Background: Upper Respiratory Tract Infections (URTIs) are among the most common causes of
morbidity worldwide, particularly in low-resource settings. Viral pathogens such as severe acute
respiratory Syndrome Coronavirus 2 (SARS-CoV-2), influenza A, and influenza B often present
with overlapping clinical symptoms, complicating diagnosis and management. Aim This study
aimed to assess the prevalence of SARS-CoV-2, influenza A, and influenza B among symptomatic
patients in Khartoum, Sudan, using a multiplex Real-Time Polymerase Chain Reaction (RT-PCR)
assay. Materials and Methods: Nasopharyngeal Aspirates (NPAs) were collected from 35
patients presenting with acute respiratory symptoms of ≤3 days duration. Multiplex RT-PCR
was performed to detect SARS-CoV-2, influenza A, and influenza B viruses. Results: Results of
the 35 patients, 42.8% tested positive for SARS-CoV-2, while no cases of influenza A, influenza
B, or viral co-infection were detected. Conclusion: These findings underscore the dominance
of SARS-CoV-2 and highlight the utility of multiplex RT-PCR for differential diagnosis in Sudan’s
surveillance efforts. The absence of influenza may reflect seasonal variation, public health
interventions, or limited sample size.
Abstract
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Keywords
SARS-CoV-2
Influenza virus
Co-infection
Multiplex RT-PCR
Nasopharyngeal
aspirates
Respiratory viral infections
Khartoum State
Sudan
Acute respiratory symptoms
Viral
RNA detection
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