SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction-based assays in Addis Ababa, Ethiopia

Objectives

This study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)-based variant detection in Addis Ababa, Ethiopia.

Methods

A cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 μl RNA and 20 μl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive.

Results

A total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30.

Conclusions

The study data demonstrated that reverse transcription-PCR-based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.

Effect of heat inactivation and bulk lysis on real-time reverse transcription PCR detection of the SARS-COV-2: an experimental study

Objective

This study aimed to investigate the effect of heat inactivation and chemical bulklysis on SARS-CoV-2 detection.

Results

About 6.2% (5/80) of samples were changed to negative results in heat inactivation at 60 °C and about 8.7% (7/80) of samples were changed to negative in heat inactivation at 100 °C. The Ct values of heat-inactivated samples (at 60 °C, at 100 °C, and bulk lysis) were significantly different from the temperature at 56 °C. The effect of heat on Ct value should be considered when interpreting diagnostic PCR results from clinical samples which could have an initial low virus concentration. The efficacy of heat-inactivation varies greatly depending on temperature and duration. Local validation of heat-inactivation and its effects is therefore essential for molecular testing.

Magnitude of H. pylori and Its Association with Preeclampsia Among Pregnant Women in Ethiopia: A Case Control Study

Background

Helicobacter pylori infections are associated with many complications of pregnancy including preeclampsia. It has been suggested that H. pylori infection could contribute to the etiopathogenesis of preeclampsia by inducing a pro-inflammatory state.

Objective

To assess the magnitude of H. pylori infection and its association with preeclamptic and non-preeclamptic pregnant women attending antenatal care in Ethiopia.

Methods

Hospital-based case control study was conducted among clinically diagnosed preeclamptic and non-preeclamptic pregnant women. Stool samples were collected for H. pylori antigen test from study participants. The collected data were analyzed using statistical methods in SPSS version 23. Simple descriptive statistics were used to present the socio-demographic and clinical characteristics of the study subjects. Association between clinical variables, preeclampsia and H. pylori infection was performed with multivariate logistic regression. A p-value of <0.05 at 95% confidence level was considered as statistically significant in all the analyses.

Results

A total of 93 cases and 186 controls were included in this study. The overall prevalence of H. pylori infection in all study participants was 38.9% (16/272). The prevalence of H. pylori infection was higher in cases than controls, 54.3% (50/92) vs 31.1% (56/180), respectively. The mean age was 29.01 (SD±4.93) years in cases and 30.37 (SD± 6.2) years in control group. A positive association was found between H. pylori infection and preeclampsia (OR: 2.45; 95% CI: 2.41–4.10).

Conclusion

H. pylori infection has been found to be associated with preeclamptic pregnant women. In this study, the prevalence of H. pylori infection was higher in cases than in controls. Age group, educational status, occupational status and body mass index were significantly associated with preeclamptic women with H. pylori. The association of H. pylori with preeclampsia needs to be further explored.