BackgroundAccurate and timely diagnosis is essential in limiting the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Real-time reverse transcription-polymerase chain reaction (rRT-PCR), the reference standard, requires specialized laboratories, costly reagents, and a long turnaround time. Antigen rapid diagnostic tests (Ag RDTs) provide a feasible alternative to rRT-PCR since they are quick, relatively inexpensive, and do not require a laboratory. The WHO requires that Ag RDTs have a sensitivity [≥]80% and specificity [≥]97%. MethodsThis evaluation was conducted at 11 health facilities in Kenya between March and July 2021. We enrolled persons of any age with respiratory symptoms and asymptomatic contacts of confirmed COVID-19 cases. We collected demographic and clinical information and two nasopharyngeal specimens from each participant for Ag RDT testing and rRT-PCR. We calculated the diagnostic performance of the Panbio Ag RDT against the US Centers for Disease Control and Preventions (CDC) rRT-PCR test. ResultsWe evaluated the Ag RDT in 2,245 individuals where 551 (24.5%, 95% CI: 22.8-26.3%) tested positive by rRT-PCR. Overall sensitivity of the Ag RDT was 46.6% (95% CI: 42.4-50.9%), specificity 98.5% (95% CI: 97.8-99.0%), PPV 90.8% (95% CI: 86.8-93.9%) and NPV 85.0% (95% CI: 83.4-86.6%). Among symptomatic individuals, sensitivity was 60.6% (95% CI: 54.3-66.7%) and specificity was 98.1% (95% CI: 96.7-99.0%). Among asymptomatic individuals, sensitivity was 34.7% (95% CI 29.3-40.4%) and specificity was 98.7% (95% CI: 97.8-99.3%). In persons with onset of symptoms <5 days (594/876, 67.8%), sensitivity was 67.1% (95% CI: 59.2-74.3%), and 53.3% (95% CI: 40.0-66.3%) among those with onset of symptoms >7 days (157/876, 17.9%). The highest sensitivity was 87.0% (95% CI: 80.9-91.8%) in symptomatic individuals with cycle threshold (Ct) values [≤]30. ConclusionThe overall sensitivity and NPV of the Panbio Ag RDT were much lower than expected. The specificity of the Ag RDT was high and satisfactory; therefore, a positive result may not require confirmation by rRT-PCR. The kit may be useful as a rapid screening tool for only symptomatic patients in high-risk settings with limited access to RT-PCR. A negative result should be interpreted based on clinical and epidemiological information and may require retesting by rRT-PCR.
INTRODUCTION: the syndromic approach to the management of sexually transmitted diseases (STIs) is recommended in areas without adequate laboratory support. We assessed the diagnostic accuracy of this approach in diagnosing Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Trichomonas vaginalis (TV) and Mycoplasma genitalium (MG) among 18 to 49 year-old individuals seeking treatment for STIs in a health centre in Nairobi, Kenya. METHODS: participants were recruited between April and June 2019. After providing written informed consent, an interviewer-administered questionnaire was completed. Endocervical swabs from women and urethral swabs from men were collected for STI testing using polymerase chain reaction (PCR). Diagnostic accuracy of reported symptoms was calculated using PCR as the gold standard. RESULTS: a total of 297 individuals (148 men and 149 women) were recruited. Majority of the participants had at least one reported symptom (130/148; 87.8% men and 145/148; 97.3% women). The most commonly diagnosed STI was NG (85/297; 28.6% 95%CI 23.5%-34.1%). Vaginal discharge syndrome had moderate (44.4%) to high (92.9%) sensitivity, low specificity, low positive predictive value (PPV) (2.4 % to 31.5%) and high negative predictive value (NPV) (68.2% to 95.2%). The lower abdominal pain syndrome had moderate to high sensitivity (40% to 71.4%), low specificity (30.9% to 35.6%), low PPV (9.9% to 15.8%) and high NPV (79.2% to 93.8%). The urethral discharge syndrome had high sensitivity (71.4% to 84.8%); moderate specificity (37.6% to 51.7%); low to moderate PPV (5.4% to 53.8%) and high NPV (83.6% to 96.4%). The kappa scores for the three syndromes were generally poor. CONCLUSION: these findings support the need for the review of the syndromic management of STIs.
Gonorrhea , Sexually Transmitted Diseases , Trichomonas vaginalis , Adolescent , Adult , Chlamydia trachomatis , Cross-Sectional Studies , Female , Humans , Kenya/epidemiology , Male , Middle Aged , Neisseria gonorrhoeae , Prevalence , Sexually Transmitted Diseases/diagnosis , Sexually Transmitted Diseases/epidemiology , Sexually Transmitted Diseases/therapy , Young Adult
BackgroundThe transmission networks of SARS-CoV-2 in sub-Saharan Africa remain poorly understood. MethodsWe undertook phylogenetic analysis of 747 SARS-CoV-2 positive samples collected across six counties in coastal Kenya during the first two waves (March 2020 - February 2021). Viral imports and exports from the region were inferred using ancestral state reconstruction (ASR) approach. ResultsThe genomes were classified into 35 Pango lineages, six of which accounted for 79% of the sequenced infections: B.1 (49%), B.1.535 (11%), B.1.530 (6%), B.1.549 (4%), B.1.333 (4%) and B.1.1 (4%). Four identified lineages were Kenya specific. In a contemporaneous global subsample, 990 lineages were documented, 261 for Africa and 97 for Eastern Africa. ASR analysis identified >300 virus location transition events during the period, these comprising: 69 viral imports into Coastal Kenya; 93 viral exports from coastal Kenya; and 191 inter-county import/export events. Most international viral imports (58%) and exports (92%) occurred through Mombasa City, a key touristic and commercial Coastal Kenya center; and many occurred prior to June 2020, when stringent local COVID-19 restriction measures were enforced. After this period, local virus transmission dominated, and distinct local phylogenies were seen. ConclusionsOur analysis supports moving control strategies from a focus on international travel to local transmission. FundingThis work was funded by Wellcome (grant#: 220985) and the National Institute for Health Research (NIHR), project references: 17/63/and 16/136/33 using UK aid from the UK Government to support global health research, The UK Foreign, Commonwealth and Development Office.
We generated 274 SARS-CoV-2 genomes from samples collected during the early phase of the Kenyan pandemic. Phylogenetic analysis identified 8 global lineages and at least 76 independent SARS-CoV-2 introductions into Kenyan coast. The dominant B.1 lineage (European origin) accounted for 82.1% of the cases. Lineages A, B and B.4 were detected from screened individuals at the Kenya-Tanzania border or returning travellers but did not lead to established transmission. Though multiple lineages were introduced in coastal Kenya within three months following the initial confirmed case, none showed extensive local expansion other than cases characterised by lineage B.1, which accounted for 45 of the 76 introductions. We conclude that the international points of entry were important conduits of SARS-CoV-2 importations. We speculate that early public health responses prevented many introductions leading to established transmission, but nevertheless a few undetected introductions were sufficient to give rise to an established epidemic.
