Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya

Newcastle disease (ND) is an endemic viral disease affecting poultry and causing massive economic losses. This cross-sectional purposive study detected coinfections that are associated with the Newcastle disease virus among poultry from selected regions in Kenya. Cloacal (n = 599) and oral-pharyngeal (n = 435) swab samples were collected and pooled into 17 and 15 samples, respectively. A total of 17,034,948 and 7,751,974 paired-end reads with an average of 200 nucleotides were generated from the cloacal and oral-pharyngeal swab samples, respectively. Analysis of the de novo assembled contigs identified 177 and 18 cloacal and oral-pharyngeal contigs, respectively with hits to viral sequences, as determined by BLASTx and BLASTn analyses. Several known and unknown representatives of Coronaviridae, Picobirnaviridae, Reoviridae, Retroviridae, and unclassified Deltavirus were identified in the cloacal swab samples. However, no Newcastle disease virus (family Paramyxoviridae) was detected in the cloacal swabs, although they were detected in the oropharyngeal swabs of chickens sampled in Nairobi, Busia, and Trans Nzoia. Additionally, sequences representative of Paramyxoviridae, Coronaviridae, and Retroviridae were identified in the oral-pharyngeal swab samples. Infectious bronchitis virus and rotavirus were chickens' most prevalent coinfections associated with the Newcastle disease virus. The detection of these coinfections suggests that these viruses are significant threats to the control of Newcastle disease as the Newcastle disease virus vaccines are known to fail because of these coinfections. Therefore, this study provides important information that will help improve disease diagnosis and vaccine development for coinfections associated with the Newcastle disease virus

Quantitative Outcomes of a One Health Approach to Investigate the First Outbreak of African Swine Fever in the Republic of Sierra Leone

African swine fever (ASF) outbreaks have been reported in Sub-Saharan countries, including West Africa states, but has never been notified in the Republic of Sierra Leone. This is the first report describing field epidemiological and laboratory investigations into the outbreak of fatal pig disease in western rural and urban districts, Freetown. A preliminary finding indicated that pigs exhibited clinical and necropsy signs suggestive of ASF. Serological (ELISA) and molecular (qRT-PCR) methods used to confirm and investigate the outbreak yielded three positive results for the ASF antibody and all negative for Swine flu; thus, confirming ASF as the etiology agent

Insights from social network analysis are helping to build understanding of African Swine Fever epidemiology

Pig movements are likely to play a signficant role in the spread of important infectious diseases such as the African Swine Fever. Characterization of movement networks from farm-to-farm and through other types of farm or household operations can provide useful information on the role that networks play in acquiring and spreading infectious diseases. Analysis of social networks that underpin these pig movements can also reveal structures that are important in the transmission of disease, trade of commodities, the spread of knowledge and norms of social behavior. Our study assessed pig movements among pig keeping households within Kenya and Uganda and across the Kenya-Uganda border to help understand within country and trans-boundary pig movements.Villages were sampled using randomized cluster design. Data was collected through interviews in 2012/13 of 683 smallholder pig-keeping households in 38 villages. NodeXL software was used to analyze pig movement networks at village level. Movement of pigs occurred through agistment, sow service, restocking of household pigs and sale of finished pigs for slaughter. Most sow services occurred within the same villages or villages that were close by. Cross-border boar service between Uganda and Kenya was also recorded. Internal and unmonitored trade in both directions was prevalent. Most pig sales during ASF outbreak were to traders or other farmers who were most likely not coming from the same village. Close social relationships between actors in pig movement networks indicate the potential for possible interventions to develop shared norms amongst smallholder pig keepers to manage risk of ASF contraction and transmission

Molecular Characterization of Newcastle Disease Virus from Backyard Poultry Farms and Live Bird Markets in Kenya

Newcastle disease (ND) is a serious disease of poultry that causes significant economic losses. Despite rampant ND outbreaks that occur annually in Kenya, the information about the NDV circulating in Kenya is still scarce. We report the first countrywide study of NDV in Kenya. Our study is aimed at evaluating the genetic characteristics of Newcastle disease viruses obtained from backyard poultry in farms and live bird markets in different regions of Kenya. We sequenced and analyzed fusion (F) protein gene, including the cleavage site, of the obtained viruses. We aligned and compared study sequences with representative NDV of different genotypes from GenBank. The fusion protein cleavage site of all the study sequences had the motif 112RRQKRFV118 indicating their velogenic nature. Phylogenetic analysis revealed that the NDV from various sites in Kenya was highly similar genetically and that it clustered together with NDV of genotype V. The study samples were 96% similar to previous Ugandan and Kenyan viruses grouped in subgenotype Vd This study points to possible circulation of NDV of similar genetic characteristics between backyard poultry farms and live bird markets in Kenya. The study also suggests the possible spread of velogenic NDV between Kenya and Uganda possibly through cross-border live bird trade. Our study provides baseline information on the genetic characteristics of NDV circulating in the Kenyan poultry population. This highlights the need for the ND control programmes to place more stringent measures on cross-border trade of live bird markets and poultry products to prevent the introduction of new strains of NDV that would otherwise be more difficult to control

Metagenomic Characterization of Poultry Cloacal and Oropharyngeal Swabs in Kenya Reveals Bacterial Pathogens and Their Antimicrobial Resistance Genes

Poultry enteric bacterial diseases are of significant economic importance because they are responsible for production losses due to weight loss, increased morbidity and mortality, and increased cost of production arising from poor feed conversion and treatment. This cross-sectional purposive study characterized enteric bacterial pathogens in poultry from selected agroclimatic regions in Kenya and investigated their antimicrobial resistance gene profiles. Cloacal (n = 563) and oropharyngeal (n = 394) swabs were collected and pooled into 16 and 14 samples, respectively, to characterize bacterial pathogens and their antimicrobial resistance gene profiles. We report that Proteobacteria, Chlamydiae, and Firmicutes are the most dominant phyla present in both cloacal and oropharyngeal swabs of the six poultry species studied, indicating the colonization of the poultry gut by many pathogenic bacteria. Using KEGG and COG databases, some pathways related to metabolism, genetic information, and cellular processing were detected. We also report the abundance of antimicrobial resistance genes that confer resistance to β-lactamases, aminoglycosides, and tetracycline in most of the poultry analyzed, raising concern about the dangers associated with continuous and inappropriate use of these antibiotics in poultry production. The antimicrobial resistance gene data generated in this study provides a valuable indicator of the use of antimicrobials in poultry in Kenya. The information generated is essential for managing bacterial diseases, especially in backyard poultry raised under scavenging conditions

Molecular Analysis of East African Lumpy Skin Disease Viruses Reveals a Mixed Isolate with Features of Both Vaccine and Field Isolates

International audienceLumpy skin disease (LSD), an economically significant disease in cattle caused by lumpy skin disease virus (LSDV), is endemic to nearly all of Africa. Since 2012, LSDV has emerged as a significant epizootic pathogen given its rapid spread into new geographical locations outside Africa, including the Middle East, Eastern Europe, and Asia. To assess the genetic diversity of LSDVs in East Africa, we sequenced and analyzed the RPO30 and GPCR genes of LSDV in twenty-two archive samples collected in Ethiopia, Kenya, and Sudan before the appearance of LSD in the Middle East and its incursion into Europe. We compared them to publicly available sequences of LSDVs from the same region and those collected elsewhere. The results showed that the East African field isolates in this study were remarkably similar to each other and to previously sequenced field isolates of LSDV for the RPO30 and GPCR genes. The only exception was LSDV Embu/B338/2011, a field virus collected in Kenya, which displayed mixed features between the LSDV Neethling vaccine and field isolates. LSDV Embu/B338/2011 had the same 12-nucleotide insertion found in LSDV Neethling and KS-1 vaccines. Further analysis of the partial EEV glycoprotein, B22R, RNA helicase, virion core protein, NTPase, and N1R/p28-like protein genes showed that LSDV Embu/B338/2011 differs from previously described LSDV variants carrying the 12-nucleotide insertion in the GPCR gene. These findings highlight the importance of the constant monitoring of genetic variation among LSDV isolates

A Phylogeographic Analysis of Porcine Parvovirus 1 in Africa

Porcine parvovirus 1 (PPV1) is recognized as a major cause of reproductive failure in pigs, leading to several clinical outcomes globally known as SMEDI. Despite being known since the late 1960s its circulation is still of relevance to swine producers. Additionally, the emergence of variants such as the virulent 27a strain, for which lower protection induced by vaccines has been demonstrated, is of increasing concern. Even though constant monitoring of PPV1 using molecular epidemiological approaches is of pivotal importance, viral sequence data are scarce especially in low-income countries. To fill this gap, a collection of 71 partial VP2 sequences originating from eight African countries (Burkina Faso, Côte d’Ivoire, Kenya, Mozambique, Namibia, Nigeria, Senegal, and Tanzania) during the period 2011–2021 were analyzed within the context of global PPV1 variability. The observed pattern largely reflected what has been observed in high-income regions, i.e., 27a-like strains were more frequently detected than less virulent NADL-8-like strains. A phylogeographic analysis supported this observation, highlighting that the African scenario has been largely shaped by multiple PPV1 importation events from other continents, especially Europe and Asia. The existence of such an international movement coupled with the circulation of potential vaccine-escape variants requires the careful evaluation of the control strategies to prevent new strain introduction and persistence