Extractionless nucleic acid detection: a high capacity solution to COVID-19 testing.

We describe an extractionless real-time reverse transcriptase-PCR (rRT-PCR) protocol for SARS-CoV-2 nucleic acid detection using heat as an accurate cost-effective high-capacity solution to COVID-19 testing. We present the effect of temperature, transport media, rRT-PCR mastermixes and gene assays on SARS-CoV-2 gene amplification and limits of detection. Utilizing our heated methodology, our limits of detection were 12.5 and 1 genome copy/reaction for singleplex E- and N1-gene assays, respectively, and 1 genome copy/reaction by utilizing an E/N1 or Orf1ab/N1 multiplex assay combination. Using this approach, we detected up to 98% of COVID-19 positive patient samples analyzed in our various cohorts including a significant percentage of weak positives. Importantly, this extractionless approach will allow for >2-fold increase in testing capacity with existing instruments, circumvent the additional need for expensive extraction devices, provide the sensitivity needed for COVID-19 detection and significantly reduce the turn-around time of reporting COVID-19 test results.

Addressing the global surge of COVID-19 cases: Insights from diagnostics, improved treatment strategies, vaccine development and application.

BACKGROUND AND AIM: As the rage of coronavirus disease 2019 (COVID-19) pandemic continues to spread globally, much effort is being directed to contain it through various efforts - genomic studies, drug discoveries, clinical trials, vaccine development, and the innovation of diagnostic techniques. However, some pertinent areas involving accurate and sensitive diagnostics, immunoglobulin specificity, evolution of mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the drug combination strategy to combat it still require more attention. METHODS: This review critically examines the COVID-19 response and containment operations. It also addresses some standing challenges involving the areas of diagnostics, vaccine development and prospect, and treatment strategies in relation to antiviral drug treatment and immunotherapy. Designated set of keywords such as "SARS-CoV-2;" "coronavirus;" "severe acute respiratory syndrome coronavirus;" "repurposed;" "vaccination;" "containment;" "laboratory diagnostic;" "immunotherapy;" "antiviral;" "antiparasitic;" "antibiotic;" "antiprotozoal;" "antibody;" "anti-inflammatory;" "antitumor;" "corticosteroid;" "hypertensive drug;" "statin;" "supplement;" and "biological" along with "COVID-19" were inserted on electronic databases to retrieve articles and clinical trial information relevant to the study objectives. The search databases included ClinicalTrials.gov, NIH.gov, PubMed, Scinapse, CINAHL, Medline, Google Scholar, Academic Search Premier, SAGE, EBSCO Host, and Scopus. RELEVANCE FOR PATIENTS: The difficulties associated with SARS-CoV-2 rapid mutations are unceasingly evolving and re-evolving. These pose serious concerns and downplay the efficacy and effectiveness of the current pipeline antiviral drugs and vaccines. Entities encompassing immunotherapy, antiviral drug therapies, viral genomics, protein-protein interaction, and improved diagnostics as well as drug combination strategy against the emerging genetic variability of SARS-CoV-2 were critically appraised. This study suggests that robust collaborations in the development of more sensitive, rapid and accurate diagnostics, development of immunoglobulin specific agents and improved anti-viral treatment focus against multiple mutant genes of SARS-CoV-2 should be aggressively pursued for the overall benefits of COVID-19 patients.

Understanding the implications of SARS-CoV-2 re-infections on immune response milieu, laboratory tests and control measures against COVID-19.

Several months after the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), cases of re-infection after recovery were reported. The extent and duration of protective immunity after SARS-CoV-2 infection is not fully understood. As such, the possibility of re-infection with SARS-CoV-2. Furthermore, cases of re-infection were mainly due to different variants or mutant SARS-CoV-2. Following the fast and pandemic-scale spread of COVID-19, mutations in SARS-CoV-2 have raised new diagnostic challenges which include the redesign of the oligonucleotide sequences used in RT-PCR assays to avoid potential primer-sample mismatches, and decrease sensitivities. Since the initial wave of the pandemic, some regions had experienced fresh outbreaks, predisposing people to be susceptible to SARS-CoV-2 re-infection. Hence, this article sought to offer detailed biology of SARS-CoV-2 re-infections and their implications on immune response milieu, diagnostic laboratory tests and control measures against COVID-19.

Leveraging on the genomics and immunopathology of SARS-CoV-2 for vaccines development: prospects and challenges.

The incidence and case-fatality rates (CFRs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, the etiological agent for Coronavirus Disease 2019 (COVID-19), have been rising unabated. Even though the entire world has been implementing infection prevention and control measures, the pandemic continues to spread. It has been widely accepted that preventive vaccination strategies are the public health measures for countering this pandemic. This study critically reviews the latest scientific advancement in genomics, replication pattern, pathogenesis, and immunopathology of SARS-CoV-2 infection and how these concepts could be used in the development of vaccines. We also offer a detailed discussion on the anticipated potency, efficacy, safety, and pharmaco-economic issues that are and will be associated with candidate COVID-19 vaccines.

Immunological and anti-oxidant profiles of malarial children in Abuja, Nigeria.

BACKGROUND: The clinical symptoms, cellular immune response, and serum cytokine homeostasis during falciparum malaria among children living in endemic regions depend on the parasite densities. This study aims to evaluate the CD4+ and CD8+ T cells, leucocytes subpopulations, IL-6, IL-10 and biomarkers of oxidative stress among children infected with varying grades of malaria attending the University of Abuja Teaching Hospital and National Hospital, Abuja, Nigeria. MATERIALS AND METHODS: This case-control study involved blood samples collected from 165 children (between 5 and 12 years). This comprised 45 children with mild malaria, 40 each with moderate, severe malaria and apparently healthy (control). Serum cytokines, ferritin, malonaldehyde (MDA), ascorbate, α-tocopherol levels were determined by Enzyme-Linked ImmunoSorbent Assay (ELISA). Leucocytes differentials and CD4+/CD8+ T cells counts were enumerated by automated hematology analyzer and flow cytometry, respectively. RESULTS: All malarial children had only Plasmodium falciparum. The male to female ratio of children with mild malaria was 1.5:1 (mean ± SD age of 8.5 ± 1.9 years). However, other groups had 1:1 male to female ratio and mean ages of 9.2 ± 2.3, 9.8 ± 2.2, 8.5 ± 1.5 for children with moderate, severe malaria and control, respectively. There was a positive but not significant association of neutrophils and monocytes with the 3 grades of malaria parasitemia (p>0.05). There was a negative and significant correlation between severe malaria and lymphocyte count (p = 0.048; r = -0.647). However, there was positive and significant correlation between eosinophil with moderate (p = 0.03; r = 0.994) and severe malaria (p = 0.006; r = 0.825). There was a significant decline in serum ascorbate with increased malaria density (p<0.0001). However, there was no difference in the serum α-tocopherol concentration within the 4 groups of children (p = 0.182). Serum ferritin and MDA significantly elevated with an increase in malaria density (p<0.0001). There was a significant decline in CD4+ T and CD8+ T cells counts with an increase in malaria densities (p<0.0001). Serum IL-10 and IL-6 significantly elevated with increased malaria density (p<0.0001). CONCLUSION: Based on these findings, severe malaria was significantly associated with declined CD4+ and CD8+ T cell counts, upregulation of IL-6, and high serum levels of oxidative stress biomarkers.

Spectrum of pulmonary fungal pathogens, associated risk factors, and anti-fungal susceptibility pattern among persons with presumptive tuberculosis at Gombe, Nigeria.

Background: Pulmonary mycosis (PM) poses a great diagnostic challenge due to the lack of pathognomonic and radiological features, especially in the absence of mycology laboratory tests. This study was aimed to isolate, phenotypically identify, determine the prevalence of pulmonary fungal pathogens and antifungal susceptibility pattern of isolates of presumptive tuberculosis (PTB) patients attending Federal Teaching Hospital (FTH) Gombe, Nigeria. Methods: After ethical approval, three consecutive early morning sputa were collected from 216 participants with presumptive of PTB attending FTH Gombe, between May 2, 2017 and May 30, 2018. Samples were processed using standard mycological staining, microscopy, sugar biochemistry, and antifungal susceptibility test protocols. Sociodemographic variables and risk factors of pulmonary fungal infection were assessed through structured questionnaires. Pulmonary fungal infection was defined by the positive culture in at least two sputa. PTB was defined by Genexpert® nested polymerase chain reaction. Results: Of the 216 participants, 19.9% had PTB and 73.6% had pulmonary fungal pathogens. Among the isolated pulmonary fungal pathogens, Aspergillus fumigatus made the highest occurrence, while 6.5% had PTB-fungal co-infection. No significant association existed between the prevalence of PM with age and sex of participants (P < 0.05). Cigarette smoking (adjusted odds ratio [aOR] = 15.9 [95% confidence interval (CI): 0.9-268.8]), prolong antibiotic use (aOR = 77.9 [95% CI: 4.7-1283]) and possession of domestic pet (aOR = 77.9 [95% CI: 4.7-1283]) were significant risk factors of PM (P < 0.05). Penicillium citrinum, Mucor spp. and Aspergillus flavus are more susceptible to voriconazole, and Candida albicans was found to be more susceptible to Nystatin. Of the 159 fungal isolates, 92.5% were resistant to fluconazole. Conclusion: Findings from this study revealed high level pulmonary fungal pathogens, especially among PTB patients. A majority of fungal isolates were resistant to fluconazole. It's recommended that persons should do away with or minimize risk factors for pulmonary fungal pathogens identified in this study.

A close look at the biology of SARS-CoV-2, and the potential influence of weather conditions and seasons on COVID-19 case spread.

BACKGROUND: There is sufficient epidemiological and biological evidence of increased human susceptibility to viral pathogens such as Middle East respiratory syndrome coronavirus, respiratory syncytial virus, human metapneumovirus and influenza virus, in cold weather. The pattern of outbreak of the coronavirus disease 2019 (COVID-19) in China during the flu season is further proof that meteorological conditions may potentially influence the susceptibility of human populations to coronaviruses, a situation that may become increasingly evident as the current global pandemic of COVID-19 unfolds. MAIN BODY: A very rapid spread and high mortality rates have characterized the COVID-19 pandemic in countries north of the equator where air temperatures have been seasonally low. It is unclear if the currently high rates of COVID-19 infections in countries of the northern hemisphere will wane during the summer months, or if fewer people overall will become infected with COVID-19 in countries south of the equator where warmer weather conditions prevail through most of the year. However, apart from the influence of seasons, evidence based on the structural biology and biochemical properties of many enveloped viruses similar to the novel severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 (aetiology of COVID-19), support the higher likelihood of the latter of the two outcomes. Other factors that may potentially impact the rate of virus spread include the effectiveness of infection control practices, individual and herd immunity, and emergency preparedness levels of countries. CONCLUSION: This report highlights the potential influence of weather conditions, seasons and non-climatological factors on the geographical spread of cases of COVID-19 across the globe.

Exploring the genetics, ecology of SARS-COV-2 and climatic factors as possible control strategies against COVID-19

The world has been thrown into pandemonium due to the recent Coronavirus Disease-19 (COVID-19) pandemic. Early available clinical data have indicated that geriatric persons cum those with comorbidity such as cardiovascular, metabolic and immunological disorders suffered severe form of COVID-19. All countries and territories of the world are currently exploring available strategies to control the pandemic with the hope to significantly minimize its morbidity and mortality rate. This present study critically reviewed available and latest research progress on the genetics and ecology of SARS-CoV-2, as well as the influence of climatic factors on the spread of COVID-19, and thus, discussed how these concepts could be harnessed for COVID-19 control and further scientific advancements in resolving the pandemic.

Epidemiology and Synergistic Hepatopathology of Malaria and Hepatitis C Virus Coinfection.

Malaria and hepatitis C virus (HCV) infections are very common causes of human suffering with overlapping global geographic distributions. With the growing incidence of HCV infections in malaria-endemic zones and malaria in areas with exceptionally high HCV prevalence, coinfections and syndemism of both pathogens are likely to occur. However, studies of malaria and HCV coinfections are very rare despite the fact that liver-stage plasmodiasis and hepatitis C develop in hepatocytes which may synergistically interact. The fact that both pathogens share similar entry molecules or receptors in early invasive steps of hepatocytes further makes hepatopathologic investigations of coinfected hosts greatly important. This review sought to emphasize the public health significance of malaria/HCV coinfections and elucidate the mechanisms of pathogens' entrance and invasion of susceptible host to improve on existing or develop antiplasmodial drugs and hepatitis C therapeutics that can intervene at appropriate stages of pathogens' life cycles.

Survey of malaria and anti-dengue virus IgG among febrile HIV-infected patients attending a tertiary hospital in Abuja, Nigeria.

BACKGROUND: Dengue and malaria are infections, of great public health concern, especially in sub-Saharan Africa where the burden of HIV infection is high. This study was conducted to determine the seroprevalence of dengue virus IgG antibodies and dengue/malaria coinfection among febrile HIV-infected patients attending the University of Abuja Teaching Hospital, Gwagwalada, Abuja. METHODS: In this cross-sectional study, blood samples from 178 consenting HIV-infected patients receiving antiretroviral therapy were collected and tested for plasmodiasis and anti-Dengue virus IgG using malaria microscopy and ELISA, respectively. Interviewer-based questionnaires were used to assess subjects' sociodemographic variables and dengue risk factors. RESULTS: Of the 178 screened participants, 44.4% were seropositive for dengue virus IgG antibody, whereas 29.2% were positive for Plasmodium falciparum. About 44.2% were positive for both dengue virus and P. falciparum. There was a statistical association between anti-dengue IgG and occupation (p=0.03) but not with age, residential area, educational level and patients' gender (p>0.05). Seroprevalence of anti-dengue specific IgG was relatively higher in participants who adopted protective measures. There was a statistical association between seroprevalence of anti-dengue IgG and adoption of preventive measures (p<0.05). CONCLUSION: The high prevalence of malaria and dengue virus IgG indicates the need to strengthen vector control and dengue surveillance programs.