between Jan...

The first era of genomics started with the publication of Watson and Crick’s notable work on the description of the DNA double helix in 1953. This era lasted 50 years, until the publication of the human genome in April 2003. The second era is associated with the period between the completion of the human genome and the present day. I argue that, wi...

Background: Italy was significantly affected by the COVID-19 pandemic, experiencing multiple waves of infection following the sequential emergence of new variants. Understanding the transmission patterns and evolution of SARS-CoV-2 is vital for future preparedness. Methods: We conducted an analysis of viral genome sequences, integrating epidemiolog...

Chronic Hepatitis B Virus (HBV) infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is an enveloped virus, classified into ten phylogenetically distinct genotypes (A – J). Tests to determine HBV genotypes are based on full-genome sequencing or reverse hybridization. In practice, both a...

Chronic Hepatitis B Virus (HBV) infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is an enveloped virus, classified into ten phylogenetically distinct genotypes (A – J). Tests to determine HBV genotypes are based on full-genome sequencing or reverse hybridization. In practice, both a...

Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here, we prop...

From the perspective of developing relevant interventions for treating HIV and controlling its spread, it is particularly important to comprehensively understand the underlying diversity of the virus, especially in countries where the virus has been present and evolving since the cross-species transmission event that triggered the global pandemic....

The Oropouche virus, initially detected in Trinidad and Tobago in 1955, has been historically confined to the Amazon Basin. However, since late 2022, it has been reported elsewhere, from northern Brazil to urban centers in Bolivia, Colombia, Cuba, and Peru. In this report we describe the doubling of publicly available full genomes by generating 133...

Health consequences arising from climate change are threatening to offset advances made to reduce the damage of infectious diseases, which vary by region and the resilience of the local health system. Here we discuss how climate change-related migrations and infectious disease burden are linked through various processes, such as the expansion of pa...

Background The World Health Organization (WHO) recommends that HIV treatment scale-up is accompanied by a robust assessment of drug resistance emergence and transmission. The WHO HIV Drug Resistance (HIVDR) monitoring and surveillance strategy includes HIVDR testing in adults both initiating and receiving antiretroviral therapy (ART). Due to limite...

The Chikungunya virus (CHIKV) poses a significant global public health concern, especially in Africa. Since its first isolation in Tanzania in 1953, CHIKV has caused recurrent outbreaks, challenging healthcare systems in low-resource settings. Recent outbreaks in Africa highlight the dynamic nature of CHIKV transmission and the challenges of underr...

42 In Ethiopia, dengue virus (DENV) infections have been reported in several regions, however, little 43 is known about the circulating genetic diversity. Here, we conducted clinical surveillance for 44 DENV during the 2023 nationwide outbreak and sequenced DENV whole genomes for the first 45 time in Ethiopia. We enrolled patients at three sentinel...

During the coronavirus disease 2019 (COVID-19) pandemic, the number and types of dashboards produced increased to convey complex information using digestible visualizations. The pandemic saw a notable increase in genomic surveillance data, which genomic epidemiology dashboards presented in an easily interpretable manner. These dashboards have the p...

The Chikungunya virus (CHIKV) poses a significant global public health concern, especially in Africa. Since its first isolation in Tanzania in 1953, CHIKV has caused recurrent outbreaks, challenging healthcare systems in low-resource settings. Recent outbreaks in Africa highlight the dynamic nature of CHIKV transmission and the challenges of underr...

Outbreaks of monkeypox (mpox) have historically resulted from zoonotic spillover of clade I monkeypox virus (MPXV) in Central Africa and clade II MPXV in West Africa. In 2022, subclade IIb caused a global epidemic linked to transmission through sexual contact. Here we describe the epidemiological and genomic features of an mpox outbreak in a mining...

During the SARS-CoV-2 pandemic, next-generation sequencing (NGS) technologies like the Ion Torrent S5 and Illumina MiSeq, alongside advanced software, improved genomic surveillance Detective and NextClade, showing Ion Torrent S5 and Illumina MiSeq success rates of 96% and 94%, respectively. The study focused on genomic coverage (above 80%) and muta...

HIV-1 group M (HIV-1M) lineages downregulate HLA-I and CD4 expression via their Nef proteins. We hypothesized that these Nef functions may be partially responsible for the differences in prevalence of viruses from different lineages that co-circulate within an epidemic. Here, we characterized these two Nef activities in HIV-1M isolates from Cameroo...

Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here we propo...

Background: The dengue virus is a significant global public health concern that poses a threat to Africa. Particularly, African countries are at risk of viral introductions through air travel connectivity with areas of South America and Asia that experience frequent explosive outbreaks. Limited reporting and diagnostic capacity hinder a comprehensi...

The SARS-CoV-2 genome occupies a unique place in infection biology – it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable re...

SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We asse...

Introduction The World Health Organization (WHO) recommends that HIV treatment scale-up is accompanied by a robust assessment of drug resistance emergence and transmission. Included in the WHO HIV Drug Resistance (HIVDR) monitoring and surveillance strategy is HIVDR testing in adults both initiating and receiving antiretroviral therapy (ART). Due t...

Chronic hepatitis B virus (HBV) infection remains a significant public health concern, particularly in Africa, where there is a substantial substantial. HBV is an enveloped virus, with isolates being classified into ten phylogenetically distinct genotypes (A-J) determined based on full-genome sequence data or reverse hybridization-based diagnostic...

Africa bears a disproportionate burden of infectious diseases, accounting for a substantial percentage of global cases. Malaria, HIV/AIDS, tuberculosis, cholera, Ebola , Lassa fever, and other tropical diseases , such as dengue and chikungunya, have had a profound impact on morbidity and mortality. Various factors contribute to the higher prevalenc...

We investigated intra-host genetic evolution using two SARS-CoV-2 isolates from a fully vaccinated (primary schedule x2 doses of AstraZeneca plus a booster of Pfizer), >70-year-old woman with a history of lymphoma and hypertension who presented a SARS-CoV-2 infection for 3 weeks prior to death due to COVID-19. Two full genome sequences were determi...

One mechanism of variant formation may be evolution during long-term infection in immunosuppressed people. To understand the viral phenotypes evolved during such infection, we tested SARS-CoV-2 viruses evolved from an ancestral B.1 lineage infection lasting over 190 days post-diagnosis in an advanced HIV disease immunosuppressed individual. Sequenc...

Wastewater-based surveillance (WBS) has become a useful public health tool as an early warning system revealing emergence/re-emergence of pathogenic diseases and spread of antimicrobial resistance (AMR). WBS is crucial in development of rapid response and increasing public health awareness to curb dangers associated with disease emergence and antib...

Omicron BA.2.86 subvariant differs from Omicron BA.2 as well as recently circulating variants by over 30 mutations in the spike protein alone. Here we report on the isolation of the live BA.2.86 subvariant from a diagnostic swab collected in South Africa which we tested for escape from neutralizing antibodies and viral replication properties in cel...

Chikungunya (CHIKV) is a re-emerging endemic arbovirus in West Africa. Since July 2023, Senegal and Burkina Faso have been experiencing an ongoing outbreak, with over 300 confirmed cases detected so far in the regions of Kedougou and Tambacounda in Senegal, the largest recorded outbreak yet. CHIKV is typically maintained in a sylvatic cycle in Sene...

The 2010 cholera epidemic in Haiti was thought to have ended in 2019, and the Prime Minister of Haiti declared the country cholera-free in February 2022. On September 25, 2022, cholera cases were again identified in Port-au-Prince. We compared genomic data from 42 clinical Vibrio cholerae strains from 2022 with data from 327 other strains from Hait...

Background In Angola, COVID‐19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS‐CoV‐2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID‐19 pandem...

BACKGROUND In low- and middle-income countries (LMICs) such as South Africa, there is paucity of data on SARS-CoV-2 infections among children attending school, including seroprevalence and transmission dynamics. OBJECTIVE This pilot study aims to assess (1) the prevalence of self-reported or confirmed SARS-CoV-2 prior infections, COVID-19 symptoms...

Omicron BA.2.86 subvariant differs from Omicron BA.2 as well as recently circulating variants by over 30 mutations in the spike protein alone. Here we report on the first isolation of the live BA.2.86 subvariant from a diagnostic swab collected in South Africa which we tested for escape from neutralizing antibodies and viral replication properties...

Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phyloge-netic and epidemiological models, we reconstructed the recent transmission history of YFV within different epidemic seasons in Bra...

Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phyloge-netic and epidemiological models, we reconstructed the recent transmission history of YFV within different epidemic seasons in Bra...

While the world recovers from the COVID-19 pandemic, another crisis continues to spiral at a much faster speed than was expected. Climate change is dominating our lives and causing a high level of distress. Countries all over the world are struggling to survive the damage caused by extreme events. They are trying to control wildfires, rebuild roads...

Since early 2022, in the aftermath of two extreme weather events, Malawi experienced its largest ever cholera outbreak, with over 58,000 reported cases and 1,761 deaths as of May 2023. We generated 49 high-quality, near-complete Vibrio cholerae genomes in Malawi from isolates collected between December 2022 and March 2023 from all three regions of...

To design effective vaccines and other immune interventions against a pathogen, it is necessary to know which aspect of immunity associates with protection. We investigated whether neutralizing antibodies associate with infection clearance in long-term SARS-CoV-2 infection during HIV-mediated immunosuppression. We monitored neutralizing antibody ac...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) now arise in the context of heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron BA.1 genomes, we identified >6,000 introductions of the antigenically distinct VOC into England and analyzed thei...

Antimicrobial resistance is increasing despite new treatments being employed, so novel strategies are required to ensure that bacterial infections remain treatable. Bacteriophages (phages; bacteria viruses) have the potential to be used as natural antimicrobial methods to control bacterial pathogens such as Salmonella spp. A Salmonella phage, Wara,...

In the original publication [...].

Background: In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1,900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence, and epidemic progression during the peak of the COVID-19 pan...

Background: Concerns around accuracy and performance of rapid antigen tests continue to be raised with the emergence of new SARS-CoV-2 variants. Objective: To evaluate the performance of two widely used SARS-CoV-2 rapid antigen tests during BA.4/BA.5 SARS-CoV-2 wave in South Africa (May - June 2022). Study design: A prospective field evaluatio...

The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the disper...

Intra-host diversity studies are used to characterise the mutational heterogeneity of SARS-CoV-2 infections in order to understand the impact of virus-host adaptations. This study investigated the frequency and diversity of the spike (S) protein mutations within SARS-CoV-2 infected South African individuals. The study included SARS-CoV-2 respirator...

SARS-CoV-2 lineages and variants of concern (VOC) have gained more efficient transmission and immune evasion properties with time. We describe the circulation of VOCs in South Africa and the potential role of low-frequency lineages on the emergence of future lineages. Whole genome sequencing was performed on SARS-CoV-2 samples from South Africa. Se...

The global pandemic caused by SARS-CoV-2 has increased the demand for scalable sequencing and diagnostic methods, especially for genomic surveillance. Although next-generation sequencing has enabled large-scale genomic surveillance, the ability to sequence SARS-CoV-2 in some settings has been limited by the cost of sequencing kits and the time-cons...

The spread of vector-borne viruses, such as CHIKV, is a significant public health concern in the Americas, with over 120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiological techniques, we characterized the ongoing large CHIKV epidemic in Paraguay. Article Summary Line Genom...

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and 7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In...

Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020 and it has since spread to all provinces in the country. To investigate the introductions and spread of SARS-CoV-2 in Mozambique, 1 142 whole genome sequences sampled within Mozambique were phylogenetically analyzed against a globally representative set, reflect...

HIV associated neurocognitive disorder (HAND) remains an important HIV-associated comorbidity despite antiretrovirals (ARVs). Cerebrospinal fluid (CSF) escape/discordance is now recognised in the context of individuals with a reconstituted immune system with an estimated prevalence of 10%. However, the contribution of CSF escape/discordance to HAND...

Background: Rifampicin resistance missed by commercial rapid molecular assays but detected by phenotypic assays may lead to discordant susceptibility results and affect patient management. Objective: This study was conducted to evaluate the causes of rifampicin resistance missed by the GenoType MTBDRplus and its impact on the programmatic manageme...

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499 000 cases, and ~7 500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. I...

Pathogen genomes harbor critical information necessary to support genomic investigations that inform public health interventions such as treatment, control, and eradication. To extract this information, their sequences are analysed to identify structural variations such as single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)...

Despite the considerable morbidity and mortality of Yellow fever virus (YFV) infections in Brazil, as well as its widespread presence in non-human primate host, our understanding of disease outbreaks is hampered by limited viral genomic data. Determining the timing and spatial corridors of YFV spread, as well as the geographic hotspots that link th...

SARS-CoV-2 variants of concern (VOCs) arise against the backdrop of increasingly heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron genomes, we identified >6,000 independent introductions of the antigenically distinct virus into England and reconstructed the dispersal history of...

[This corrects the article DOI: 10.1371/journal.pntd.0009591.].

Recurrent disease outbreaks caused by a range of emerging and resurging pathogens over the past decade reveal major gaps in public health preparedness, detection, and response systems in Africa. Underlying causes of recurrent disease outbreaks include inadequacies in the detection of new infectious disease outbreaks in the community, in rapid patho...

The SARS-CoV-2 Africa dashboard is an interactive tool that enables visualization of SARS-CoV-2 genomic information in African countries. The customizable app allows users to visualize the number of sequences deposited in each country, and the variants circulating over time. Our dashboard enables near real-time exploration of public data that can i...

In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon of global viral lineage displacement was observed...

The milder clinical manifestations of Omicron infection relative to pre-Omicron SARS-CoV-2 raises the possibility that extensive evolution results in reduced pathogenicity. To test this hypothesis, we quantified induction of cell fusion and cell death in SARS-CoV-2 evolved from ancestral virus during long-term infection. Both cell fusion and death...

Background: Genomic surveillance, with the aid of next-generation sequencing (NGS) technologies, revolutionized the SARS-CoV-2 pandemic. Coupled with high-performance analysis software, methodologies such as the Ion Torrent S5 and Illumina MiSeq dramatically improved the genomic surveillance capacity within South Africa during the height of the pan...

Background Human mobility changed in unprecedented ways during the SARS-CoV-2 pandemic. In March and April 2020, when lockdowns and large travel restrictions began in most countries, global air-travel almost entirely halted (92% decrease in commercial global air travel in the months between February and April 2020). Initial recovery in global air t...

Background Relationships between distinct antiretroviral therapy (ART) adherence patterns and risk of drug resistance are not well understood. Methods We conducted a nested case–control analysis within a longitudinal cohort study of individuals initiating efavirenz-based ART. Primary outcomes of interest, measured at 6 and 12 months after treatmen...

Lymphoid tissues are an important HIV reservoir site that persists in the face of antiretroviral therapy and natural immunity. Targeting these reservoirs by harnessing the antiviral activity of local tissue-resident memory (TRM) CD8⁺ T-cells is of great interest, but limited data exist on TRM-like cells within lymph nodes of people living with HIV...