Seroprevalence of dengue in the Democratic Republic of Congo, Ghana and Senegal: results of the SERODEN study

Methods: A total of 97 bat guano samples were collected from three caves in urban areas of Algeria.After nucleic acid extraction, pan-coronavirus screening was conducted using a nested RT-PCR system.Subsequently, PCR amplicons were cloned into pGEM-T Easy vectors, transformed into E. coli, and screened via blue/white screening.Positive clones were sequenced using an ABI Prism 310 DNA Sequencer.For full genome recovery, libraries were prepared with NEBNext kits for the Illumina NextSeq platform, followed by sequencing and data analysis utilizing CLC Genomics Workbench and Diamond.Phylogenetic analysis was conducted using the IQ-TREE web server.Results: PCR screening unveiled four alphacoronaviruses and two betacoronaviruses in bat species including Rhinolophus ferrumequinum, Myotis punicus, Miniopterus schreibersii, and Plecotus gaisleri.Particularly noteworthy was the identification of an alphacoronavirus in Plecotus gaisleri for the first time.Furthermore, the co-circulation of alpha and beta coronaviruses in Rhinolophus ferrumequinum was emphasized, and a full betacoronavirus genome was recovered.It formed a sister clade with the Khosta-1 Russian coronavirus, sharing 89.48% nucleotide identity.Discussion: The alphacoronavirus isolated from Myotis punicus clustered with another Algerian alphacoronavirus detected in Miniopterus schreibersii from a different city.This highlights the impact of their co-roosting habits on viral diversity and supports previous theories on the lack of association between coronaviruses and their sampling locations.Interestingly, the first described coronavirus from Plecotus gaisleri clustered with Rhinolophus-related alphacoronaviruses found in Kenya and Guinea, rather than Algeria.Data on coronaviruses in Plecotus gaisleri are sparse, hence further investigations are needed.Additionally, the evidence of co-circulation of an alphacoronavirus and a betacoronavirus in Rhinolophus ferrumequinum aligns with previous observations in other species, raising concerns about potential recombination events and new coronaviruse emergence.The clustering of the Algerian betacoronavirus with the Russian sequence point toward the role of bat migration in viral spread.Conclusion: Despite limited research in regions like Algeria, our study emphasizes the importance of understanding bat-related viral zoonoses within a One Health framework to mitigate zoonotic disease risks.The identification of diverse coronaviruses in Algerian bats underscores the necessity for continued surveillance and research to prevent future outbreaks.