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Data on spatiotemporal distribution of rotavirus diarrhea are limited in many endemic settings. This study determined the prevalence and seasonal distribution of rotavirus among Nigerian children with diarrhea. Here, a total of 406 fecal samples were collected from patients attending six health facilities in Lagos between January – December 2019. Socio-demographic data of each enrolled child were collected. Rotavirus VP6 antigen was detected by enzyme-linked immunoassay (ELISA) and confirmation by VP7 gene detection by reverse transcription polymerase-chain reaction. The overall rotavirus diarrhea prevalence was 16.3% by ELISA with children above 2 years having 29.2% of this prevalence and higher occurrence in females (59.1%) than males (40.9%) (P <.05). Rotavirus diarrhea diagnosis using RT-PCR showed 100% concordance with ELISA. Cases of rotavirus diarrhea were detected from March to July and from September to November with the highest number of cases detected in May and June (22.7% each), followed by July (21.2%). The prevalence of rotavirus diarrhea remains high in Lagos with an emerging higher disease activity in children above 2. A different rotavirus transmission dynamics compared to previous studies from Nigeria and other African countries was found. VP6 ELISA may reliably be used for continuous rotavirus surveillance in Nigeria. [ABSTRACT FROM AUTHOR]

Background: There have been suggestions that hematologic abnormalities in COVID-19 are linked with the progression and severity of diseases and mortality. Lymphopenia, sepsis, and thrombocytopenia were highly reported in patients with COVID-19. This study investigated the significance of hematologic abnormalities in patients with COVID-19 in Lagos, Nigeria, and its potential as a diagnostic tool for COVID-19 severity. Results: This was a retrospective observational study with a total of 340 patients with COVID-19 (236 patients included in the analysis). These patients were categorized into two groups, comprising 71 patients with severe COVID-19 (SCP) and 165 patients with non-severe COVID-19 (NSCP). The majority were males in both categories (SCP 74.6% and NSCP 63.6%). The mean ± SD ages for SCP and NSCP were 52.28 ± 16.87 and 42.44 ± 17.18 years, respectively. The SCP (52.1%) and NSCP (20.0%) had underlying health conditions. The SCP exhibited significantly higher neutrophil counts (P < 0.05) and significantly lower mean hemoglobin, red blood cell (RBC), packed cell volume (PCV), and lymphocyte values (P < 0.05). Anemia and lymphocytopenia were more prominent in the SCP group than in the NSCP group (P < 0.05). Hemoglobin, RBC, PCV, and lymphocytes were inversely correlated with age-group in the SCP, while only lymphocytes and platelets were inversely correlated with age-group in the NSCP. The highest area under the ROC curve (AUC) for neutrophils was 0.739 with a sensitivity of 62.0% and specificity of 80.0%, while white blood cells had an AUC of 0.722 with a sensitivity of 73.2% and specificity of 61.2%. The AUC for neutrophil–lymphocyte ratio (NLR) was 0.766 with a sensitivity of 63.3% and specificity of 83.5%, while that for the platelet–lymphocyte ratio (PLR) was 0.695 with a sensitivity and specificity of 61.7% and 77.8%. Conclusions: COVID-19 affected the levels of hemoglobin, RBC, PCV, and lymphocytes in the blood, and the differences were significant between the SCP and NSCP. The significant changes in neutrophil and lymphocyte counts may be useful in the prognosis and management of COVID-19 severity in hospital settings. Furthermore, NLR and PLR may be used in the prognosis and management of severe COVID-19 infection, as well as provide an objective basis for early identification and management in low-resource settings. [ABSTRACT FROM AUTHOR]

Background: A common complication of any respiratory disease by a virus could be a secondary bacterial infection, which is known to cause an increase in severity. It is, however, not clear whether the presence of some opportunistic pathogens called pathobionts contributes to the severity of the disease. In COVID-19 patients, undetected bacterial co-infections may be associated with the severity of the disease. Therefore, we investigated the implications of bacterial co-infections in COVID-19 cases. Results: This is a cross-sectional study that involved archived specimens collected from nasopharyngeal samples of 150 people for COVID-19 screening in Lagos. DNA extraction from the samples was carried out to determine the presence of five respiratory bacterial pathogens using nested real-time PCR, and data were analysed using the Chi-square test. Of the 150 samples collected, 121 (80.7%) were positive for SARs-CoV-2 infection and 29 were negative. The proportion of patients with bacteria co-infection in COVID-19-negative, asymptomatic, and mild cases were 93.1%, 70.7%, and 67.5%, respectively. There was no statistically significant difference between mild COVID-19 conditions and bacteria co-infection (p = 0.097). There was also no significant difference in the nasal carriage of Staphylococcus aureus, Mycoplasma pneumoniae, and Haemophilus spp. However, there was a statistically significant increase in the carriage of Moraxella catarrhalis and Chlamydophila pneumoniae among COVID-19-negative patients when compared with the positive patients (p value = 0.003 and 0.000 for Moraxella catarrhalis and Chlamydophila pneumoniae, respectively). Conclusions: The current study shows that bacterial co-infection and superinfection with COVID-19 are not associated with mild and asymptomatic COVID-19 cases in our setting. However, given the high prevalence of Staphylococcus aureus and Mycoplasma pneumoniae among the mild COVID-19 cases seen in this study, early diagnosis and treatment of these bacterial co-infections are still encouraged to mitigate the effect on the severity of COVID-19. [ABSTRACT FROM AUTHOR]

A key element in containing the spread of the SARS-CoV-2 infection is quality diagnostics which is affected by several factors. We now report the comparative performance of five real-time diagnostic assays. Nasopharyngeal swab samples were obtained from persons seeking a diagnosis for SARS-CoV-2 infection in Lagos, Nigeria. The comparison was performed on the same negative, low, and high-positive sample set, with viral RNA extracted using the Qiagen Viral RNA Kit. All five assays are one-step reverse transcriptase real-time PCR assays. Testing was done according to each assay's manufacturer instructions for use using real-time PCR platforms. 63 samples were tested using the five qPCR assays, comprising of 15 negative samples, 15 positive samples (Ct = 16–30; one Ct = 35), and 33 samples with Tib MolBiol E-gene Ct value ranging from 36–41. All assays detected all high positive samples correctly. Three assays correctly identified all negative samples while two assays each failed to correctly identify one different negative sample. The consistent detection of positive samples at different Ct/Cq values gives an indication of when to repeat testing and/or establish more stringent in-house cut-off value. The varied performance of different diagnostic assays, mostly with emergency use approvals, for a novel virus is expected. Comparative assays' performance reported may guide laboratories to determine both their repeat testing Ct/Cq range and/or cut-off value. [ABSTRACT FROM AUTHOR]