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Context: Background: Chikungunya is an emerging global threat because of the unprecedented magnitude of its spread and highly debilitating disease. Objective: This study was informed by the need to use serological methods to unmask the chikungunya virus (CHIKV) from suspected malaria patients. Methodology: The ELISA IgM and PRNT90 (nAb) were used to assess the presence of CHIKV antibodies. Findings: Of 530 patients, 129 (24.3%) had CHIKV IgM, 199 (37.5%) neutralizing antibody (nAb) and 23 (4.3%) IgM + nAb. Only 4.3% of the patients and 43.9% of the IgM negatives had CHIKV nAb indicating acute and past infections respectively. Of 200 patients from Adamawa State, 6.5%, 42.5%, and 3.5% were CHIKV IgM, nAb, and IgM + nAb respectively. In Borno State, 47.0% were IgM, 49.0% nAb and 4.5% were IgM+ nAb . Of 130 samples from Bauchi State, 72.3% had IgM, 16 (12.3%) nAb, and 5.4% IgM + nAb. CHIKV infections in Bauchi and Borno were significantly higher than in Adamawa but residents of the three states are at risk. This study also detected co-infections between CHIKV and flaviviruses at varied degrees: dengue viruses (DENV) (17.7%), Zika virus (ZIKV) (1.5%, West Nile virus (WNV) (4.0%), and yellow fever virus (YFV) (1.3%). The type of settlement, gender, age, and yellow fever vaccination status of the patients were not significantly associated with CHIKV nAb. However, patients aged >60 years were more likely to have experienced CHIKV infections than younger age groups. CHIKV nAb and samples collected 1-7 days after the onset of symptoms were significantly different from those within 7-10 days. CHIKV nAb among recipients of anti-malaria anti/antibiotics treatments and those untreated were significantly associated. Conclusion: The persistent misdiagnosis of CHIKV infections poses a global public health threat in the phase of climate change if unchecked. Misuse of antibiotics/antimalaria could lead to antimicrobial resistance
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