High pathogenicity avian influenza virus (HPAIV) H5N1 reached the sub-Antarctic and Antarctica in 2023, subsequently spreading to remote locations within this region where it had devastating impacts on seal, penguin and albatross populations. The threat to marine wildlife over this broad area exemplifies the need to understand H5N1 long-distance dispersal and evolution. We obtained 104 novel viral genomic sequences from samples that we collected at South Georgia, Kerguelen, Crozet, Prince Edward, Falklands/Malvinas Islands and the Antarctic Peninsula in a region spanning 8,000 kilometers. Using recent phylogeographic modeling advances we show that H5N1 spread encompassed numerous transmission events between distant locations, accumulating mammalian-adaptive mutations in the process. Seals are the most affected species, but we reveal that the long-distance eastward virus dispersal better aligns with the long-distance movements of large petrels and albatrosses. The risk of H5N1 endemisation, dispersal to other locations and ongoing evolution are highly concerning.

The International Alliance for Biological Standardization (IABS), in collaboration with the World Organization for Animal Health (WOAH) convened a hybrid meeting on 22-23 October 2024 at the WOAH Headquarters (HQ) in Paris, France to discuss the global state of vaccination and surveillance for high pathogenicity avian influenza (HPAI) in poultry. The primary objective of the meeting was to advance vaccination acceptance to both control virus spread and reduce disease. Vaccination is increasingly recognized as a tool to complement biosecurity, movement controls and stamping-out of infected flocks. However, concerns persist regarding the risk of undetected, sustained transmission (silent infection) in vaccinated flocks as a result of inadequate surveillance. This has contributed to both vaccination hesitancy and trade barriers. The meeting aimed to assess the current state of the art regarding HPAI surveillance programs in vaccinated populations and their effectiveness. Representatives of multiple stakeholders were invited to share their experiences and perspectives on the use of vaccination and accompanying surveillance to control the growing H5N1 panzootic and its global impact. Several conclusions and recommendations emerged as essential to advancing the acceptance of vaccination strategies. These included (1) the utility of quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) as a sensitive, specific and economical tool to detect virus in vaccinated populations, (2) regular testing of dead birds within a flock as a highly effective method for early detection of outbreaks in vaccinated flocks and demonstrating freedom from infection and, (3) the importance of collecting information on circulating field strains in the selection of candidate vaccine antigens to ensure adequate efficacy. Testing sentinel birds was deemed less effective for surveillance and serological testing of vaccinated birds was considered more useful for assessing immunity levels than for determining the infection status of a flock. There was broad agreement on the need to standardize surveillance outcomes in terms of accepted confidence levels to promote safe and fair trade. However, it was acknowledged that context and pragmatic considerations will shape the development of situation specific plans, which must be statistically valid, scientifically sound, economically feasible and operationally sustainable for both governments and industry. Concomitantly, it was recommended that trade policies tied to vaccination and surveillance should be based solely on science and risks. To this end, enforcement of existing international rules and resolution of disputes are considered a shared responsibility. Peer reviewed publications were proposed as a central mechanism for developing the stronger guidelines needed to facilitate fair trade agreements and enable implementation of global vaccination programs. Rapid dissemination of information, consistent messaging and exchange of virus isolates were also seen as critical for coordinating an effective global response to controlling HPAI.

Equine influenza (EI) is a highly contagious acute respiratory disease of wild and domesticated horses, donkeys, mules, and other Equidae. EI is caused by the Equine Influenza virus (EIV), is endemic in many countries and outbreaks still have a severe impact on the equine industry globally. Conventional EI vaccines are widely used, but a need exists for a platform that facilitates prompt manufacturing of a highly immunogenic, antigenically matched, updated vaccine product. Here we developed a plant-produced bivalent EI virus-like particle (VLP) vaccine candidate which lacks the viral genome and are therefore non-infectious. We conducted a pilot safety/dose response study of a plant produced bivalent VLP vaccine expressing the HA proteins of Florida clade (FC) 1 and FC2 EIV in 1:1 ratio. Groups of three EIV seronegative horses were vaccinated using four antigen levels (0 sham control, 250, 500, 1000 HAU/dose component). Two doses of vaccines were administered one month apart, and horses were observed for adverse reactions, which were minimal. Sera were collected for hemagglutination inhibition (HI) testing using FC1 and FC2 viruses. One month after the second dose, all horses were challenged with the aerosolized FC1 virus. Horses were observed daily for clinical signs, and nasopharyngeal swabs were collected to quantify viral RNA using qPCR and infectious virus by titration in embryonated hens' eggs. Results showed that all vaccinated groups seroconverted prior to challenge. Post-challenge, both clinical scores and virus shedding were much reduced in all vaccinates compared to the sham-vaccinated controls. We conclude that the VLP vaccines were safe and effective in this natural host challenge model. A safe, efficacious, new-generation bivalent EI VLP vaccine produced in plants, which can promptly and regularly be antigenically matched to ensure optimal protection, will pave the way to highly competitive commercially viable vaccine products for all economic environments globally.

Africa's vast geographic and climatic diversity makes it a critical region for the ecology and spread of avian influenza viruses, particularly due to its role as a wintering ground for Palearctic migratory waterbirds. The continent has experienced multiple waves of clade 2.3.4.4b A/H5Nx high pathogenicity avian influenza (HPAI), which has caused widespread outbreaks in poultry and wild birds since 2017. From 2023 to mid-2025, clade 2.3.4.4b A/H5N1 outbreaks were reported across West and Southern Africa, with severe impacts on poultry production and conservation of endangered wild bird species. Concurrently, South Africa and Mozambique battled an unprecedented A/H7N6 HPAI epizootic in 2023, leading to the culling or loss of over 6.8 million chickens. Additionally, the A/H9N2 subtype, particularly G5.5 sublineage strains, continues to circulate in North, West, and East Africa, with reassortant viruses with A/H5Nx viruses reported in Egypt. Underreporting and limited surveillance hamper accurate epidemiological assessment. Despite these challenges, advancements in noninvasive environmental sampling offer promising tools for early detection. Strengthening regional cooperation and surveillance is essential for mitigating future outbreaks and protecting both animal and public health.

Infectious bronchitis virus (IBV) affects the respiratory, urogenital and reproductive systems of chickens and causes major economic losses. Biosecurity and vaccinations are used to limit the disease's impact, and identifying the circulating strains is important for selecting appropriate vaccines. The partial spike (S1) genes of 364 IBVs, isolated from commercial chickens in Botswana, Eswatini, Namibia and South Africa from 2010 to 2020, were phylogenetically analyzed. Seven genotypes were identified: 184 viruses (50,5 %) were classified as genotype GI-19 (QX) and 78 (21,4 %) were GI-1 (Mass/H120). Thirty-nine (10,7 %) were genotype GI-13 (4/91), 29 (8,0 %) were GVI-1 (TC07-2), 19 (5,2 %) were GI-23 (Variant 2), and 13 (3,6 %) were GI-11 (UFMG/G-Brazil). Two (0.5 %) viruses belonged to the GIV-1 (DE/072/92) genotype. Genotype GI-11 had not been reported outside South America before but has evidently circulated in South Africa for at least a decade. Similarly, genotype GVI-1, previously thought to be restricted to Asia, has been present in southern Africa since at least 2010. Prior to 2013, only Mass and H120 vaccines were permitted to be used in South Africa, but since 2013 793/B (GI-13), QX (GI-19), 4-91 (GI-13) and Variant 2 (GI-23) live attenuated vaccines were permitted. Accordingly, the four IBV variants we identified were putative recombinants of genotypes G1-1 and G1-19, G1-13 and G1-19, or G1-13 and unknown IBV strains, but these variant viruses did not spread extensively or persist in the region. The phylogenetic evidence points to imported contaminated poultry and poultry products as the source of new IBV genotypes in southern Africa.

INTRODUCTION:Pigeon paramyxovirus type 1 (PPMV-1) is an antigenic variant of Avian Orthoavulavirus 1 (AOAV-1) (Newcastle disease virus) with a global distribution that causes lethal infections in pigeon and dove species. AOAV-1's infecting humans normally cause mild, self-limiting conjunctivitis, but since 2003, PPMV-1 has been associated with an increased number of severe and lethal respiratory and neurological infections in immunocompromised persons in the Netherlands, the USA, France, China and Australia. METHODS:PPMV-1's isolated from free-living pigeons and doves across South Africa from 2012 to 2024 were sequenced using conventional or next generation technologies. Maximum likelihood and time-scaled phylogenetic analyses were conducted. Cases of human infections with AOAV-1 were reviewed, and where the genotypes were not previously assigned, the sequence data were re-analysed for classification purposes. RESULTS:PPMV-1 sub-genotype VI.2.1.1.2.1, present in South Africa since at least 2005, continued to circulate in 2021. Sub-genotype VI.2.1.1.2.2, that is widely distributed across Europe, Asia and Australia, was identified in South Africa for the first time, with introduction estimated around September 2017 (95% HPD January 2016-June 2019). Previously unclassified viruses causing lethal human infections in the Netherlands (2003), the USA (2007) and France (2021) were identified as sub-genotypes VI.2.1.1.2.2, VI.2.1.1.1 and XXI.1.1, respectively. CONCLUSIONS:Five recorded AOAV-1-associated human fatalities since 1953 were all caused by PPMV-1. Three out of the five human fatalities, plus one seriously ill survivor, were associated with sub-genotype VI.2.1.1.2.2 viruses, and sub-genotypes VI.2.1.1.1 and XXI.1.1 each caused one human death. PPMV-1's, found widely in pigeons and doves, pose a serious health risk to immunocompromised persons.

A high pathogenicity avian influenza (HPAI) subtype H7N6 virus emerged in South African poultry in 2023 and later spread to Mozambique, the first documented emergence of H7 HPAI in the African continent. A total of 6.82 million birds succumbed to the disease or were culled, representing about 20% of the South African egg-laying flock and almost 30% of the broiler breeder flock. The complete genomes of 68 outbreak viruses were sequenced and analyzed, tracing the phylogenetic origins of the ancestral H7N6 virus to a reassortment of various subtypes that circulated in southern African wild birds. Molecular clock analysis determined that the virus emerged in the first week of May 2023, probably in a smallholder chicken flock, before spreading to commercial farms, where the disease was first reported in early June. The multibasic hemagglutinin protein cleavage site (HA0) was derived from a nonhomologous recombination event with chicken 28S ribosomal ribonucleic acid (RNA). Few genetic markers associated with an increased risk to humans were present in the translated viral proteins. The intravenous pathogenicity index (IVPI) value of the index case isolate was 1.67, reflecting that 50% of the specific pathogen-free chickens died within 4 days of infection. Surviving birds showing mostly mild clinical signs and recovered by day 10 postinfection. Prior to death, chickens shed the virus primarily through the respiratory route, with lower amounts shed from the cloaca, but in the survivors, the virus was still being shed from the cloaca on day 10. Fomites were the likely source of disease spread between farms, and the amount of H7N6 HPAI virus per gram of feces was calculated at ~383,193 (5.58 log10) egg infectious dose 50 (EID50) equivalents, chicken feather follicles contained on average 739,712.43 (5.87 log10) EID50 equivalents, and 20 µg of feather dust contained 14,976.96 (4.175 log10) EID50 equivalents.

In the quest for heightened protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, we engineered a prototype vaccine utilizing the plant expression system of Nicotiana benthamiana, to produce a recombinant SARS-CoV-2 virus-like particle (VLP) vaccine presenting the S-protein from the Beta (B.1.351) variant of concern (VOC). This innovative vaccine, formulated with either a squalene oil-in-water emulsion or a synthetic CpG oligodeoxynucleotide adjuvant, demonstrated efficacy in a golden Syrian Hamster challenge model. The Beta VLP vaccine induced a robust humoral immune response, with serum exhibiting neutralization not only against SARS-CoV-2 Beta but also cross-neutralizing Delta and Omicron pseudoviruses. Protective efficacy was demonstrated, evidenced by reduced viral RNA copies and mitigated weight loss and lung damage compared to controls. This compelling data instills confidence in the creation of a versatile platform for the local manufacturing of potential pan-sarbecovirus vaccines, against evolving viral threats.

Village poultry plays a vital role in providing essential nutrition and income for rural communities in Africa. In this context, poultry are often traded through live bird markets (LBMs), which serve as central trading hubs where producers connect with traders and consumers, facilitating the flow of poultry products along the value chain. While they serve as important trading hubs, these markets create an environment where avian pathogens, like Newcastle disease virus (NDV) and avian influenza virus, can easily emerge and spread. Improving our understanding of the epidemiology of NDV in LBMs is important for assessing disease risks and identifying factors that contribute to its persistence. Local chickens at the Mawenzi LBM in Morogoro municipality were surveyed for NDV presence, its temporal and spatial distribution, and risk factors for NDV infection. Twenty-three percent of 659 local chickens sampled over a 1-year period were positive for NDV based on PCR. Increased odds of NDV infection were identified in chickens that had been in the market for 2 or more days prior to sampling and during the period extending from August through October. Four significant spatiotemporal clusters of NDV-positive chickens encompassing 13 villages were detected between August and October 2020, illustrating geographic hotspots of infection when NDV was most prevalent. Similar to the other LBMs, this market had enclosures with high densities of birds of mixed species, limited biosecurity, and the presence of birds with observable illness. Bird traders who source the chickens from the villages, described long transit times in mixed enclosures with limited sanitation practices and without consideration of sick birds or vaccination status prior to arriving at the LBM. This study highlights the need to invest in improvements to infrastructure and biosecurity for LBMs as well as training opportunities for increasing traders' knowledge on hygiene and sanitation practices, animal welfare, and poultry biosecurity measures.

In 2023, South Africa continued to experience sporadic cases of clade 2.3.4.4b H5N1 high-pathogenicity avian influenza (HPAI) in coastal seabirds and poultry. Active environmental surveillance determined that H5Nx, H7Nx, H9Nx, H11Nx, H6N2, and H12N2, amongst other unidentified subtypes, circulated in wild birds and ostriches in 2023, but that H5Nx was predominant. Genome sequencing and phylogenetic analysis of confirmed H5N1 HPAI cases determined that only two of the fifteen sub-genotypes that circulated in South Africa in 2021–2022 still persisted in 2023. Sub-genotype SA13 remained restricted to coastal seabirds, with accelerated mutations observed in the neuraminidase protein. SA15 caused the chicken outbreaks, but outbreaks in the Paardeberg and George areas, in the Western Cape province, and the Camperdown region of the KwaZulu-Natal province were unrelated to each other, implicating wild birds as the source. All SA15 viruses contained a truncation in the PB1-F2 gene, but in the Western Cape SA15 chicken viruses, PA-X was putatively expressed as a novel isoform with eight additional amino acids. South African clade 2.3.4.4b H5N1 viruses had comparatively fewer markers of virulence and pathogenicity compared to European strains, a possible reason why no spillover to mammals has occurred here yet.

Prior to 2017, chicken production in South Africa had only ever been affected by an endemic strain of H6N2 low pathogenic avian influenza (LPAI), but since 2017, an outbreak of Goose/Guangdong clade 2.3.4.4b H5N8 high pathogenicity avian influenza (HPAI) introduced by wild birds, followed by clade 2.3.4.4b H5N1 HPAI (2021-present), affected the country. In the present study, the viruses from seven cases of H6N2 LPAI from commercial poultry between October 2019 and August 2020 were genome-sequenced along with an H5N2 HPAI virus, and phylogenetic analysis was performed. The H5N2 HPAI virus caused localized outbreaks in a small-scale chicken farm and a large commercial layer farm in the KwaZulu-Natal province between late October and early December 2022. The phylogenetic results confirmed the first incidence of the chicken-adapted H6N2 lineage in commercial ostriches in the Western Cape province, with a likely epidemiological origin in chickens from the KwaZulu Natal province. The results also showed that the H5N2 HPAI virus was a novel reassortant of PB2, PB1, PA, NP and NA genome segments derived from a parental H6N2 virus that circulated in region, whereas the HA, M and NS genome segments were derived from sub-genotype SA10 H5N1 HPAI parental virus that had circulated in the local wild bird reservoir since July 2021.

Newcastle disease (ND) is a highly contagious viral respiratory and neurological disease that has a severe impact on poultry production worldwide. In the present study, an expression platform was established for the transient production in N.bethamiana of ND virus-like particles (VLPs) for use as vaccines against ND. The expression of the ND Fusion (F) and/or Hemagglutinin-neuraminidase (HN) proteins of a genotype VII.2 strain formed ND VLPs in planta as visualized under the transmission electron microscope, and HN-containing VLPs agglutinated chicken erythrocytes with hemagglutination (HA) titres of up to 13 log2.The immunogenicity of the partially-purified ND VLPs was confirmed in specific-pathogen-free White leghorn chickens. Birds receiving a single intramuscular immunization with 1024 HA units (10 log2) of the F/HN ND VLPs administered with 20% [v/v] Emulsigen®-P adjuvant, seroconverted after 14 days with F- and HN-specific antibodies at ELISA titres of 5705.17 and HI geometric mean titres (GMTs) of 6.2 log2, respectively. Furthermore, these ND-specific antibodies successfully inhibited viral replication in vitro of two antigenically closely-related ND virus isolates, with virus-neutralization test GMTs of 3.47 and 3.4, respectively. Plant-produced ND VLPs have great potential as antigen-matched vaccines for poultry and other avian species that are highly immunogenic, cost-effective, and facilitate prompt updating to ensure improved protection against emerging ND field viruses.

Infectious bronchitis (IB) Gammacoronavirus causes a highly contagious respiratory disease in chickens that is listed by the World Organisation for Animal Health (WOAH). Its high mutation ability has resulted in numerous variants against which the commercially available live or recombinant vaccines singly offer limited protection. Agrobacterium-mediated transient expression in Nicotiana benthamiana (tobacco) plants was used here to produce a virus-like particle (VLP) vaccine expressing a modified full-length IBV spike (S) protein of a QX-like IB variant. In a challenge study with the homologous live IB QX-like virus, VLP-vaccinated birds produced S protein-specific antibodies comparable to those produced by live-vaccinated birds seroconverting with mean geometric titers of 6.8 and 7.2 log2, respectively. The VLP-vaccinated birds had reduced oropharyngeal and cloacal viral shedding compared to an unvaccinated challenged control and were more protected against tracheal ciliostasis than the live-vaccinated birds. While the results appeared similar, plant-produced IB VLPs are safer, more affordable, easier to produce and update to antigenically match any emerging IB variant, making them a more suitable alternative to IBV control than live-attenuated vaccines.

High pathogenicity avian influenza (HPAI) clade 2.3.4.4b H5N8 virus was detected in coastal seabirds in late 2017 in South Africa, following a devastating epidemic in the commercial poultry and ostrich industries. By May 2018, the infection had been confirmed in fifteen seabird species at 31 sites along the southern coast, with the highest mortality recorded in terns (Family Laridae, Order Charadriiformes). Over 7,500 positive or suspected cases in seabirds were reported. Among those infected were three endangered species: African penguins (Spheniscus demersus Linnaeus, 1758), Cape cormorants (Phalacrocorax capensis Wahlberg, 1855), and Cape gannets (Morus capensis Lichtenstein, 1823). The scale and impact of this outbreak were unprecedented in southern African coastal seabirds and raised logistical challenges in resource allocation, risk mitigation, and outbreak response. It required the collaboration of multiple stakeholder groups, including a variety of government departments and nongovernmental organizations. With another HPAI outbreak in South African seabirds in 2021 and major incursions in seabird species in the northern hemisphere in 2022, it is vital to share and consolidate knowledge on the subject. We describe the epidemic, the lessons learned, and recommendations for developing contingency plans.

Newcastle disease (ND) is among the most important poultry diseases worldwide. It is the major threat to poultry production in Africa and causes major economic losses for both local and commercial chickens. To date, half of ND class II genotypes have been reported in Africa (I, IV, V, VI, VII, XI, XIII, XIV, XVII, XVIII, and XXI). The information on the circulating NDV genotypes is still scarce despite the endemic nature of ND in most countries on the African continent.A total of 659 oro-cloacal swabs were collected from local chickens in Mawenzi live bird market located in Morogoro, Tanzania, between June 2020 and May 2021. Newcastle disease virus was detected by using reverse transcription real-time polymerase chain reaction (RT-qPCR) and conventional PCR followed by sequencing of PCR products. The prevalence of NDV in the surveilled live bird markets was 23.5%. Sequencing and phylogenetic analysis revealed the presence of sub-genotype VII.2. The detected sub-genotype VII.2 has phylogenetic links to Zambian NDV strains implying a Southeast dissemination of the virus, considering that it was first detected in Mozambique. This study underscores the need of active NDV surveillance to determine the distribution of this NDV genotype in the country and monitor its spread and contribution to the emergence of new ND viruses.

Introduction:Salmonella enterica subspecies enterica serovar Gallinarum biovar Gallinarum (SG) is associated with fowl typhoid fever, and the attenuated rough strain SG9R is widely used as a vaccine in many regions. Reversion to virulence of vaccine strains was suspected as the cause during recent fowl typhoid fever outbreaks in poultry in South Africa and Eswatini.Methods:To compare nine field isolates with global wild-type SG9 strains and the two commercial SG9R vaccines in use, Nobilis® SG9R and Cevac®-SG, we used whole-genome comparison with single-nucleotide polymorphism (SNP) detection.Results:SNP phylogenic analysis showed that all the southern African field isolates were more closely related to the vaccine strains than wild-type SG9 strains. Furthermore, SNPs in the pyruvate dehydrogenase (aceE) and/or lipopolysaccharide 1,2-glucosyltransferase (rfaJ) genes, which are known markers of attenuation, were found in four of the field isolates along with intact spv, SPI-1, and SPI-2 gene clusters, providing conclusive evidence that these four isolates were originally vaccine strains that reverted to virulence. Five other field isolates lacked the SG9R attenuation markers, but variant analysis identified an SNP in the yihX gene, insertions in the ybjX and hydH genes, and deletions in the ftsK and sadA genes that were shared between the field isolates and vaccine strains but absent in wild-type SG9, indicating that these field isolates were also likely revertant vaccines.Discussion:Overall, this study highlights different mechanisms of reversion of two commercial vaccines, where virulence caused by field isolates closely related to the Nobilis® SG9R vaccine was associated with the restoration of intact virulence gene clusters, and those derived from the Cevac®-SG vaccine were characterized by point mutations resulting in restored aceE and rfaJ genes. A possible new marker of attenuation was identified as a point mutation in the yihX gene, as well as four new candidate genes that could potentially be used to distinguish current vaccine strains from wild-type strains using PCR assays.

BACKGROUND:High-pathogenicity avian influenza (HPAI) has become a conservation threat to wild birds. Therefore, suitable vaccine technology and practical application methods require investigation.METHODS:Twenty-four African penguins (Spheniscus demersus) were vaccinated with either a conventional inactivated clade 2.3.4.4b H5N8 HPAI whole virus or a tobacco leaf-produced H5 haemagglutinin-based virus-like particle (VLP). Six birds received a second dose of the inactivated vaccine. Antibody responses were assessed and compared by employing haemagglutination inhibition tests.RESULTS:A second dose of inactivated vaccine was required to induce antibody titres above the level required to suppress virus shedding, while a single dose of VLP vaccine produced these levels by day 14, and one bird still had antibodies on day 430.LIMITATIONS:Bacterial contamination of the VLP vaccine limited the monitoring period and sample size in that treatment group, and it was not possible to perform a challenge study with field virus.CONCLUSION:VLP vaccines offer a more practical option than inactivated whole viruses, especially in logistically challenging situations involving wild birds.

The outbreak of the SARS-CoV-2 global pandemic heightened the pace of vaccine development with var-ious vaccines being approved for human use in a span of 24 months. The SARS-CoV-2 trimeric spike (S) surface glycoprotein, which mediates viral entry by binding to ACE2, is a key target for vaccines and ther-apeutic antibodies. Plant biopharming is recognized for its scalability, speed, versatility, and low produc-tion costs and is an increasingly promising molecular pharming vaccine platform for human health. We developed Nicotiana benthamiana-produced SARS-CoV-2 virus-like particle (VLP) vaccine candidates dis-playing the S-protein of the Beta (B.1.351) variant of concern (VOC), which triggered cross-reactive neu-tralising antibodies against Delta (B.1.617.2) and Omicron (B.1.1.529) VOCs. In this study, immunogenicity of the VLPs (5 mu g per dose) adjuvanted with three independent adjuvants i.e. oil-in-water based adjuvants SEPIVAC SWETM (Seppic, France) and "AS IS" (Afrigen, South Africa) as well as a slow-release synthetic oligodeoxynucleotide (ODN) adjuvant designated NADA (Disease Control Africa, South Africa) were evaluated in New Zealand white rabbits and resulted in robust neutralising antibody responses after booster vaccination, ranging from 1:5341 to as high as 1:18204. Serum neutralising anti-bodies elicited by the Beta variant VLP vaccine also showed cross-neutralisation against the Delta and Omicron variants with neutralising titres ranging from 1:1702 and 1:971, respectively. Collectively, these data provide support for the development of a plant-produced VLP based candidate vaccine against SARS-CoV-2 based on circulating variants of concern.(c) 2023 The Author(s). Published by Elsevier Ltd.

In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild birds in Lesotho and Botswana. In this study, the complete or partial genomes of 117 viruses from the SA outbreaks in 2021–2022 were analyzed to decipher the sub-regional spread of the disease. Our analysis showed that seven H5N1 sub-genotypes were associated with the initial outbreaks, but by late 2022 only two sub-genotypes still circulated. Furthermore, SA poultry was not the source of Lesotho’s outbreaks, and the latter was most likely an introduction from wild birds. Similarly, SA and Botswana’s outbreaks in 2021 were unrelated, but viruses of Botswana’s unique sub-genotype were introduced into SA later in 2022 causing an outbreak in ostriches. At least 83% of SA’s commercial poultry cases in 2021–2022 were point introductions from wild birds. Like H5N8 HPAI in 2017–2018, a coastal seabird-restricted sub-lineage of H5N1 viruses emerged in the Western Cape province in 2021 and spread to Namibia, causing mortalities in Cape Cormorants. In SA ~24,000 of this endangered species died, and the loss of >300 endangered African penguins further threatens biodiversity.