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Mpox is a reemerging infectious disease caused by monkeypox virus (MPXV). Whole-genome sequencing provides comprehensive surveillance of MPXV but is challenging in resource-limited outbreak settings and on clinical samples with low viral load. We developed a low-cost, high-throughput partial-genome sequencing strategy and a freeware Nextflow pipeline for MPXV genomic surveillance. We targeted 2 genomic regions of MPXV by using short overlapping amplicons. This amplicon-based approach generated high-quality sequences over the 2 genomic regions from clinical specimens, including samples with low viral DNA and from formalin-fixed tissues. This partial-genome sequencing approach can determine MPXV subclades and offers an attractive strategy to lower cost and improve MPXV surveillance during outbreaks in mpox-endemic and -nonendemic countries.

The real-time generation of information about pathogen genomes has become a vital goal for transmission analysis and characterisation in rapid outbreak responses. In response to the recently established genomic capacity in the Democratic Republic of the Congo, we explored the real-time generation of genomic information at the start of the 2018 Ebola virus disease (EVD) outbreak in North Kivu Province. We used targeted-enrichment sequencing to produce two coding-complete Ebola virus genomes 5 days after declaration of the EVD outbreak in North Kivu. Subsequent sequencing efforts yielded an additional 46 genomes. Genomic information was used to assess early transmission, medical countermeasures, and evolution of Ebola virus. The genomic information demonstrated that the EVD outbreak in the North Kivu and Ituri Provinces was distinct from the 2018 EVD outbreak in Équateur Province of the Democratic Republic of the Congo. Primer and probe mismatches to Ebola virus were identified in silico for all deployed diagnostic PCR assays, with the exception of the Cepheid GeneXpert GP assay. The first two coding-complete genomes provided actionable information in real-time for the deployment of the rVSVΔG-ZEBOV-GP Ebola virus envelope glycoprotein vaccine, available therapeutics, and sequence-based diagnostic assays. Based on the mutations identified in the Ebola virus surface glycoprotein (GP12) observed in all 48 genomes, deployed monoclonal antibody therapeutics (mAb114 and ZMapp) should be efficacious against the circulating Ebola virus variant. Rapid Ebola virus genomic characterisation should be included in routine EVD outbreak response procedures to ascertain efficacy of medical countermeasures. Defense Biological Product Assurance Office.

The ongoing mpox clade Ib outbreak was first detected in the eastern Democratic Republic of Congo (DRC) and was associated with sexual transmission. It emerged in Kamituga, a mining city and spread rapidly in surrounding health zones and reached cities like Bukavu and Goma. Here, we describe the clinical, epidemiological, and virological characteristics of the first case of clade Ib in Kinshasa, the capital city in the western DRC. The case involved a young adult woman from Kinshasa who reported unprotected sexual contact with an occasional partner, a former friend, and subsequently developed genital lesions, including vesicles and pustules. These lesions evolved and spread to the entire body, including the limbs, eyes, and soles. The diagnosis was confirmed by PCR and sequencing allowed us to assign clade Ib. We show that infection with mpox clade Ib through sexual transmission can lead to limbal nodular keratoconjunctivitis and focal conjunctivitis as complications. Importantly, these results suggest that clade Ib may have been circulating silently in Kinshasa prior to the official declaration by the Ministry of Health. This also raises concerns about the potential risk of global spread, as is currently being observed. Further studies are needed to investigate whether subsequent outbreaks of clade Ib in Kinshasa may have emerged independently of introductions from Kivu, pointing to a more complex pattern of co-circulation that could define the mpox epidemic in the capital.

Monkeypox virus (MPXV) Clade Ib, a new MPXV subclade associated with sustained human-to-human transmission, emerged in eastern DRC in late 2023. Early spread mainly occurred among the adult population, primarily through sexual contact. We investigate how key epidemiological characteristics of the new MPXV Clade Ib outbreak in the DRC differ by transmission mode. We estimate the mean serial interval to be 8.57 days (95% CI 7.15 − 9.91 days). The serial interval is approximately four days shorter for putative sexual compared to non-sexual transmission. We estimate the mean incubation period to be 9.56 days (95% CrI 8.22 − 11.02 days), and approximately two days shorter for putative sexual compared to non-sexual transmission. These observed differences in serial interval and incubation period estimates by transmission mode suggest that the context in which an outbreak occurs is an essential factor to consider when devising public health policies. The study found that the serial interval and incubation period of monkeypox virus Clade Ib are shorter for putative sexual versus non-sexual transmission, indicating that epidemiological context is crucial for developing effective public health policies.

The 2018 Ebola virus disease (EVD) outbreak in Équateur Province, Democratic Republic of the Congo, began on May 8, and was declared over on July 24; it resulted in 54 documented cases and 33 deaths. We did a retrospective genomic characterisation of the outbreak and assessed potential therapeutic agents and vaccine (medical countermeasures). We used target-enrichment sequencing to produce Ebola virus genomes from samples obtained in the 2018 Équateur Province outbreak. Combining these genomes with genomes associated with known outbreaks from GenBank, we constructed a maximum-likelihood phylogenetic tree. In-silico analyses were used to assess potential mismatches between the outbreak strain and the probes and primers of diagnostic assays and the antigenic sites of the experimental rVSVΔG-ZEBOV-GP vaccine and therapeutics. An in-vitro flow cytometry assay was used to assess the binding capability of the individual components of the monoclonal antibody cocktail ZMapp. A targeted sequencing approach produced 16 near-complete genomes. Phylogenetic analysis of these genomes and 1011 genomes from GenBank revealed a distinct cluster, confirming a new Ebola virus variant, for which we propose the name “Tumba”. This new variant appears to have evolved at a slower rate than other Ebola virus variants (0·69 × 10−3 substitutions per site per year with “Tumba” vs 1·06 × 10−3 substitutions per site per year without “Tumba”). We found few sequence mismatches in the assessed assay target regions and antigenic sites. We identified nine amino acid changes in the Ebola virus surface glycoprotein, of which one resulted in reduced binding of the 13C6 antibody within the ZMapp cocktail. Retrospectively, we show the feasibility of using genomics to rapidly characterise a new Ebola virus variant within the timeframe of an outbreak. Phylogenetic analysis provides further indications that these variants are evolving at differing rates. Rapid in-silico analyses can direct in-vitro experiments to quickly assess medical countermeasures. Defense Biological Product Assurance Office.

Cholera remains a significant public health burden in many countries in sub-Saharan Africa, though the exact mechanisms of bacterial emergence and spread remain largely undefined. We generated genomic data from 763 Vibrio cholerae O1 isolates predominantly collected between 2019-2024 to create the largest dataset of V. cholerae genomes sequenced locally in Africa. This dataset enabled us to interrogate recent patterns of spread, including the rapid circulation of the AFR15 lineage associated with unusually large outbreaks in Southern Africa. We provide evidence for the movement of the AFR15 lineage into new African Union Member States and confirm previously observed differences in V. cholerae transmission dynamics in West versus East Africa, though cross-border transmission is prevalent on both sides of the continent. Despite observed differences, evolutionary processes are similar across lineages and we find no evidence for significant changes in antimicrobial resistance genotypes. Overall, our findings emphasize the importance of regionally coordinated cross-border surveillance and interventions, while also demonstrating the critical role of locally generated genomic data in understanding the spread of cholera in Africa. Cholera remains a significant public health burden in sub-Saharan Africa, but the mechanisms of continental and regional spread remain undefined. Here, the authors investigate recent patterns of spread using Vibrio cholerae genomic surveillance data collected by a consortium of seven African Union member states from 2019-2024.

Summary Background One year after the coronavirus disease 2019 (COVID-19) pandemic, the focus of attention has shifted to the emergence and spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs). The aim of the study was to assess the frequency of VOCs in patients followed for COVID-19 at Kinshasa university hospital (KUH) during the 3rd and 4th waves of the pandemic in Kinshasa. Hospital mortality was compared to that of the first two waves. Method The present study included all patients in whom the diagnosis of SARS-CoV-2 infection was confirmed by the polymerase chain reaction (PCR). The laboratory team sequenced a subset of all SARS-CoV-2 positive samples with high viral loads define as Ct < 25 to ensure the chances to generate complete genome sequence. RNA extraction was performed using the Viral RNA Mini Kit (Qiagen). Depending on the platform, we used the iVar bioinformatics or artic environments to generate consensus genomes from the raw sequencing output in FASTQ format. Results During the study period, the original strain of the virus was no longer circulating. The Delta VOC was predominant from June (92%) until November 2021 (3rd wave). The Omicron VOC, which appeared in December 2021, became largely predominant one month later (96%) corresponding the 4th wave. In-hospital mortality associated with COVID-19 fell during the 2nd wave (7% vs. 21% 1st wave), had risen during the 3rd (16%) wave before falling again during the 4th wave (7%) (p < 0.001). Conclusion The Delta (during the 3rd wave) and Omicron VOCs (during the 4th wave) were very predominant among patients followed for Covid-19 in our hospital. Contrary to data in the general population, hospital mortality associated with severe and critical forms of COVID-19 had increased during the 3rd wave of the pandemic in Kinshasa.

Human Mpox cases are increasingly reported in Africa, with the highest burden in the Democratic Republic of Congo (DRC). While case reporting on a clinical basis can overestimate infection rates, laboratory confirmation by PCR can underestimate them, especially on suboptimal samples like blood, commonly used in DRC. Here we used a Luminex-based assay to evaluate whether antibody testing can be complementary to confirm cases and to identify human transmission chains during outbreak investigations. We used left-over blood samples from 463 patients, collected during 174 outbreaks between 2013 and 2022, with corresponding Mpox and VZV PCR results. In total, 157 (33.9%) samples were orthopox-PCR positive and classified as Mpox+; 124 (26.8%) had antibodies to at least one of the three Mpox peptides. The proportion of antibody positive samples was significantly higher in Mpox positive samples (36.9%) versus negative (21.6%) (p < 0.001). By combining PCR and serology, 66 additional patients were identified, leading to an Mpox infection rate of 48.2% (223/463) versus 33.9% when only PCR positivity is considered. Mpox infections were as such identified in 14 additional health zones and 23 additional outbreaks (111/174 (63.8%) versus 88/174 (50.6%)). Our findings highlight the urgent need of rapid on-site diagnostics to circumvent Mpox spread.

In this report from the Democratic Republic of Congo, Ebola virus disease (EVD) developed in a young man, and he recovered after treatment with a monoclonal antibody. Six months later, EVD recrudesced, and he transmitted the virus to others and died from EVD.

DR Congo has the highest global burden of mpox, a disease caused by infection with the monkeypox virus. The incidence has risen since 1980, but recent analyses of epidemiological trends are lacking. We aimed to describe trends in suspected and confirmed mpox cases in DR Congo using epidemiological and laboratory mpox surveillance data collected from 2010 to 2023, and provide insights that can better inform the targeting and monitoring of control strategies. We analysed aggregated national epidemiological surveillance data and individual-level laboratory data from 2010 to 2023. We calculated incidence based on suspected cases, case-fatality ratios, and percentage of laboratory-confirmed cases and assessed geospatial trends. Demographic and seasonal trends were investigated using generalised additive mixed models. Between Jan 1, 2010, and Dec 31, 2023, a total of 60 967 suspected cases and 1798 suspected deaths from mpox were reported in DR Congo (case-fatality ratio 2·9%). The number of reporting provinces increased from 18 of 26 provinces in 2010 to 24 of 26 provinces in 2023. The annual incidence increased from 2·97 per 100 000 in 2010 to 11·46 per 100 000 in 2023. The highest incidence (46·38 per 100 000) and case-fatality ratio (6·0%) were observed in children younger than 5 years. Incidence was higher in rural compared with urban areas. PCR testing was performed for 7438 suspected cases (12·2%), with 4248 (57·1%) of 7438 samples testing positive. Median age of confirmed cases (13·0 years [IQR 6·0–25·0]) remained stable, although the 95th percentile of age increased over time. The incidence and geographical distribution of suspected mpox cases have increased substantially since 2010. Improvements in surveillance and decentralised testing are essential to monitor mpox trends and direct interventions effectively, to address the public health emergency declarations issued in August, 2024. Belgian Directorate-General Development Cooperation and Humanitarian Aid; European and Developing Countries Clinical Trials Partnership; Research Foundation–Flanders; European Civil Protection and Humanitarian Aid Operations; Department of Economy, Science, and Innovation of the Flemish Government; Canadian Institutes of Health Research; and the International Development Research Centre.