Clinical and epidemiological significance of RT-PCR and non-structural glycoprotein-1 assays in the diagnosis of dengue virus infections

Background: Due to the rapid geographic expansion, dengue has attracted much global attention. Hence, many research outputs have emanated from clinical and epidemiological studies. However, most of these studies, especially those from low- and middle-income countries, heavily relied on enzyme-linked immunosorbent assay (ELISA). Objective: In view of this, we sought to comment and remind dengue researchers within virology, immunology, and epidemiology disciplines regarding the limitations of ELISA protocols in establishing diagnosis of dengue virus (DENV) infections. Subsequently, we provided an update on the current diagnostic algorithm for dengue. Method: Extensive literature search was done using special key words on “PubMed”, “Scopus”, “Web of Science” and “Hinari”. Suitable articles were selected and subjected to scrutiny for inclusion in this study. Result: It was discovered that over 90% of published articles from LMICs inferred about dengue mainly from available commercial serological kits, without further confirmation using more accurate, sensitive and specific protocols. In some instances (less than 5%), combination of either RNA positive and anti-DENV IgM or dengue NS1 and anti-DENV IGM were used to diagnose acute primary dengue; while presence anti-DENV IgG and DENV RNA were considered non-primary dengue. Conclusion: In view of the limitations of every protocol used for investigations of dengue virus infections, its necessary to utilize appropriate combination tests to differentiate primary from non-primary dengue in order to generate reliable clinical and epidemiological inferences

Seroprevalence and associated risk factors of hepatitis E virus infection among pregnant women attending Maiduguri teaching hospital, Nigeria

Background: Hepatitis E Virus (HEV) is a major public health problem in developing countries and often fatal among pregnant women in the third trimester. Objectives: The study investigated the sero-prevalence and risk factors of HEV infection among pregnant women attendee of University of Maiduguri Teaching Hospital, Maiduguri, Nigeria. Methods: The cross-sectional study was carried out between 4th January 2016 to 30th May, 2016. One hundred and eighty blood samples from pregnant women who consented and enrolled for the study were analyzed for anti – HEV IgM using a quality assured commercial Enzyme Linked Immunosorbent Assay (ELISA) kit. Structured questionnaires were used to collate the sociodemographic characteristics and risk factor of study subjects. Results: Out of the 180 pregnant women sampled, the anti-HEV IgM seroprevalence of 13.3% was recorded.  The seroprevalence was significantly higher in the age range of 31 – 35 years (26.5%) and least in age range ≤ 20 years (4.9%) (p=0.009).  The highest seroprevalence was recorded in the third trimester 14.1% followed by second (p>0.05). After logistic regression, nature of toilet system, and source of water consumption were significant risk factors for active HEV infection (p˂0.05). Conclusion: Based on the 10.8 % pooled national prevalence of HEV infection in Nigeria, this study recorded a significantly high level of anti – HEV IgM seropositivity, an indication of recent and active HEV infection among pregnant women at the study area. Also, these infections are most among the pregnant women in their third trimester. HEV infection was related to personal, water and environmental hygiene

Molecular Detection of Influenza A(H1N1)Pdm09 Virus Among Chronic Kidney Disease Patients: A Peripheral Blood Sample Approach and Assessment of the Associated Risk Factors

Introduction: Chronic kidney disease (CKD) is a progressive loss of functional nephron characterized by various risk factors. Influenza virus has been found to cause rhabdomyolysis, which is toxic to the kidneys and can initiate or worsen CKD. This study aims to investigate the frequency and molecular detection of Influenza A(H1N1)Pdm09 Virus gene among CKD patients attending University of Maiduguri Teaching Hospital, Nigeria.Materials and Methods: Peripheral blood samples were collected from 150 CKD patients. One-step RT-PCR was performed for detection of influenza virus using the Centers for Disease Control and Prevention protocol. Relevant clinical data were collected in standardized questionnaires from each patient, and medical history was obtained from their hospital records.Results: Conventional PCR analysis revealed that 16% of the CKD patients tested positive for Inf A/Pdm H1N1. The virus frequency was found to be higher among patients in CKD stage 5 (end-stage CKD) and lower in CKD stage 3 (moderate CKD). Additionally, female CKD patients and those in the age group of 55-64 years showed a higher susceptibility to Inf A/Pdm H1N1 infection.Discussion: The study provides evidence of the presence of Inf A/Pdm H1N1 in CKD patients, aligning with previous research showing its involvement in kidney disease aggravation. CKD patients often exhibit immune dysregulation, which might facilitate the virus's invasion and persistence. Conclusion: This study provides evidence of an association between Influenza A(H1N1)Pdm09 viraemia and decreased kidney function among CKD patients. The findings highlight the importance of monitoring and preventing influenza infection in CKD patients to prevent further kidney damage

Human Bocaviruses Are Highly Diverse, Dispersed, Recombination Prone, and Prevalent in Enteric Infections

International audienceA new species of parvovirus, tentatively named human bocavirus 4 (HBoV4), was genetically characterized. Among 641 feces samples obtained from children and adults, the most commonly detected bocavirus species were, in descending order, HBoV2, HBoV3, HBoV4, and HBoV1, with an HBoV2 prevalence of 21% and 26% in Nigerian and Tunisian children, respectively. HBoV3 or HBoV4 species were found in 12 of 192 patients with non-polio acute flaccid paralysis in Tunisia and Nigeria and 0 of 96 healthy Tunisian contacts (P = .01). Evidence of extensive recombination at the NP1 and VP1 gene boundary between and within bocavirus species was found. The high degree of genetic diversity seen among the human bocaviruses found in feces specimens, relative to the highly homogeneous HBoV1, suggest that this worldwide-distributed respiratory pathogen may have recently evolved from an enteric bocavirus after acquiring an expanded tropism favoring the respiratory tract. Elucidating the possible role of the newly identified enteric bocaviruses in human diseases, including acute flaccid paralysis and diarrhea, will require further epidemiological studies

Evidence of arbovirus co-infection in suspected febrile malaria and typhoid patients in Nigeria

Introduction: Clinical symptoms of malaria and typhoid infections are virtually indistinguishable from those initially seen in many arbovirus infections. Here we describe arbovirus co-infection detected in 310 sera samples collected from febrile, clinically suspected malaria/typhoid patients in Borno State, Nigeria. Methodology: Tested initially for Plasmodium falciparum by microscopy and for Salmonella Typhi by Widal test, samples were subsequently tested for chikungunya (CHIKV), yellow fever (YFV), dengue (DENV) and West Nile viruses (WNV) by plaque reduction neutralization test. Results: While 92% of patients tested positive for malaria, typhoid, an arbovirus infection, or a combination of one or more of these types of infections, less than 1% of the patients tested positive for malaria alone and only 3.9% tested positive for typhoid alone. Approximately half of the patients tested positive for infection with a single arbovirus (48%) regardless of the presence or absence of malaria or typhoid. Of those who showed 90% to 95% virus neutralization, 67.7% had neutralizing antibodies against DENV, 50% against CHIKV, 25% against WNV and 8.7% against YFV. Eight per cent tested negative against all six pathogens, suggesting that other arboviruses not tested for in this study may also be circulating in Nigeria. Conclusions: The results suggest that misdiagnosis of arbovirus co-infections as malaria infections, combined with a lack of virus surveillance and underreporting of arbovirus infections, increases the potential for undetected and uncontrolled spread of important vector-borne arboviruses becoming serious underlying public health concerns in Nigeria

Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.

Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Letter to the Editor: Why is severe dengue rare in Nigeria: an ecologicepidemiology and host genetic perspective?

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