Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018.

During 2018, an unusual increase in Lassa fever cases occurred in Nigeria, raising concern among national and international public health agencies. We analyzed 220 Lassa virus genomes from infected patients, including 129 from the 2017-2018 transmission season, to understand the viral populations underpinning the increase. A total of 14 initial genomes from 2018 samples were generated at Redeemer's University in Nigeria, and the findings were shared with the Nigerian Center for Disease Control in real time. We found that the increase in cases was not attributable to a particular Lassa virus strain or sustained by human-to-human transmission. Instead, the data were consistent with ongoing cross-species transmission from local rodent populations. Phylogenetic analysis also revealed extensive viral diversity that was structured according to geography, with major rivers appearing to act as barriers to migration of the rodent reservoir.

Setting up a molecular diagnostic laboratory for SARS-CoV-2 testing: Experience of a single centre in a resource-constrained setting.

BACKGROUND: Molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is at the forefront of the global response to the coronavirus disease 2019 (COVID-19) pandemic. However, molecular diagnostic capabilities are poorly developed in many African countries. Efforts by the Nigeria Centre for Disease Control and other public health agencies to scale up facilities for molecular testing across the continent are well documented, but there are few accounts from the laboratories at the frontline. INTERVENTION: As part of an institutional response to the COVID-19 pandemic, the University of Benin Teaching Hospital, Benin City, Nigeria, signed a memorandum of understanding with a World Bank-supported institution to obtain a non-proprietary testing platform, renovated an existing molecular virology laboratory and validated the test process to make SARS-CoV-2 testing readily available for decision-making by frontline health workers. These efforts resulted in the University of Benin Teaching Hospital's inclusion in the Nigeria Centre for Disease Control COVID-19 molecular laboratory network. The laboratory achieved a turnover of 12 123 tests within 7 months of operation. Challenges faced and dealt with include incompatible equipment, limited skilled manpower, unstable (unreliable) electric power supply, disrupted procurement and supply chain, and significant overhead costs. LESSONS LEARNT: Molecular diagnostic capability is essential in laboratory preparedness for pandemic response and can be achieved by establishing collaborative networks in low-resource settings. RECOMMENDATIONS: Molecular diagnostic capabilities attained during the COVID-19 pandemic should be maintained by governmental support of the local biotechnology sector, collaboration with partners and stakeholders and the expansion of diagnostics to include other diseases of public health importance.

Field evaluation of a Pan-Lassa rapid diagnostic test during the 2018 Nigerian Lassa fever outbreak.

Lassa virus (LASV) is the causative agent of Lassa fever (LF), an often-fatal hemorrhagic disease. LF is endemic in Nigeria, Sierra Leone and other West African countries. Diagnosis of LASV infection is challenged by the genetic diversity of the virus, which is greatest in Nigeria. The ReLASV Pan-Lassa Antigen Rapid Test (Pan-Lassa RDT) is a point-of-care, in vitro diagnostic test that utilizes a mixture of polyclonal antibodies raised against recombinant nucleoproteins of representative strains from the three most prevalent LASV lineages (II, III and IV). We compared the performance of the Pan-LASV RDT to available quantitative PCR (qPCR) assays during the 2018 LF outbreak in Nigeria. For patients with acute LF (RDT positive, IgG/IgM negative) during initial screening, RDT performance was 83.3% sensitivity and 92.8% specificity when compared to composite results of two qPCR assays. 100% of samples that gave Ct values below 22 on both qPCR assays were positive on the Pan-Lassa RDT. There were significantly elevated case fatality rates and elevated liver transaminase levels in subjects whose samples were RDT positive compared to RDT negative.

Molecular diagnostics for lassa fever at Irrua specialist teaching hospital, Nigeria: lessons learnt from two years of laboratory operation.

BACKGROUND: Lassa fever is a viral hemorrhagic fever endemic in West Africa. However, none of the hospitals in the endemic areas of Nigeria has the capacity to perform Lassa virus diagnostics. Case identification and management solely relies on non-specific clinical criteria. The Irrua Specialist Teaching Hospital (ISTH) in the central senatorial district of Edo State struggled with this challenge for many years. METHODOLOGY/PRINCIPAL FINDINGS: A laboratory for molecular diagnosis of Lassa fever, complying with basic standards of diagnostic PCR facilities, was established at ISTH in 2008. During 2009 through 2010, samples of 1,650 suspected cases were processed, of which 198 (12%) tested positive by Lassa virus RT-PCR. No remarkable demographic differences were observed between PCR-positive and negative patients. The case fatality rate for Lassa fever was 31%. Nearly two thirds of confirmed cases attended the emergency departments of ISTH. The time window for therapeutic intervention was extremely short, as 50% of the fatal cases died within 2 days of hospitalization--often before ribavirin treatment could be commenced. Fatal Lassa fever cases were older (p = 0.005), had lower body temperature (p<0.0001), and had higher creatinine (p<0.0001) and blood urea levels (p<0.0001) than survivors. Lassa fever incidence in the hospital followed a seasonal pattern with a peak between November and March. Lassa virus sequences obtained from the patients originating from Edo State formed--within lineage II--a separate clade that could be further subdivided into three clusters. CONCLUSIONS/SIGNIFICANCE: Lassa fever case management was improved at a tertiary health institution in Nigeria through establishment of a laboratory for routine diagnostics of Lassa virus. Data collected in two years of operation demonstrate that Lassa fever is a serious public health problem in Edo State and reveal new insights into the disease in hospitalized patients.