Molecular detection of SARS-CoV-2 infection in three geo-political zones of Nigeria: a cross-sectional study.

Introduction: sequel to the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its subsequent spread to all continents of the world, humans have continued to experience severe devastation to their health and economies. To control the spread of this virus, it is important to detect the infection in recently infected and asymptomatic individuals who are capable of infecting others. This study was designed to detect ongoing SARS-CoV-2 Infection among asymptomatic individuals in open markets across three geopolitical zones in Nigeria. Methods: nasal and oropharyngeal swab samples were collected from 2,158 study participants between December 20th, 2020 and March 20th, 2021 from large open markets across three geo-political zones (Southwest, Northwest and Southeast) of Nigeria. Virus RNA was extracted from these swab samples and real time reverse transcription polymerase chain reaction (RT-PCR) was carried out for the detection of SARS-CoV-2 specific genes. Data were analysed using descriptive statistics. Results: a total of 163 (7.6%) of the 2,158 participants enrolled for the study tested positive for SARS-CoV-2 by RT-PCR. The rate of infection was significantly higher in the North-western States of the country when compared to the western and Eastern regions (P=0.000). Similarly, the rate of infection was higher among buyers than sellers (P=0.000) and among males when compared with females, though the difference was not significant (p=0.31). Conclusion: this study shows that there is a continuous spread of SARS-CoV-2, especially among active, asymptomatic individuals across many States in the country. There is therefore need to continuously educate citizens on the need to adhere to both the non-pharmaceutical and pharmaceutical preventive measures to protect themselves and ultimately curb the spread of the virus.

Human Seasonal Influenza Viruses in Swine Workers in Lagos, Nigeria: Consequences for Animal and Public Health.

The influenza A virus has been scarcely investigated in pigs in Africa, with rare detection prior to 2009. The spread of A(H1N1)pdm09 changed the epidemiology due to frequent human-to-swine transmission and the emergence of various new reassortants. This study therefore aimed at estimating the level of circulation and characterizing influenza A viruses at the interface between swine workers, who are crucial players in the inter-species transmission of influenza A viruses, and their animals in several farms in Nigeria, a hub for pig production in Africa. This cross-sectional study showed that 24.6% (58/236) of the pig serum samples collected in 2013-2014 had anti-influenza A antibodies in the absence of vaccination programs, but none of the pig swabs (n = 1193) were positive according to RT-qPCR. Viral RNA was detected in 0.9% (2/229) of swine workers sampled at their place of work, and the strains were characterized as A(H1N1)pdm09 and seasonal A(H3N2). Our results highlight that more awareness of swine workers regarding the consequences of reverse zoonosis for animal and public health is warranted. Annual vaccination and the wearing of masks when experiencing influenza-like symptoms would help decrease influenza inter-species transmission, while surveillance should be adequately supported for early detection.

Molecular detection of SARS-CoV-2 infection in three geo-political zones of Nigeria: a cross-sectional study

Introduction: sequel to the emergence of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) and its subsequent spread to all continents of the world, humans have continued to experience severe devastation to their health and economies. To control the spread of this virus, it is important to detect the infection in recently infected and asymptomatic individuals who are capable of infecting others. This study was designed to detect ongoing SARS-CoV-2 Infection among asymptomatic individuals in open markets across three geopolitical zones in Nigeria. Methods: nasal and oropharyngeal swab samples were collected from 2,158 study participants between December 20th, 2020 and March 20th, 2021 from large open markets across three geo-political zones (Southwest, Northwest and Southeast) of Nigeria. Virus RNA was extracted from these swab samples and real time RT-PCR was carried out for the detection of SARS-CoV-2 specific genes. Data was analysed using descriptive statistics. Results: a total of 163 (7.6%) of the 2,158 participants enrolled for the study tested positive for SARS-CoV-2 by RT-PCR. The rate of infection was significantly higher in the North-western states of the country when compared to the western and Eastern regions (P=0.000). Similarly, the rate of infection was higher among buyers than sellers (P=0.000) and among males when compared with females, though the difference was not significant (p=0.31). Conclusion: this study shows that there is a continuous spread of SARS-CoV-2, especially among active, asymptomatic individuals across many states in the country. There is therefore need to continuously educate citizens on the need to adhere to both the non-pharmaceutical and pharmaceutical preventive measures to protect themselves and ultimately curb the spread of the virus.

Saliva sample for detection of SARS-CoV-2: A possible alternative for mass testing.

Molecular diagnostic testing has played a critical role in the global response to the novel Coronavirus disease (COVID-19) pandemic, since its first outbreak in late 2019. At the inception of the COVID-19 pandemic, nasopharyngeal swab sample analysis for COVID-19 diagnosis using the real-time polymerase chain reaction (RT-PCR) technique was the most widely used. However, due to the high cost and difficulty of sample collection, the number of available sample types for COVID-19 diagnosis is rapidly increasing, as is the COVID-19 diagnostic literature. The use of nasal swabs, saliva, and oral fluids as viable sample options for the effective detection of SARS-CoV-2 has been implemented successfully in different settings since 2020. These alternative sample type provides a plethora of advantages including decreasing the high exposure risk to frontline workers, enhancing the chances of home self-sampling, reducing the cost, and significantly increasing testing capacity. This study sought to ascertain the effectiveness of Saliva samples as an alternative for COVID-19 diagnosis in Nigeria. Demographic data, paired samples of Nasopharyngeal Swab and Drooling Saliva were obtained from 309 consenting individuals aged 8-83 years presenting for COVID-19 testing. All samples were simultaneously assayed for the detection of SARS-CoV-2 RdRp, N, and E genes using the GeneFinder™ COVID-19 Plus RT-PCR test kit. Out of 309 participants, only 299 with valid RT-PCR results comprising 159 (53.2%) males and 140 (46.8%) females were analyzed in this study using the R Statistical package. Among the 299 samples analyzed, 39 (13.0%) had SARS-CoV-2 detected in at least one specimen type. Both swabs and saliva were positive in 20 (51.3%) participants. Ten participants (25.6%) had swab positive/saliva-negative results and 9 participants (23.1%) had saliva positive/swab-negative results. The percentage of positive and negative agreement of the saliva samples with the nasopharyngeal swab were 67% and 97% respectively with positive and negative predictive values as 69% and 96% respectively. The findings indicate that drooling saliva samples have good and comparable diagnostic accuracy to the nasopharyngeal swabs with moderate sensitivities and high specificities.

From Ebola to COVID-19: emergency preparedness and response plans and actions in Lagos, Nigeria.

BACKGROUND: Lagos state is the industrial nerve centre of Nigeria and was the epicentre of the 2014 Ebola outbreak in Nigeria as it is now for the current Coronavirus Disease (COVID-19) outbreak. This paper describes how the lessons learned from the Ebola outbreak in 2014 informed the emergency preparedness of the State ahead of the COVID-19 outbreak and guided response. DISCUSSION: Following the Ebola outbreak in 2014, the Lagos State government provided governance by developing a policy on emergency preparedness and biosecurity and provided oversight and coordination of emergency preparedness strategies. Capacities for emergency response were strengthened by training key staff, developing a robust surveillance system, and setting up a Biosafety Level 3 laboratory and biobank. Resource provision, in terms of finances and trained personnel for emergencies was prioritized by the government. With the onset of COVID-19, Lagos state was able to respond promptly to the outbreak using the centralized Incident Command Structure and the key activities of the Emergency Operations Centre. Contributory to effective response were partnerships with the private sectors, community engagement and political commitment. CONCLUSION: Using the lessons learned from the 2014 Ebola outbreak, Lagos State had gradually prepared its healthcare system for a pandemic such as COVID-19. The State needs to continue to expand its preparedness to be more resilient and future proof to respond to disease outbreaks. Looking beyond intra-state gains, lessons and identified best practices from the past and present should be shared with other states and countries.

Immunological screening of Lassa Virus among Health workers and Contacts of patients of Lassa fever in Ondo State.

BACKGROUND: The increasing trends of morbidity and mortality of Lassa fever is becoming more alarming in Nigeria. Information about immune response to the virus is limited. At exposure, the level of immunity plays a vital role in the vulnerability of individuals infected. OBJECTIVE: Investigating the immune status of health workers, infected cases and contacts of infected cases of Lassa fever in Ondo State. STUDY DESIGN: Blood samples were collected from 233 individuals comprising 102 health workers, 22 infected cases and 109 contacts of infected cases from Owo and Ose Local Government Areas and transported in triple level packaging. Plasma samples were analyzed for IgG and IgM markers using ReLASV® Pan-Lassa NP IgG/IgM ELISA Kit (Zalgen Labs, LLC, USA) while RNAs extracted from IgM positive samples were analyzed for LASV RNA according to manufacturers' instructions. RESULT: Among the health workers, 20/102 (19.6%) and 2/102 (2.0%) were IgG and IgM positive respectively. While 16/22 (72.7%) and 14/22 (63.6%) were IgG and IgM positive respectively among the infected cases. Of the contacts of infected cases screened, 64/109 (58.7%) were IgG positive while 4/109 (3.7%) were positive for IgM. There was no detectable LASV RNA in the samples analyzed. CONCLUSION: These findings suggest that majority of the health workers are naïve to the virus and hence may be prone to the viral infection. It could also be suggestive that a good personal protective procedure is been practiced by the health workers, hence the low exposure. However, most of the contacts of infected cases show exposure to the virus.

Comparative performance of SARS-CoV-2 real-time PCR diagnostic assays on samples from Lagos, Nigeria.

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.

Full length genomic sanger sequencing and phylogenetic analysis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Nigeria.

In an outbreak, effective detection of the aetiological agent(s) involved using molecular techniques is key to efficient diagnosis, early prevention and management of the spread. However, sequencing is necessary for mutation monitoring and tracking of clusters of transmission, development of diagnostics and for vaccines and drug development. Many sequencing methods are fast evolving to reduce test turn-around-time and to increase through-put compared to Sanger sequencing method; however, Sanger sequencing remains the gold standard for clinical research sequencing with its 99.99% accuracy This study sought to generate sequence data of SARS-CoV-2 using Sanger sequencing method and to characterize them for possible site(s) of mutations. About 30 pairs of primers were designed, synthesized, and optimized using endpoint PCR to generate amplicons for the full length of the virus. Cycle sequencing using BigDye Terminator v.3.1 and capillary gel electrophoresis on ABI 3130xl genetic analyser were performed according to the manufacturers' instructions. The sequence data generated were assembled and analysed for variations using DNASTAR Lasergene 17 SeqMan Ultra. Total length of 29,760bp of SARS-CoV-2 was assembled from the sample analysed and deposited in GenBank with accession number: MT576584. Blast result of the sequence assembly shows a 99.97% identity with the reference sequence. Variations were noticed at positions: nt201, nt2997, nt14368, nt16535, nt20334, and nt28841-28843, which caused amino acid alterations at the S (aa614) and N (aa203-204) regions. The mutations observed at S and N-gene in this study may be indicative of a gradual changes in the genetic coding of the virus hence, the need for active surveillance of the viral genome.

Predictive ability of symptomatology in COVID-19 during Active case search in Lagos State, Nigeria.

BACKGROUND: In April 2020, a community-based active case search surveillance system of coronavirus disease 2019 (COVID-19) was developed by the emergency outbreak committee in Lagos State. This followed the evidence of community transmission of coronavirus disease in the twenty Local Government Areas in Lagos State. This study assessed the value of respiratory and other symptoms in predicting positive SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR). It is hoped that if symptoms are predictive, they can be used in screening before testing. METHODS: Communities were included based on the alerts from community members through the rumour alert system set up by the state. All members of the households of the communities from where the alert came were eligible. Household members who declined to participate were excluded from the study. A standardised interviewer-administered electronic investigation form was used to collect sociodemographic information, clinical details and history for each possible case. Data was analysed to see the extent of agreement or correlation between reported symptoms and the results of PCR testing for SARS-COV-2. RESULTS: A total of 12,739 persons were interviewed. The most common symptoms were fever, general weakness, cough and difficulty in breathing. Different symptoms recorded different levels of sensitivity as follows: fever, 28.9%; cough, 21.7%; general body weakness, 10.9%; and sore throat, 10.9%. Sensitivity and specificity for fever, the most common symptom, were 28.3% and 50.2%, respectively, while similar parameters for general body weakness, the next most common symptom, were 10.9% and 73.2%, respectively. CONCLUSION: From these findings, the predictive ability of symptoms for COVID-19 diagnosis was extremely weak. It is unlikely that symptoms alone will suffice to predict COVID-19 in a patient. An additional measure, such as confirmatory test by RT-PCR testing, is necessary to confirm the disease.

Monitoring of Lassa virus infection in suspected and confirmed cases in Ondo State, Nigeria.

INTRODUCTION: Lassa virus (LASV), the causative agent of Lassa fever (LF), an endemic acute viral haemorrhagic illness in Nigeria, is transmitted by direct contact with the rodent, contaminated food or household items. Person-to-person transmission also occurs and sexual transmission has been reported. Thus, this study investigated the presence of LASV in body fluids of suspected and confirmed cases. METHODS: this was a cross-sectional study between March 2018 and April 2019 involving 112 consenting suspected and post ribavirin confirmed cases attending the Lassa fever treatment center in Ondo State. Whole blood was collected from 57 suspected and 29 confirmed cases. Other samples from confirmed cases were 5 each of High Vaginal Swab (HVS) and seminal fluid; 12 breast milk and 4 urine. All samples were analyzed using reverse transcription-PCR (RT-PCR) targeting the S-gene of LASV. RESULTS: analysis of whole blood by RT-PCR showed that 1/57 (1.8%) suspected and 1/29 (3.4%) confirmed post ribavirin treated cases were positive. While LASV was detected in 2/5 (40%) post ribavirin treated seminal fluids and 1/11 (8.3%) breast milk. However, LASV was not detected in any of the HVS and urine samples. CONCLUSION: the detection of LASV in seminal fluid and breast milk of discharged post ribavirin treated cases suggests its persistence in these fluids of recovering Nigerians. The role of postnatal and sexual transmissions in the perennial outbreak of LF needs to be further evaluated.

Caesarean delivery of first prediagnosed COVID-19 pregnancy in Nigeria.

The COVID-19 pandemic is currently causing widespread infection and deaths around the world. Since the identification of the first case in Nigeria in February 2020, the number of confirmed cases has risen to over 9,800. Although pregnant women are not necessarily more susceptible to infection by the virus, changes to their immune system in pregnancy may be associated with more severe symptoms. Adverse maternal and perinatal outcomes have been reported among pregnant women with COVID-19 infection. However, literature is scarce on the peripartum management and pregnancy outcome of a pregnant woman with COVID-19 in sub-Saharan Africa. We report the first successful and uncomplicated caesarean delivery of a pregnant woman with COVID-19 infection in Nigeria.

High multiple mutations of Plasmodium falciparum-resistant genotypes to sulphadoxine-pyrimethamine in Lagos, Nigeria.

BACKGROUND: Plasmodium falciparum-resistance to sulphadoxine-pyrimethamine (SP) has been largely reported among pregnant women. However, the profile of resistance markers to SP dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) in the general population are varied and not frequently monitored. Currently, SP is used as partner drug for artemisinin combination therapy (SP-artesunate) in some sub-Saharan African countries or as a prophylactic drug in intermittent preventive treatment of malaria during pregnancy and infants and in seasonal malaria chemoprevention (SMC). Profiling of P. falciparum-resistant genotypes to SP is dynamic and critical in providing data that would be useful for malaria control programmes. This study assessed the profile of dhfr and dhps genes genotypes among individuals with malaria in Lagos, Nigeria. METHODS: Molecular markers of SP resistance were identified by nested PCR and sequenced among malaria positive dried blood spots (DBS) that were collected from individuals attending health facilities from January 2013 to February 2014 and during community surveys from October 2010 to September 2011 across different Local Government Areas of Lagos State, Nigeria. RESULTS: A total of 242 and 167 samples were sequenced for dhfr and dhps, respectively. Sequence analysis of dhfr showed that 95.5% (231/242), 96.3% (233/242) and 96.7% (234/242) of the samples had N51I, C59R and S108N mutant alleles, respectively. The prevalence of dhps mutation at codons A437G, A613S, S436A, A581G, I431V and K540E were 95.8% (160/167), 41.9% (70/167), 41.3% (69/167), 31.1% (52/167), 25.1% (42/167), and 1.2% (2/167) respectively. The prevalence of triple mutations (CIRNI) in dhfr was 93.8% and 44.3% for the single dhps haplotype mutation (SGKAA). Partial SP-resistance due to quadruple dhfr-dhps haplotype mutations (CIRNI-SGKAA) and octuple haplotype mutations (CIRNI-VAGKGS) with rate of 42.6% and 22.0%, respectively has been reported. CONCLUSIONS: There was increased prevalence in dhfr triple haplotype mutations when compared with previous reports in the same environment but aligned with high prevalence in other locations in Nigeria and other countries in Africa. Also, high prevalence of dhfr and dhps mutant alleles occurred in the study areas in Lagos, Nigeria five to eight years after the introduction of artemisinin combination therapy underscores the need for continuous monitoring.

Clinical presentation, case management and outcomes for the first 32 COVID-19 patients in Nigeria.

INTRODUCTION: Success in curtailing the pandemic coronavirus disease (COVID-19) depends largely on a sound understanding of the epidemiologic and clinical profile of cases in a population as well as the case management approach. This study documents the presenting characteristics, treatment modalities and outcomes of the first 32 COVID-19 patients in Nigeria. METHODS: This retrospective study used medical records of the first 32 patients admitted and discharged from the Mainland Hospital, Lagos State, southwest Nigeria between February 27 and April 6, 2020. The outcomes of interest were death, promptness of admission process and duration of hospitalization. RESULTS: The mean age of the patients was 38.1 years (SD: 15.5) and 66% were male. Three-quarters (75%) of the patients presented in moderately severe condition while 16% were asymptomatic. The most common presenting symptoms were fever (59%) and dry cough (44%). The mean time between a positive test result and admission was 1.63 days (SD: 1.31). Almost all (97%) the patients were treated with lopinavir-ritonavir with no recorded death. The median duration of hospital stay was 12 days (IQR: 9-13.5). CONCLUSION: In this preliminary analysis of the first COVID-19 cases in Nigeria, clinical presentation was mild to moderate with no mortality. Processes to improve promptness of admission and reduce hospital stay are required to enhance the response to COVID-19 in Nigeria.

Parvovirus B19 DNA detection in treatment-naïve HIV anemic patients in Lagos, Nigeria: a case control study.

BACKGROUND: Parvovirus B19 (B19) has tropism for cells of the erythroid lineage, which may lead to transient inhibition of erythropoiesis. Several studies and case reports suggested that B19 infection may contribute significantly to severe chronic anemia in HIV infected persons. OBJECTIVE: To detect parvovirus B19 DNA in treatment-naïve HIV patients. METHODS: This was a case control retrospective study. One hundred nineteen anemic and 81 non-anemic treatment-naïve HIV infected patients participated in the study at the Lagos University Teaching Hospital, Lagos, Nigeria. Polymerase chain reaction was used to detect B19 DNA. RESULTS: Out of 200 patients analysed, 13(6.5%) had parvovirus B19 DNA. Eight HIV patients with anemia had B19 DNA while five non-anemic HIV patients had B19 DNA. This suggests that the presence of B19 DNA in the blood of HIV positive individuals may contribute to anemia because the majority (61.5%) who were positive for B19 DNA had anemia as compared to the non-anemic control group (38.5%). CONCLUSION: This study shows that the presence of B19 DNA in anemic HIV infected patients is not associated with chronic anaemia in HIV infection because no significant association exist.

Lassa virus RNA detection from suspected cases in Nigeria, 2011-2017.

INTRODUCTION: The diagnosis of Lassa fever is crucial to confirm cases, as well as to control/prevent nosocomial and community-based transmission and initiation of treatment, which is still limited in the country. Thus, we aimed at providing some information on the laboratory detection of Lassa from suspected cases in Nigeria. METHODS: This was a retrospective study of seasonal Lassa fever outbreaks data from 1,263 samples analyzed using Reverse Transcription-Polymerase Chain Reaction (RT-PCR) at the Virology Research Laboratory, College of Medicine, University of Lagos/Lagos University Teaching Hospital between year 2011 and 2017. Data were analyzed using the 21st edition of SPSS statistical software (2015). RESULTS: The RT-PCR test confirmed the presence of Lassa in 112 (8.9%) comprising 61 (54.4%) males, 48 (42.9%) females and 3 (2.7%) individuals without gender information. Those aged between 18 and 49 years were mostly affected. There was a decline in the detection of Lassa from 4.7% in 2011/2012 to less than 1% by the 2014/2015. However, during the 2015/2016 and 2016/2017 seasons the detection rates increased to 10.4% and 15.1% respectively. The Northern region of Nigeria reported high confirmed cases of Lassa. The South Western region also witnessed an increased Lassa fever positivity rate of 13.4% of which Lagos and Ogun states being the focal state of Lassa activity in the region. CONCLUSION: These established the need for heightening the continued surveillance for Lassa as well as the establishment of other testing facilities within these endemic regions for prompt diagnosis of Lassa fever.

Molecular confirmation and phylogeny of Lassa fever virus in Benin Republic 2014-2016.

BACKGROUND: The changing epidemiology of the Lassa virus from endemic areas to other parts of West Africa has been reported. However, there have been no documented Lassa fever transmission chains in the Benin Republic. Two outbreaks of Lassa fever (November 2014 and January 2016) in the Benin Republic were characterised by a high number of deaths (more than 50%) among 27 confirmed and other unconfirmed cases. OBJECTIVES: We report the detection, confirmation and relatedness of the Lassa virus strains from the Benin Republic with other isolates within the West African Sub-region. METHODS: A total of 70 blood samples (16 from 2014 and 54 from 2016) from suspected cases with signs and symptoms suggestive of viral haemorrhagic fever were received for molecular analysis at the Centre for Human and Zoonotic Virology, College of Medicine, University of Lagos and the Lagos University Teaching Hospital. With the detection of the Lassa virus RNA by reverse transcriptase polymerase chain reaction, sequencing and phylogenetic analyses were performed using the Sanger dideoxy sequencing technology platform and the MEGA6 software. RESULTS: S segments of the Lassa virus RNA genome were detected in 5 (7.1%) of the 70 samples analysed. Sequencing and a phylogenetic tree construction confirmed that the strain of Lassa virus had close relationships with strains previously isolated from Nigeria. CONCLUSION: We confirmed the presence of the Lassa virus in the Benin Republic, with 2 strains having molecular epidemiological links with Lineage I and II strains from Nigeria. To reduce the likelihood of outbreaks, there is a need for heightened awareness and strengthened surveillance systems about Lassa fever, particularly in the sub-region.

Kelch 13 propeller gene polymorphism among Plasmodium falciparum isolates in Lagos, Nigeria: Molecular Epidemiologic Study.

OBJECTIVE: To assess polymorphism in Kelch 13 gene of Plasmodium falciparum isolates in Lagos, Nigeria. METHODS: 195 Plasmodium falciparum-positive dried blood spots collected from individuals that accessed diagnostic care at some health facilities and during community surveys across several Local Government Areas of Lagos State, Nigeria, were investigated for the presence of mutations in the K13 gene by nested polymerase chain reaction (PCR) using haplotype-specific probes and sequencing. RESULTS: Three mutant genotypes of K13 gene were observed: A578S in 0.5%, D464N in 0.5% and Q613H in 1.5%. The frequency of K13 polymorphism was 3.1%, while the remaining parasite population had the wild K13 propeller genes. CONCLUSION: No validated Kelch 13 polymorphism associated with artemisinin resistance was seen among P. falciparum isolates from Lagos, Nigeria. As no clinical study was done, this could not be correlated with artemisinin sensitivity.

OBJECTIF: Evaluer le polymorphisme du gène Kelch 13 dans les isolats de Plasmodium falciparum à Lagos, au Nigéria. MÉTHODES: 195 gouttes de sang séchées positives pour Plasmodium falciparum recueillies auprès d'individus ayant accédé à des soins de diagnostic dans certains centres de santé et lors d'enquêtes communautaires menées dans plusieurs zones du gouvernement local de l'Etat de Lagos, au Nigéria, ont été examinées pour rechercher la présence de mutations du gène K13 par la réaction en chaîne imbriquée de la polymérase (PCR) en utilisant des sondes spécifiques à l'haplotype et par le séquençage. RÉSULTATS: Trois génotypes mutants du gène K13 ont été observés: A578S dans 0,5%, D464N dans 0,5% et Q613H dans 1,5%. La fréquence du polymorphisme K13 était de 3,1%, alors que la population parasitaire restante avait les gènes sauvages de l'hélice K13. CONCLUSION: Aucun polymorphisme validé de Kelch 13 associé à une résistance à l'artémisinine n'a été observé parmi les isolats de P. falciparum de Lagos, au Nigéria. Aucune étude clinique n'ayant été réalisée, il n'a pas été possible d'établir une corrélation entre cette observation et la sensibilité à l'artémisinine.

Complete Genome Sequence of a Hepatitis E Virus Genotype 1e Strain from an Outbreak in Nigeria, 2017.

Hepatitis E virus genotype 1 (HEV-1) is associated with large epidemics. Notably, HEV subtype 1e (HEV-1e) has caused HEV outbreaks in sub-Saharan Africa. We report here the second full-length genome sequence of an HEV-1e strain (NG/17-0503) from a recent outbreak in Nigeria in 2017. It shares 94.2% identity with an HEV-1e strain from Chad.

Ebola Virus Epidemiology and Evolution in Nigeria.

Containment limited the 2014 Nigerian Ebola virus (EBOV) disease outbreak to 20 reported cases and 8 fatalities. We present here clinical data and contact information for at least 19 case patients, and full-length EBOV genome sequences for 12 of the 20. The detailed contact data permits nearly complete reconstruction of the transmission tree for the outbreak. The EBOV genomic data are consistent with that tree. It confirms that there was a single source for the Nigerian infections, shows that the Nigerian EBOV lineage nests within a lineage previously seen in Liberia but is genetically distinct from it, and supports the conclusion that transmission from Nigeria to elsewhere did not occur.

New Hosts of The Lassa Virus.

Lassa virus (LASV) causes a deadly haemorrhagic fever in humans, killing several thousand people in West Africa annually. For 40 years, the Natal multimammate rat, Mastomys natalensis, has been assumed to be the sole host of LASV. We found evidence that LASV is also hosted by other rodent species: the African wood mouse Hylomyscus pamfi in Nigeria, and the Guinea multimammate mouse Mastomys erythroleucus in both Nigeria and Guinea. Virus strains from these animals were isolated in the BSL-4 laboratory and fully sequenced. Phylogenetic analyses of viral genes coding for glycoprotein, nucleoprotein, polymerase and matrix protein show that Lassa strains detected in M. erythroleucus belong to lineages III and IV. The strain from H. pamfi clusters close to lineage I (for S gene) and between II &III (for L gene). Discovery of new rodent hosts has implications for LASV evolution and its spread into new areas within West Africa.