The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus.

Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 are not phylogenetically closely related; however, both use the angiotensin-converting enzyme 2 (ACE2) receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario, and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2 and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.

The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus.

SARS-CoV-1 and SARS-CoV-2 are not phylogenetically closely related; however, both use the ACE2 receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda which are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario; and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2, and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.

Detection of tilapia lake virus (TiLV) infection by PCR in farmed and wild Nile tilapia (Oreochromis niloticus) from Lake Victoria.

Tilapia lake virus disease (TiLVD) has emerged to be an important viral disease of farmed Nile tilapia (Oreochromis niloticus) having the potential to impede expansion of aquaculture production. There is a need for rapid diagnostic tools to identify infected fish to limit the spread in individual farms. We report the first detection of TiLV infection by PCR in farmed and wild Nile tilapia from Lake Victoria. There was no difference in prevalence between farmed and wild fish samples (p = .65), and of the 442 samples examined from 191 fish, 28 were positive for TiLV by PCR. In terms of tissue distribution, the head kidney (7.69%, N = 65) and spleen (10.99%, N = 191), samples had the highest prevalence (p < .0028) followed by heart samples (3.45%, N = 29). Conversely, the prevalence was low in the liver (0.71%, N = 140) and absent in brain samples (0.0%, N = 17), which have previously been shown to be target organs during acute infections. Phylogenetic analysis showed homology between our sequences and those from recent outbreaks in Israel and Thailand. Given that these findings were based on nucleic acid detection by PCR, future studies should seek to isolate the virus from fish in Lake Victoria and show its ability to cause disease and virulence in susceptible fish.

Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus.

The evolutionary origins of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) are unknown. Current evidence suggests that insectivorous bats are likely to be the original source, as several 2c CoVs have been described from various species in the family Vespertilionidae Here, we describe a MERS-like CoV identified from a Pipistrellus cf. hesperidus bat sampled in Uganda (strain PREDICT/PDF-2180), further supporting the hypothesis that bats are the evolutionary source of MERS-CoV. Phylogenetic analysis showed that PREDICT/PDF-2180 is closely related to MERS-CoV across much of its genome, consistent with a common ancestry; however, the spike protein was highly divergent (46% amino acid identity), suggesting that the two viruses may have different receptor binding properties. Indeed, several amino acid substitutions were identified in key binding residues that were predicted to block PREDICT/PDF-2180 from attaching to the MERS-CoV DPP4 receptor. To experimentally test this hypothesis, an infectious MERS-CoV clone expressing the PREDICT/PDF-2180 spike protein was generated. Recombinant viruses derived from the clone were replication competent but unable to spread and establish new infections in Vero cells or primary human airway epithelial cells. Our findings suggest that PREDICT/PDF-2180 is unlikely to pose a zoonotic threat. Recombination in the S1 subunit of the spike gene was identified as the primary mechanism driving variation in the spike phenotype and was likely one of the critical steps in the evolution and emergence of MERS-CoV in humans.IMPORTANCE Global surveillance efforts for undiscovered viruses are an important component of pandemic prevention initiatives. These surveys can be useful for finding novel viruses and for gaining insights into the ecological and evolutionary factors driving viral diversity; however, finding a viral sequence is not sufficient to determine whether it can infect people (i.e., poses a zoonotic threat). Here, we investigated the specific zoonotic risk of a MERS-like coronavirus (PREDICT/PDF-2180) identified in a bat from Uganda and showed that, despite being closely related to MERS-CoV, it is unlikely to pose a threat to humans. We suggest that this approach constitutes an appropriate strategy for beginning to determine the zoonotic potential of wildlife viruses. By showing that PREDICT/PDF-2180 does not infect cells that express the functional receptor for MERS-CoV, we further show that recombination was likely to be the critical step that allowed MERS to emerge in humans.

Seroprevalence and Risk Factors for Exposure of Free-Range Poultry to Avian Influenza Viruses in Important Bird Areas in Uganda.

Avian influenza (AI) viruses cause disease in domestic and wild bird species. Although these viruses have been reported to occur in poultry in Uganda, risk factors for their introduction and spread were largely unknown. We investigated the seroprevalence and risk factors for exposure of free-range poultry to AI viruses in Important Bird Areas (IBAs) in the country. A structured questionnaire was administered to 664 respondents, and 1342 sera were collected from poultry. Sera were analyzed for antibody titers against AI using competitive ELISA. AI antibody prevalence was 7.6% (95% confidence interval [CI]: 6.2-9.0) in the Lake Victoria Basin, 8.4% (95% CI: 7.0-9.8) in the southwestern region, and none (0/432) in the Kyoga region. High proportions of risky practices were observed among respondent farmers. Significant predictors for exposure of poultry to AI viruses were the source of restocking poultry, method of disposal of inedible parts of slaughtered poultry, and waterfowl visits to a nearby body of water. In addition, visits by waterbirds to a nearby body of water during October-December were more associated with exposure to AI viruses (odds ratio = 3.6; 95% CI: 1.42-9.23) compared with January-March visits'. These results suggested the existence of several risk factors for exposure of free-range to AI viruses in IBAs in Uganda.

Predictors for Risk Factors for Spread of Avian Influenza Viruses by Poultry Handlers in Live bird markets in Uganda.

Live bird markets (LBMs) are essential for marketing poultry, but have been linked to many outbreaks of avian influenza (AI) and its spread. In Uganda, it has been observed that demographic characteristics of poultry traders/handlers influence activities and decision-making in LBMs. The study investigated the influence of socio-demographic characteristics of poultry handlers: age, sex, religion, educational background, level of income, location of residence and region of operation on 20 potential risk factors for introduction and spread of AI in LBMs. Study sites included 39 LBMs in the four regions of Uganda. Data was collected using a semi-structured questionnaire administered to 424 poultry handlers. We observed that background of education was a predictor for slaughter and processing of poultry in open sites. Location of residence was associated with slaughter of poultry from open sites and selling of other livestock species. Region influenced stacking of cages, inadequate cleaning of cages, feeders and drinkers, and provision of dirty feed and water. Specifically, bird handlers with secondary level of education (OR = 12.9, 95% CI: 2.88-57.4, P < 0.01) were more likely to be involved in open site slaughter of poultry than their counterparts without formal education. Comparatively, urbanite bird handlers were less likely to share poultry equipment (OR = 0.4, 95% CI: 0.22-0.63, P < 0.01) than rural resident handlers. Poultry handlers in Northern were 3.5 times more likely to practise insufficient cleaning of cages (OR = 3.5, 95% CI: 1.52-8.09) compared to those in Central region. We demonstrated that some socio-demographic characteristics of poultry handlers were predictors to risky practices for introduction and spread of AI viruses in LBMs in Uganda.

A review of zoonotic disease surveillance supported by the Armed Forces Health Surveillance Center.

The Armed Forces Health Surveillance Center (AFHSC), Division of Global Emerging Infections Surveillance and Response System conducts disease surveillance through a global network of US Department of Defense research laboratories and partnerships with foreign ministries of agriculture, health and livestock development in over 90 countries worldwide. In 2010, AFHSC supported zoonosis survey efforts were organized into four main categories: (i) development of field assays for animal disease surveillance during deployments and in resource limited environments, (ii) determining zoonotic disease prevalence in high-contact species which may serve as important reservoirs of diseases and sources of transmission, (iii) surveillance in high-risk human populations which are more likely to become exposed and subsequently infected with zoonotic pathogens and (iv) surveillance at the human-animal interface examining zoonotic disease prevalence and transmission within and between human and animal populations. These efforts have aided in the detection, identification and quantification of the burden of zoonotic diseases such as anthrax, brucellosis, Crimean Congo haemorrhagic fever, dengue fever, Hantaan virus, influenza, Lassa fever, leptospirosis, melioidosis, Q fever, Rift Valley fever, sandfly fever Sicilian virus, sandfly fever Naples virus, tuberculosis and West Nile virus, which are of military and public health importance. Future zoonotic surveillance efforts will seek to develop local capacity for zoonotic surveillance focusing on high risk populations at the human-animal interface.

Participatory livestock farmer training for improvement of animal health in rural and peri-urban smallholder dairy herds in Jinja, Uganda.

Within the framework of a research project investigating methods to decrease mastitis incidence, farmer groups for participatory training in a modified Farmer Field School approach were initiated in order to improve animal health and farmer knowledge in mastitis control technologies in smallholder dairy farms in the Jinja district of Uganda. Two peri-urban groups and one rural group met for common learning and training two hours per fortnight during a 12-month period, facilitated by two local extension agents together with one or two scientists from Makerere University. Farmers rotated each time between farms owned by group participants, which demanded mutual trust, openness and respect. From their own assessment the farmers felt they had improved their milk production and reduced mastitis incidence on their farms. In an evaluation workshop, they articulated how they had built up common knowledge and experience from training in systematic clinical examination of animals, evaluation of the farm environments, and identification of improvements. Much of the acquired new knowledge was about basic dairy cow management and husbandry practices. In addition, they gave examples of how they were now used as resource persons in their local communities. Principles of learning and empowerment are discussed.

Investigations of the occurrence of Avibacterium paragallinarum infections in Uganda.

Investigations were conducted to determine the occurrence of Avibacterium paragallinarum in poultry in Uganda. A total of 710 each of bacteriologic and serum samples were taken from chickens and turkeys for demonstration of A. paragallinarum and antibodies. Samples for isolation of A. paragallinarum were also subjected to direct polymerase chain reaction (PCR) for demonstration of the organism's presence. Antibodies to A. paragallinarum were demonstrated in the sera using the hemagglutination inhibition test. A total of five isolates were recovered from two out of five commercial layer chicken farms investigated where suspected cases of infectious coryza were reported, and all of them belonged to Page's serovar C. PCR detected more positive samples (11/68) than did culture (5/68). Isolates were not recovered from free-range poultry nor were there any positive samples by PCR. The overall seroprevalence was 40.5% and the seroprevalence to serovars A, B, and C were 18%, 0.5%, and 22%, respectively. Antibodies to all Page's serovars A, B, and C were demonstrated in free-range chickens but only serovar C antibodies were demonstrated in commercial chickens. No antibodies were demonstrated in turkeys. This is the first time infectious coryza has been confirmed in Uganda and the causative agent, A. paragallinarum, isolated. A high seroprevalence observed in free-range chickens seems to indicate a subclinical infection under extensive village management conditions.

Virulence characterization of Avibacterium paragallinarum isolates from Uganda.

Avibacterium paragallinarum isolates from Uganda were characterized for their virulence by comparison of their pathogenicity and their resistance to serum. Pathogenicity was evaluated using commercial Hisex Brown layer chickens, local indigenous chickens, local turkeys and local guineafowls inoculated with 108 colony-forming units of Av. paragallinarum and comparing their overall mean disease scores over a period of 20 days. Persistence of the bacteria in the host and water was also investigated for a 60-day period by culture and polymerase chain reaction as well as use of sentinel chickens. Serum resistance was measured by comparison of the growth kinetics and survival indices at 3 and 6 h. There was no difference in the virulence of the isolates. Commercial layer chickens and local indigenous chickens were equally susceptible to challenge, while turkeys and guineafowls only showed transient mild signs and did not transmit infection. Turkeys and guineafowls did not acquire the infection when placed in contact with infected chickens. The isolates were resistant in normal chicken serum at both 3 and 6 h of incubation but were resistant at 3 h and sensitive at 6 h in turkey and guineafowl sera. The resistance of the isolates to serum correlated with their pathogenicity in the different hosts. No carrier status was demonstrated in this study using polymerase chain reaction and culture. The present study demonstrates that Ugandan Av. paragallinarum isolates are pathogenic to chickens with only transient signs in turkeys and guineafowls, and that serum resistance could be a subject for further investigation as a predictor of virulence of these bacteria. The role of turkeys and guineafowls in transmission of Av. paragallinarum was not demonstrated in the present investigation.

A view on antimicrobial resistance in developing countries and responsible risk factors.

Antimicrobial resistance is one of the biggest challenges facing global public health. Although antimicrobial drugs have saved many lives and eased the suffering of many millions, poverty, ignorance, poor sanitation, hunger and malnutrition, inadequate access to drugs, poor and inadequate health care systems, civil conflicts and bad governance in developing countries have tremendously limited the benefits of these drugs in controlling infectious diseases. The development of resistance in the responsible pathogens has worsened the situation often with very little resource to investigate and provide reliable susceptibility data on which rational treatments can be based as well as means to optimise the use of antimicrobial agents. The emergence of multi-drug-resistant isolates in tuberculosis, acute respiratory infections and diarrhoea, often referred to as diseases of poverty, has had its greatest toll in developing countries. The epidemic of HIV/AIDS, with over 30 million cases in developing countries, has greatly enlarged the population of immunocompromised patients. The disease has left these patients at great risk of numerous infections and even greater risks of acquiring highly resistant organisms during long periods of hospitalisation. This review discusses antimicrobial resistance in developing countries and the risk factors responsible.

Naked DNA when co-administered intranasally with heat-labile enterotoxin of Escherichia coli primes effectively for systemic B- and T-cell responses to the encoded antigen.

In this study a novel prime-boost immunisation strategy was evaluated. Priming of BALB/c mice by the intranasal route with plasmid DNA encoding beta-galactosidase (LacZ) with or without heat-labile enterotoxin (LT) of Escherichia coli as a mucosal adjuvant, resulted in the induction of weak serum antibody and proliferative T-cell responses. However, following an intraperitoneal booster injection with the beta-galactosidase protein (beta-gal), strong antibody and proliferative T-cell responses were induced in all the mice. These responses were highest in mice primed intranasally with a mixture of LacZ+LT as compared to those mice primed with DNA (LacZ) or protein (beta-gal) alone. Moreover, LacZ+LT primed mice produced high avidity antibodies and the subclasses of serum antibodies were IgG1 and IgG2a, suggesting a mixed Th1/Th2-type response. Priming of mice with either protein (beta-gal) or DNA (LacZ) alone, produced predominantly IgG1 antibodies, suggesting a Th2-type response. These findings suggest that the use of a heterologous DNA-prime, protein-boost immunisation scheme combining different routes of administration, might be an advantageous strategy for the induction of accelerated immune responses.