Browsing by Author "Njau, Emma"

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African Swine Fever Virus (ASFV): Biology, Genomics and Genotypes Circulating in Sub-Saharan Africa
(MDPI, 2021-11-15) Njau, Emma; Machuka, Eunice; Cleaveland, Sarah; Shirima, Gabriel; Kusiluka, Lughano; Okoth, Edward; Pelle, Roger
African swine fever (ASF) is a highly infectious and fatal haemorrhagic disease of pigs that is caused by a complex DNA virus of the genus Asfivirus and Asfarviridae African suids family. The disease is among the most devastating pig diseases worldwide including Africa. Although the disease was first reported in the 19th century, it has continued to spread in Africa and other parts of the world. Globally, the rising demand for pork and concomitant increase in transboundary movements of pigs and pork products is likely to increase the risk of transmission and spread of ASF and pose a major challenge to the pig industry. Different genotypes of the ASF virus (ASFV) with varying virulence have been associated with different outbreaks in several countries in sub-Saharan Africa (SSA) and worldwide, and understanding genotype circulation will be important for ASF prevention and control strategies. ASFV genotypes unique to Africa have also been reported in SSA. This review briefly recounts the biology, genomics and genotyping of ASFV and provides an account of the different genotypes circulating in SSA. The review also highlights prevention, control and progress on vaccine development and identifies gaps in knowledge of ASFV genotype circulation in SSA that need to be addressed.
Detection and genetic characterization of sylvatic and outbreak African swine fever virus isolates in selected zones of Tanzania
(NM-AIST, 2022-07) Njau, Emma
This thesis is about African swine fever (ASF), a severe disease of domestic pigs that is notifiable according to OIE. Virus strains circulating in Tanzania have been changing from time to time making surveillance studies imperative. This research aimed at understanding the African Swine Fever Virus (ASFV) setting in the sylvatic cycle devoid of domestic pigs and genetic characterization of the ASFV genotypes circulating in the domestic pig cycle by genome sequencing of the virus so as to provide information such as the relatedness of the virus strains for other studies. In the study, blood and tissue samples from outbreaks and from selected seven agro-ecological areas of Tanzania (Northern (n=58) Southern (n=18), Southern highlands (n=60), Coastal (n=30), Western (n=40), Central (n=40) and lake zone (n=56)) were screened for ASFV using antibody ELISA and PCR techniques. The study population included domestic cycle hosts (domestic pigs (n=302) and sylvatic cycle hosts (warthogs (n=9) and soft ticks (n=300)). Snowball sampling was applied for domestic pigs following outbreak notifications from the Ministry of Livestock and Fisheries for the areas that experienced outbreaks (Southern highlands, Lake Victoria, Coastal and Northern zones). Convenient sampling was implied for non-outbreak areas (Central, Western and Southern zones) and the Saadani National Park. Blood and tissue samples from domestic pigs (n=302), blood samples from warthogs (n=19) and whole ticks (n=300) from warthog burrows (n=5) were collected from the field and transported to the laboratory for analysis. Serum samples extracted from blood were analysed for the presence of ASFV antibodies. DNA was extracted from the tissues, ticks and whole blood samples for ASFV diagnosis. Representative positive samples were Sanger sequenced for genotyping and tissue cultured for whole genome sequencing. While using standard OIE recommended ASF diagnostic and genotyping primers, positive and negative controls were used in each process to ensure reliability and validity of the obtained results. ELISA results confirmed the exposure of warthogs to ASFV although none of the animals were found to be in active viremia. As opposed to warthogs, domestic pigs did not react positively to an ELISA test but they were in active viremia following a PCR test with ASFV primers. This study reported four ASFV genotypes currently present in Tanzania. Genotypes II, IX and X were reported from domestic pigs whereas genotype XV was reported from the ticks in the sylvatic cycle. This is the first study to report the presence of genotype XV from an ecosystem that has never recorded interaction with domestic pigs. The study also released the first full genome sequence of a genotype II ASFV strain from Africa (Tanzania/ Rukwa/2017/1) generated using Illumina sequencing (Deposited in the INSDC databases through the European Nucleotide Archive (ENA) under accession number LR813622). The reported strain was observed to have a 99.961 percentage identity with the updated Georgia ii 2007/1 reference isolate (FR682468.2), 99.960% identity with Polish isolate Pol16_29413_o23 (MG939586) and 99.957% identity with Chinese isolate ASFV-wbBS01 (MK645909.1). This gave a proposition on the relatedness of genotype II strains of the virus from the known geographical hotspot given that this was the most globally spread genotype. Findings from this study add an information on what was known regarding ASFV in the sylvatic cycle in the country, and as a global hotspot for ASF. The first ASF vaccine is likely to focus on genotype II as it is the most widespread genotype. This has an implication on the global efforts to control ASF while being able to follow the molecular changes of the virus from the hotspot areas. There is also a possibility that in Tanzania, ASFV is present in new areas and distributed widely than it was previously anticipated. Information on circulating genotypes and spatial distribution is paramount for devising control interventions in Tanzania.
Detection of African swine fever virus genotype XV in a sylvatic cycle in Saadani National Park, Tanzania
(Wiley Online Library, 2020-07-22) Njau, Emma; Machuka, Eunice; Githae, Dedan; Okoth, Edward; Cleaveland, Sarah; Shirima, Gabriel; Kusiluka, Lughano; Pelle, Roger
African swine fever (ASF) is a severe haemorrhagic disease of domestic pigs caused by ASF virus (ASFV). ASFV is transmitted by soft ticks (Ornithodoros moubata complex group) and by direct transmission. In Africa, ASF is maintained in transmission cycles of asymptomatic infection involving wild suids, mainly warthogs (Phacochoerus afri canus). ASF outbreaks have been reported in many parts of Tanzania; however, active surveillance has been limited to pig farms in a few geographical locations. There is an information gap on whether and where the sylvatic cycle may occur independently of domestic pigs. To explore the existence of a sylvatic cycle in Saadani National Park in Tanzania, blood and serum samples were collected from 19 warthogs se lected using convenience sampling along vehicle-accessible transects within the na tional park. The ticks were sampled from warthog burrows. Blood samples and ticks were subjected to ASFV molecular diagnosis (PCR) and genotyping, and warthog sera were subjected to serological (indirect ELISA) testing for ASFV antibody detection. All warthog blood samples were PCR-negative, but 16/19 (84%) of the warthog sera were seropositive by ELISA confirming exposure of warthogs to ASFV. Of the ticks sampled, 20/111 (18%) were positive for ASFV by conventional PCR. Sequencing of the p72 virus gene fragments showed that ASF viruses detected in ticks belonged to genotype XV. The results confirm the existence of a sylvatic cycle of ASFV in Saadani National Park, Tanzania, that involves ticks and warthogs independent of domestic pigs. Our findings suggest that genotype XV previously reported in 2008 in Tanzania is likely to be widely distributed and involved in both wild and domestic infection cycles. Whole-genome sequencing and analysis of the ASFV genotype XV circulating in Tanzania is recommended to determine the phylogeny of the viruses.
The first genotype II African swine fever virus isolated in Africa provides insight into the current Eurasian pandemic
(Scientific Reports, 2021-06-22) Njau, Emma; Entfellner, Jean-Baka; Machuka, Eunice; Bochere, Edwina; Cleaveland, Sarah; Shirima, Gabriel; Kusiluka, Lughano; Upton, Chris; Bishop, Richard; Pelle, Roger; Okoth, Edward
African swine fever (ASF) caused by the African swine fever virus (ASFV) is ranked by OIE as the most important source of mortality in domestic pigs globally and is indigenous to African wild suids and soft ticks. Despite two ASFV genotypes causing economically devastating epidemics outside the continent since 1961, there have been no genome-level analyses of virus evolution in Africa. The virus was recently transported from south-eastern Africa to Georgia in 2007 and has subsequently spread to Russia, eastern Europe, China, and south-east Asia with devastating socioeconomic consequences. To date, two of the 24 currently described ASFV genotypes defined by sequencing of the p72 gene, namely genotype I and II, have been reported outside Africa, with genotype II being responsible for the ongoing pig pandemic. Multiple complete genotype II genome sequences have been reported from European, Russian and Chinese virus isolates but no complete genome sequences have yet been reported from Africa. We report herein the complete genome of a Tanzanian genotype II isolate, Tanzania/Rukwa/2017/1, collected in 2017 and determined using an Illumina short read strategy. The Tanzania/Rukwa/2017/1 sequence is 183,186 bp in length (in a single contig) and contains 188 open reading frames. Considering only un-gapped sites in the pairwise alignments, the new sequence has 99.961% identity with the updated Georgia 2007/1 reference isolate (FR682468.2), 99.960% identity with Polish isolate Pol16_29413_o23 (MG939586) and 99.957% identity with Chinese isolate ASFV-wbBS01 (MK645909.1). This represents 73 single nucleotide polymorphisms (SNPs) relative to the Polish isolate and 78 SNPs with the Chinese genome. Phylogenetic analysis indicated that Tanzania/Rukwa/2017/1 clusters most closely with Georgia 2007/1. The majority of the differences between Tanzania/Rukwa/2017/1 and Georgia 2007/1 genotype II genomes are insertions/deletions (indels) as is typical for ASFV. The indels included differences in the length and copy number of the terminal multicopy gene families, MGF 360 and 110. The Rukwa2017/1 sequence is the first complete genotype II genome from a precisely mapped locality in Africa, since the exact origin of Georgia2007/1 is unknown. It therefore provides baseline information for future analyses of the diversity and phylogeography of this globally important genetic sub-group of ASF viruses.