: Unexplained fever poses significant diagnostic challenges in resource-limited settings like Bamako, Mali, where overlapping endemic diseases include malaria, HIV/AIDS, yellow fever, typhoid, and others. This study aimed to elucidate the infectious etiologies of acute febrile illnesses in this context. Acute febrile patients of any age were enrolled after informed consent or assent. Baseline clinical and demographic data were collected, and samples were analyzed by using rapid diagnostic tests, reverse transcriptase polymerase chain reaction, ELISA, and virus-targeted metagenomic sequencing (virome capture sequencing platform for vertebrate viruses [VirCapSeq-VERT]). Among 108 enrolled subjects, most were male (51.9%) and under 15 years old (56.5%). Measles virus was identified in 39.8% of cases, primarily among children. Other findings included Plasmodium spp. (12%), Salmonella spp. (13%), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; 8.7%). The virome capture sequencing platform for vertebrate viruses was used for 101 subjects, corroborating many routine test results and identifying additional cases of measles virus (1), SARS-CoV-2 (5), and numerous other agents. Notably, nearly all subjects showed evidence of herpesviruses (90%) and anelloviruses (98%). Hemorrhagic fever viruses were not observed. With the inclusion of VirCapSeq-VERT, identifiable pathogens were found in 79.6% of cases, leaving 20.4% without a clear etiology. The identification of more than one concurrent pathogen was common (41.5%). Integrating metagenomic sequencing with routine laboratory diagnostic testing enhances the detection of pathogens in acute febrile illnesses, highlighting its potential value in identifying infectious etiologies in resource-limited settings.

We utilized a pan-viral capture sequencing assay, VirCapSeq-VERT, to assess viral diversity in rodents from the Eastern Province of Zambia as a model for pre-pandemic viral reservoir surveillance. We report rodent adeno-, parvo-, paramyxo-, and picornaviruses that represent novel species or isolates, including murine adenovirus 4, two additional species in the genus Chaphamaparvovirus, two paramyxoviruses distantly related to unclassified viruses in the genus Jeilongvirus, and the first Aichivirus A sequence identified from rodents in Africa. Our results emphasize the importance of rodents as a reservoir for potential zoonotic viruses.

We report the first confirmed cases of Zika virus (ZIKV) disease (ZVD) in Kenya and provide the associated genomic sequences. The study is part of a prospective febrile illness surveillance study in Kenya. A cluster of ZVD cases was identified in patients with fever presenting at King Fahd Referral Hospital, Lamu Island. Clinical signs resembled those caused by dengue or malaria and included fever, chills, muscle and joint pains, and headache. The Biofire Film Array Global fever panel (BioFire Diagnostics, UT, USA) identified ZIKV in three of five blood samples. RNA extracted from plasma was used for sequence library preparation and subsequent viral enrichment using the VirCapSeq-VERT probe set designed at the Center for Infection and Immunity, Columbia University. Enriched libraries were sequenced on the NextSeq 2000 (Illumina, San Diego, CA, USA). Assembled genomes were classified into lineages and a spatio-temporal phylogeny inferred with Nextstrain v8.5.3. Assembled genomes produced contigs covering between 3363 and 10,950 nt that mapped to the Asian lineage of ZIKV and branched with genomes from India. Mutation profiling revealed viral strains with potentially enhanced transmission and immune evasion capabilities. The presence of the more transmissible Asian lineage ZIKV that has previously caused large outbreaks of ZVD in the Americas raises significant public health concern.

: Dengue fever, a vector-borne disease caused by four serotypes of dengue virus (DENV), ranges from asymptomatic to severe illness, including hemorrhagic fever and shock syndrome. A 2023 outbreak (August 2023–May 2024) in Mali affected six districts in Bamako, causing 1,422 confirmed cases with a 2.7% fatality rate. In this study, viral sequencing provided insights into the molecular epidemiology and transmission dynamics of this outbreak. From September to October 2023, 23 of 42 suspected cases detected through national dengue surveillance activities were tested using the pan-vertebrate virus metagenomics method (virome capture sequencing platform for vertebrate viruses [VirCapSeq-VERT]). Sequencing data were analyzed using the Rapid Identification of Microbes pipeline, and Bayesian phylogenetic inference with Monte Carlo methods was used to assess viral genomic evolution. Among 23 patients, 61% were male, and the median age was 37 years (range: 20–74). The most common symptoms were fever (93.1%), headache (56.5%), and asthenia (47.8%). The largest proportion experienced dengue with warning signs (65.2%), followed by dengue without warning signs (30.4%) and severe dengue (4.4%). The successful sequencing of 19 samples revealed dengue virus serotype 3 (DENV-3; genotype III) in 15 (65.21%) samples and dengue virus serotype 1 (DENV-1; genotype III) in 4 (17.39%) samples. The DENV-1 sequences were analogous to West African sequences, and the DENV-3 were clustered with West African, Asian, and Caribbean sequences. In this study of DENV in Mali, we offer insights into the molecular epidemiology of the virus and underscore the benefits of the genomic surveillance of arboviruses in West Africa.

: Orthobunyaviruses, one of the largest and most diverse genera of viruses, include numerous reassortant viruses and present diagnostic challenges due to similar clinical presentations with other arboviral infections. The detection and isolation of a group C orthobunyavirus from a patient with acute febrile illness from Puerto Ospina, Putumayo Department, Colombia during the 2023–2024 Latin American Oropouche fever regional outbreaks are reported in the present study. Using a vertebrate virus-focused metagenomics sequencing approach with VirCapSeq-VERT, a virus related to the Caraparu complex was identified, and a virus isolate was obtained. Although limited to a single case and without serological or longitudinal clinical confirmation, these findings underscore the value of unbiased molecular approaches for unresolved febrile illness diagnosis in endemic settings such as the Amazon basin.

The authors wish to make the following correction to this paper