RESULTS
In the four sentinel sites, 1271 individuals who met the predefined inclusion criteria were enrolled in the study. Among the participants, 510 (40.1%) were male, while 761 (59.9%) were female. The study cohort comprised 90.8% (N=1154) adults and 9.2% (N=117) minors. The median age of the study participants was 37 years, with an age range spanning from 3 to 98 years. The prevalence of SARS-CoV-2 during the study period was 13.93% (N=177), with higher rates among females (15.5%) compared to males (11.6%). Influenza A was the most common influenza subtype, with a prevalence of 5.7% (N=73), while influenza B was 1.96% (N=25). Influenza A was more prevalent among males (7.4%) compared to females (4.4%), whereas influenza B had similar rates among males (1.96%) and females (1.97%). There were RSV showed a prevalence of 0.94%, with similar rates among males (0.8%) and females (1.1%) (Table 1).
Among the positive samples for influenza A, the influenza A (H1N1)pdm 2009 subtype accounted for 50.6% (N=37), none were identified as Influenza A-H1 or Influenza A-H3, while 49.4% (N=36) could not be classified into specific subtypes. 50% (N=6) of the samples tested positive for RSV subtype B, and 8.3% (N=1) were identified as RSV subtype A while the rest could not be sub-typed (Supplementary Table 1).
SARS-CoV-2, Influenza A and influenza B were found to be circulating in all the sentinel sites, while RSV was present in three sites (Table 1). The prevalence varied widely across the sites, with Molo having the highest of SARS-CoV-2 and influenza A while Iten had the lowest in both cases. Olenguruone had the highest prevalence of influenza B. There were two instances of co-infection involving both influenza A and influenza B, one instance of co-infection with influenza A and RSV, and one case where all three pathogens (influenza A, influenza B, and RSV) were present simultaneously (Supplementary Table 2).
There were two major spikes in the incidence of SARS-CoV-2 and Influenza A. The spike in SARS-CoV-2 occurred in January and June-July due to the 5th and the 6th COVID-19 waves around the same time. The spike in Influenza A cases happened in June-July and September, reflecting seasonal patterns of influenza occurrence in Kenya.
The most common symptom in SARS-CoV-2 infected patients was rhinorrhoea (68.4%), then myalgia (53.7%), fatigue (54.1%), fever (52%) and anosmia (24.9%), whereas the most reported comorbidities were diabetes (5, 2.8%) and HIV (2, 1.1%) (Table 2). A summary of associations between various symptoms and comorbidities with SARS-CoV-2 status is shown in Table 2. Statistical analysis revealed a significant association between rhinorrhoea and SAR-CoV-2 (OR = 2.463, 95% CI = 1.731 - 3.523, p < 0.001). Influenza A patients commonly presented with symptoms of rhinorrhoea (66.7%) followed by fever (54.2%), myalgia (51.4%), and fatigue (48.6%), while those with influenza B commonly presented with rhinorrhoea(76%), fever(60%), fatigue(56%), and myalgia (56%). Among RSV-positive patients, myalgia (75%) and fever (58.3%) were the most frequent presenting symptoms (Table 2).
29.9% (N=53) of the SARS-CoV-2 positive samples were co-infected with one or more acute respiratory pathogens. The most detected co-infecting pathogen was Streptococcus pneumoniae 16.4% (N=29), followed byHaemophilus influenzae 10.7%, (N=19), HCoV OC43 5.9% (N=9), HCoV 229E 4% (N=7), Influenza A 2.3% (N=4), Influenza B 2.3% (N=4), human rhinovirus 2.3%(N=4) and HCoV NL63 1.1% (N=2). RSV, PIV 3, PIV 4, Metapneumovirus (MPV), Adenovirus (AdV), Enterovirus (HEV), Bocavirus 1/2/3/4 (HBoV), Bordetella parapertussis (BPP), Bordetella pertussis (BP), Chlamydophila pneumoniae (CP), Legionella pneumophila (LP), and Mycoplasma pneumoniae (MP) were however not detected as co-infecting with SARS-CoV-2 (Supplementary table 3).
Seventeen co-infection patterns with SARS-CoV-2 were found in this study (Table 4). There were 31 cases where one pathogen co-infecting with SARS-CoV-2, 18 cases of two pathogens, 2 cases of three pathogens, and 1 case where four pathogens co-infected with SARS-CoV-2. A high proportion of co-infection patterns was SARS-CoV-2 and Streptococcus pneumoniae, accounting for 22.6% (N=12) of all co-infections observed.