DISCUSSION
The timely detection and monitoring of ARIs is essential for understanding disease patterns and trends, developing appropriate prevention and control strategies, and informing public health decision-making. In this study, we implemented an active sentinel surveillance system for SARS-CoV-2 in four sites in the Rift Valley, focusing on detecting SARS-CoV-2 and co-infections with other acute respiratory pathogens. This study offers a glimpse of the respiratory pathogen landscape and the co-infection of SARS-CoV-2 with viral and bacterial ARIs in the Rift Valley, Kenya, providing valuable insights into disease burden, prevalence rates, and co-infection patterns.
As of December 2022, Kenya has had seven waves of SARS-CoV-2. The trend of SARS-CoV-2 infection corresponded to the national trend, with similar peaks during the fifth and sixth waves . This study captures a snapshot of the fifth wave on the decline. SARS-CoV-2 positivity of 13.93% rate is similar to that reported in Bukavu City in the Democratic Republic of Congo.
The trend of influenza A is consistent with the seasonality of influenza in Kenya, which corresponds to the winter season in the Southern hemisphere The prevalence of influenza A, 5.6%, influenza B, 1.96% and RSV, 0.95, is much lower than those from previous studies in Kenya. There is a significant dominance in the circulation of Influenza A (H1N1)pdm 2009 compared to what has been reported in previous studies suggesting a shift in the viral landscape and highlights, thus having a potential impact on the local disease burden. Whereas the study found a significant association between rhinorrhoea and SARS-CoV-2, it is inconsistent with previous studies, which found it to be a rarer symptom of SARS-CoV-2.
One of the most significant findings of this study was the high proportion of co-infections observed in patients with SARS-CoV-2 infection, with approximately 29.9% of the SARS-CoV-2 positive samples being co-infected with one or more acute respiratory pathogens.Streptococcus pneumoniae and Haemophilus influenzae were the most co-infecting ARI pathogens, which is similar to previous studies that identified these two pathogens as some of the most common co-infecting pathogens in ARIs . Bacterial aetiologies are often not investigated in most ARI cases as they usually present as secondary infections following a viral infection and require further diagnostic approaches, including culturing and antibiotic susceptibility. Co-infections, especially with bacterial pathogens, have been shown to complicate patients’ clinical course, leading to poor disease outcomes. This study’s findings thus underscore the importance of diagnosing bacterial ARI pathogens to address challenges arising from co-infections and prevent unnecessary antibiotic use, which could potentially lead to antimicrobial resistance.
Another notable finding was that human coronaviruses were the common viral aetiologies co-infected with SARS-COV-2. The circulation of human coronaviruses in Kenya has been reported before the emergence of SARS-CoV-2; hence little is understood about the clinical implications of co-infection . This highlights the importance of understanding potential interactions and cross-reactivity between different coronaviruses as this potentially impacts disease severity, immune response, clinical outcomes, and therapeutic strategies.
These findings thus demonstrate that other underlying pathologies warrant syndromic testing for evidence-based clinical interventions to improve patient outcomes. The main limitation of this study was that it was not possible to make further assessments of the impact of ARIs and co-infections on patient outcomes due to lack of information on clinical severity, hospitalization, recovery, and treatment. Additionally, the study relied on self-reported symptoms, which may not accurately reflect the clinical presentation of ARIs.