Systematic review, meta-analysis and whole genome sequence analysis studies of avian influenza virus, influenza d virus, newcastle disease virus, and severe acute respiratory syndrome coronavirus 2.
| dc.contributor.author | Kalonda, Annie | |
| dc.date.accessioned | 2025-01-15T11:51:13Z | |
| dc.date.available | 2025-01-15T11:51:13Z | |
| dc.date.issued | 2023 | |
| dc.description | Thesis of Doctor of Philosophy in Virology. | |
| dc.description.abstract | Avian influenza and Newcastle disease are respiratory and often fatal diseases of birds caused by avian influenza virus (AIV) and Newcastle disease virus (NDV), respectively. They are zoonotic diseases that affect a wide range of avian species and cause substantial economic losses. Moreover, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans strained the global economy and healthcare systems. Despite disease control efforts, these viruses have continued to circulate. Therefore, the study aimed to evaluate the circulation and genetic characteristics of AIVs, influenza D virus (IDV), NDV and SARS-CoV-2. A total of 2851 and 1150 faecal samples were obtained from wild waterfowl and poultry, respectively, and 198 nasopharyngeal swabs were collected from humans in Zambia. Systematic reviews and meta-analysis were conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, and standard methods and next-generation sequencing were used to identify and genetically characterise the viruses. The systematic review revealed an overall prevalence and seroprevalence of 3.0% and 4.1% of AIV in African birds, with H5N1 being the most detected subtype. The meta-analysis demonstrated an estimated pooled prevalence and seroprevalence of IAV in pigs in Africa of 1.6% and 14.9%, respectively, while IDV seroprevalence was at 87.2% in camels, 9.3% in cattle and 2.2% in small ruminants. IAV subtypes H1N1 and H1N1pdm09 were commonly detected in pigs. In Zambian wild waterfowl, 85 (3.0%) low pathogenicity AIVs belonging to various subtypes and 2 (0.07%) avirulent NDVs were isolated. While no AIVs were detected in poultry, 4 (0.3%) virulent NDV were isolated. Moreover, the study reports, for the first time in Africa, the isolation of AIV in glossy ibis and the detection of H2N9, H8N4, and H10N8 AIV subtypes. Phylogenetic analysis of AIVs revealed that all the isolates belonged to the Eurasian lineage, with their closest relatives being viruses from wild and/or domestic birds in Africa, Asia, and Europe, and were grouped into distinct clusters based on the year of isolation. Furthermore, some internal protein genes of the viruses were closely related to H7 low pathogenicity AIVs. Analysis of the NDV strains revealed that the isolates from wild waterfowl belonged to class I viruses. In contrast, those from poultry belonged to class II, genotype VII and were closely related to viruses isolated from the Eastern Province of Zambia in 2015. Genetic analysis of 40 SARS-CoV-2 revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants. Furthermore, 292 mutations were observed, with the majority being missense mutations. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 variants in Zambia from different European and African countries. This study highlights the circulation of low pathogenicity AIVs and NDV in wild waterfowls, NDV in poultry and co-circulations of SARS-CoV-2 variants in the human population in the Southern Province of Zambia. Therefore, the study stresses the need for continuous surveillance and monitoring of AIVs and NDV in wild waterfowl and poultry for a better understanding of the eco-epidemiology and evolutionary dynamics of AIVs in Africa as well as SARS-CoV-2 circulation in Zambia | |
| dc.identifier.uri | https://dspace.unza.zm/handle/123456789/9082 | |
| dc.language.iso | en | |
| dc.publisher | The University of Zambia | |
| dc.title | Systematic review, meta-analysis and whole genome sequence analysis studies of avian influenza virus, influenza d virus, newcastle disease virus, and severe acute respiratory syndrome coronavirus 2. | |
| dc.type | Thesis |