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.