Classic human astrovirus 4, 8, MLB-3, and likely new genotype 5 sublineage in stool samples of children in Nigeria.

Human astrovirus (HAstV) is a nonenveloped RNA virus and has been implicated in acute gastroenteritis among children and elderly. However, there exists a substantial dearth of information on HAstV strains circulating in Nigeria. Viral-like particles were purified from archived 254 stool samples of children with acute flaccid paralysis between January and December 2020 from five states in Nigeria, using the NetoVIR protocol. Extracted viral RNA and DNA were subjected to a reverse transcription step and subsequent random polymerase chain reaction amplification. Library preparation and Illumina sequencing were performed. Using the virome paired-end reads pipeline, raw reads were processed into genomic contigs. Phylogenetic and pairwise identity analysis of the recovered HAstV genomes was performed. Six near-complete genome sequences of HAstV were identified and classified as HAstV4 (n = 1), HAstV5 (n = 1), HAstV8 (n = 1), and MLB-3 (n = 3). The HAstV5 belonged to a yet unclassified sublineage, which we tentatively named HAstV-5d. Phylogenetic analysis of open reading frames 1a, 1b, and 2 suggested recombination events inside the MAstV1 species. Furthermore, phylogenetic analysis implied a geographic linkage between the HAstV5 strain from this study with two strains from Cameroon across all the genomic regions. We report for the first time the circulation of HAstV genotypes 4, 8, and MLB-3 in Nigeria and present data suggestive for the existence of a new sublineage of HAstV5. To further understand the burden, diversity, and evolution of HAstV, increased research interest as well as robust HAstV surveillance in Nigeria is essential.

Towards an effective poliovirus laboratory containment strategy in Nigeria.

BACKGROUND: The Global Commission for the Certification of the Eradication of Poliomyelitis will declare the world free of wild poliovirus transmission when no wild virus has been found in at least 3 consecutive years, and all laboratories possessing wild poliovirus materials have adopted appropriate measures of containment. Nigeria has made progress towards poliomyelitis eradication with the latest reported WPV type 1 on 21 Aug 2016 after 2 years without any case. This milestone achievement was followed by an inventory of biomedical laboratories completed in November 2015 with the destruction of all identified infectious materials. This paper seeks to describe the poliovirus laboratory containment process in Nigeria on which an effective containment system has been built to minimize the risk of virus re-introduction into the population from the laboratories. METHODS: A national survey of all biomedical facilities, as well as an inventory of laboratories from various sectors, was conducted from June-November 2015. National Task Force (NTF) members and staff working on polio administered an on-site questionnaire in each facility. Laboratory personnel were sensitized with all un-needed materials destroyed by autoclaving and incineration. All stakeholders were also sensitized to continue the destruction of such materials as a requirement for phase one activities. RESULTS: A total of 20,638 biomedical facilities were surveyed with 9575 having laboratories. Thirty laboratories were found to contain poliovirus or potentially infectious materials. The 30 laboratories belonged to the ministries of health, education, defence and private organizations. CONCLUSIONS: This article is amongst the first in Africa that relates poliovirus laboratory containment in the context of the tOPV-bOPV switch in alignment with the Global Action Plan III. All identified infectious materials were destroyed and personnel trained to continue to destroy subsequent materials, a process that needs meticulous monitoring to mitigate the risk of poliovirus re-introduction to the population.