Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Seropositive Camel Handlers in Kenya

Epidemiological connectivity between humans and animals across an urban landscape

Urbanization is predicted to be a key driver of disease emergence through human exposure to novel, animal-borne pathogens. However, while we suspect that urban landscapes are primed to expose people to novel animal-borne diseases, evidence for the mechanisms by which this occurs is lacking. To address this, we studied how bacterial genes are shared between wild animals, livestock, and humans (n = 1,428) across Nairobi, Kenya-one of the world's most rapidly developing cities. Applying a multilayer network framework, we show that low biodiversity (of both natural habitat and vertebrate wildlife communities), coupled with livestock management practices and more densely populated urban environments, promotes sharing of Escherichia coli-borne bacterial mobile genetic elements between animals and humans. These results provide empirical support for hypotheses linking resource provision, the biological simplification of urban landscapes, and human and livestock demography to urban dynamics of cross-species pathogen transmission at a landscape scale. Urban areas where high densities of people and livestock live in close association with synanthropes (species such as rodents that are more competent reservoirs for zoonotic pathogens) should be prioritized for disease surveillance and control.

A scoping review of zoonotic parasites and pathogens associated with abattoirs in Eastern Africa and recommendations for abattoirs as disease surveillance sites

Abattoirs are facilities where livestock are slaughtered and are an important aspect in the food production chain. There are several types of abattoirs, which differ in infrastructure and facilities, sanitation and PPE practices, and adherence to regulations. In each abattoir facility, worker exposure to animals and animal products increases their risk of infection from zoonotic pathogens. Backyard abattoirs and slaughter slabs have the highest risk of pathogen transmission because of substandard hygiene practices and minimal infrastructure. These abattoir conditions can often contribute to environmental contamination and may play a significant role in disease outbreaks within communities. To assess further the risk of disease, we conducted a scoping review of parasites and pathogens among livestock and human workers in abattoirs across 13 Eastern African countries, which are hotspots for zoonoses. Our search results (n = 104 articles) showed the presence of bacteria, viruses, fungi, and macroparasites (nematodes, cestodes, etc.) in cattle, goats, sheep, pigs, camels, and poultry. Most articles reported results from cattle, and the most frequent pathogen detected was Mycobacterium bovis, which causes bovine tuberculosis. Some articles included worker survey and questionnaires that suggested how the use of PPE along with proper worker training and safe animal handling practices could reduce disease risk. Based on these findings, we discuss ways to improve abattoir biosafety and increase biosurveillance for disease control and mitigation. Abattoirs are a 'catch all' for pathogens, and by surveying animals at abattoirs, health officials can determine which diseases are prevalent in different regions and which pathogens are most likely transmitted from wildlife to livestock. We suggest a regional approach to biosurveillance, which will improve testing and data gathering for enhanced disease risk mapping and forecasting. Next generation sequencing will be key in identifying a wide range of pathogens, rather than a targeted approach.

Extended Viral Shedding of MERS-CoV Clade B Virus in Llamas Compared with African Clade C Strain

Middle East respiratory syndrome coronavirus (MERS-CoV) clade B viruses are found in camelids and humans in the Middle East, but clade C viruses are not. We provide experimental evidence for extended shedding of MERS-CoV clade B viruses in llamas, which might explain why they outcompete clade C strains in the Arabian Peninsula.

Serum immunoglobulin G and mucosal immunoglobulin A antibodies from prepandemic samples collected in Kilifi, Kenya, neutralize SARS-CoV-2 in vitro

OBJECTIVES

Many regions of Africa have experienced lower COVID-19 morbidity and mortality than Europe. Pre-existing humoral responses to endemic human coronaviruses (HCoV) may cross-protect against SARS-CoV-2. We investigated the neutralizing capacity of SARS-CoV-2 spike reactive and nonreactive immunoglobulin (Ig)G and IgA antibodies in prepandemic samples.

METHODS

To investigate the presence of pre-existing immunity, we performed enzyme-linked immunosorbent assay using spike antigens from reference SARS-CoV-2, HCoV HKU1, OC43, NL63, and 229E using prepandemic samples from Kilifi in coastal Kenya. In addition, we performed neutralization assays using pseudotyped reference SARS-CoV-2 to determine the functionality of the identified reactive antibodies.

RESULTS

We demonstrate the presence of HCoV serum IgG and mucosal IgA antibodies, which cross-react with the SARS-CoV-2 spike. We show pseudotyped reference SARS-CoV-2 neutralization by prepandemic serum, with a mean infective dose 50 of 1: 251, which is 10-fold less than that of the pooled convalescent sera from patients with COVID-19 but still within predicted protection levels. The prepandemic naso-oropharyngeal fluid neutralized pseudo-SARS-CoV-2 at a mean infective dose 50 of 1: 5.9 in the neutralization assay.

CONCLUSION

Our data provide evidence for pre-existing functional humoral responses to SARS-CoV-2 in Kilifi, coastal Kenya and adds to data showing pre-existing immunity for COVID-19 from other regions.

Meta-analysis of seroprevalence and zoonotic infections of Middle East respiratory syndrome coronavirus (MERS-CoV): A one-health perspective

The zoonotic Middle East respiratory syndrome (MERS) is caused by an emerging beta-coronavirus (CoV). The majority of MERS studies have included scattered data from sub-Saharan Africa and the Middle East, and these data have not been analyzed collectively. In this work, a meta-analysis of these studies was conducted to coalesce these results, determine the prevalence and seroprevalence of MERS-CoV in camels and humans, and examine how zoonotic infection rates in dromedary camels are related to human infection rates. After extracting the collected data, the prevalence and seroprevalence at a 95% confidence interval (CI) using a fixed-effects inverse-variance meta-analysis was conducted. Thirteen studies were included. Eight studies included 2905 samples from dromedary camels, of which 1108 (38.14%) were positive for the virus. The prevalence was 8.75[−13.47, 30.98] at 95% CI in dromedary camels and 0.03[−35.23, 35.28] at 95% CI in humans. Ten studies included 7176 serum samples, 5788 (80.66%) of which were positive. The seroprevalence was 20.69[−4.60, 45.99] at 95% CI. The prevalence of MERS-CoV was moderate to high, but the seroprevalence was high. Despite the high prevalence of the virus in camel herds, zoonotic transmissions were not widespread. Further longitudinal and cross-sectional follow-up studies are recommended to provide solid control of MERS-CoV transmission.

Knowledge, attitudes, and practices on camel respiratory diseases and conditions in Garissa and Isiolo, Kenya

Background

Livestock farmers' attitudes, practices, and behaviors are major factors in infection prevention and control of animal diseases. Kenya has the fourth largest global camel population, and the industry has grown over the last two decades, transforming beyond the traditional camel-keeping areas to include peri-urban camel trade and value chain growth. The dromedary camel is resilient, and it is a preferred species in the arid and semi-arid areas (ASALs) of Kenya. However, it still faces many health and production challenges; to identify infection drivers and risky behaviors for camel respiratory illnesses and conditions in Kenya, we conducted a knowledge, attitudes, and practices (KAP) survey.

Method

Using a set of tools (questionnaires, key informant interviews, and focus group discussions), we interviewed camel owners, herders, agro-veterinary outlets, and other relevant value chain stakeholders in Garissa and Isiolo counties (n = 85). Data were analyzed using descriptive and analytic statistics.

Results

Most camel owners/herders are male and most are relatively uneducated (85.5%). The camels were used primarily for milk and meat production, income generation, and transport. Larger herd sizes (>30 camels) and owner/herder's lack of formal education are risk factors for owner-reported respiratory illnesses in camels. Major clinical signs of respiratory conditions were coughing (85.7%), nasal discharge (59.7%), and fever (23.4%). Diseases, lack of feeds, theft, and marketing challenges are the major constraints to camel production in Kenya. Owners-herders use drugs indiscriminately and this may contribute to antimicrobial resistance challenges.

Conclusion

Practitioners in the camel value chain want more commitment from the government and animal health officials on support services and access to veterinary services. Watering points, grazing areas, and marketing points are the primary areas for congregating camels and have a significant potential for disease spread. Kenya camels have a massive capacity for rural and ASALs' livelihoods transformation but the identified health challenges, and other issues must be addressed. Further studies on the Kenyan camels' respiratory microbial ecology are important to understand microbial risks and reduce the burden of zoonotic infections. Intensification of risk communication and community engagement, and messaging targeted at behavior change interventions should be directed at camel value chain actors.

Outbreak of Middle East Respiratory Syndrome Coronavirus in Camels and Probable Spillover Infection to Humans in Kenya

The majority of Kenya’s > 3 million camels have antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV), although human infection in Africa is rare. We enrolled 243 camels aged 0−24 months from 33 homesteads in Northern Kenya and followed them between April 2018 to March 2020. We collected and tested camel nasal swabs for MERS-CoV RNA by RT-PCR followed by virus isolation and whole genome sequencing of positive samples. We also documented illnesses (respiratory or other) among the camels. Human camel handlers were also swabbed, screened for respiratory signs, and samples were tested for MERS-CoV by RT-PCR. We recorded 68 illnesses among 58 camels, of which 76.5% (52/68) were respiratory signs and the majority of illnesses (73.5% or 50/68) were recorded in 2019. Overall, 124/4692 (2.6%) camel swabs collected from 83 (34.2%) calves in 15 (45.5%) homesteads between April−September 2019 screened positive, while 22 calves (26.5%) recorded reinfections (second positive swab following ≥ 2 consecutive negative tests). Sequencing revealed a distinct Clade C2 virus that lacked the signature ORF4b deletions of other Clade C viruses. Three previously reported human PCR positive cases clustered with the camel infections in time and place, strongly suggesting sporadic transmission to humans during intense camel outbreaks in Northern Kenya.

Serosurvey for Middle East respiratory syndrome coronavirus antibody in dromedary camels and human patients at a secondary care hospital, Illela, Northwest Nigeria

Middle East respiratory syndrome (MERS) is a serious emerging zoonosis. It is characterized by severe infection of the respiratory tract in humans. Dromedary camels are considered to be the most probable origin of the pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV). This cross-sectional survey was carried out to ascertain the seroprevalence of MERS-CoV in dromedary camels at Illela border and human patients in a secondary care hospital in Illela, Sokoto State, Nigeria from November 2016 to January 2017. Serum samples from 74 camels and 39 human patients were collected while a data form was administered to the camel handlers (40) and human patients to obtain information on zoographic characteristics of dromedary camels, demographic characteristics of camel handlers and human patients and some practices of both groups which are likely to predispose to MERS-CoV infection. The serum samples were analyzed for antibodies against MERS-CoV using the indirect Enzyme-Linked Immuno-Sorbent Assay (ELISA). All the camels sampled were seropositive against MERS-CoV and 74% of the human patients had antibodies against MERS. All handlers treated their camels without consulting veterinarians and there was little or no biosecurity measures undertaken. Age, sex, and occupation were not significant determinants for the presence of MERS-CoV antibody in human patients sampled. This study serves as a baseline for similar researches and due to the high seroprevalence obtained in this study for both camels and humans, there is need for trained personnel, surveillance and diagnostic tools at our border posts and animal markets.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00580-022-03351-3.

Coronavirus, the King Who Wanted More Than a Crown: From Common to the Highly Pathogenic SARS-CoV-2, Is the Key in the Accessory Genes?

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that emerged in late 2019, is the etiologic agent of the current "coronavirus disease 2019" (COVID-19) pandemic, which has serious health implications and a significant global economic impact. Of the seven human coronaviruses, all of which have a zoonotic origin, the pandemic SARS-CoV-2, is the third emerging coronavirus, in the 21st century, highly pathogenic to the human population. Previous human coronavirus outbreaks (SARS-CoV-1 and MERS-CoV) have already provided several valuable information on some of the common molecular and cellular mechanisms of coronavirus infections as well as their origin. However, to meet the new challenge caused by the SARS-CoV-2, a detailed understanding of the biological specificities, as well as knowledge of the origin are crucial to provide information on viral pathogenicity, transmission and epidemiology, and to enable strategies for therapeutic interventions and drug discovery. Therefore, in this review, we summarize the current advances in SARS-CoV-2 knowledges, in light of pre-existing information of other recently emerging coronaviruses. We depict the specificity of the immune response of wild bats and discuss current knowledge of the genetic diversity of bat-hosted coronaviruses that promotes viral genome expansion (accessory gene acquisition). In addition, we describe the basic virology of coronaviruses with a special focus SARS-CoV-2. Finally, we highlight, in detail, the current knowledge of genes and accessory proteins which we postulate to be the major keys to promote virus adaptation to specific hosts (bat and human), to contribute to the suppression of immune responses, as well as to pathogenicity.

In Vitro Inhibitory Analysis of Rationally Designed siRNAs against MERS-CoV Replication in Huh7 Cells

MERS-CoV was identified for the first time in Jeddah, Saudi Arabia in 2012 in a hospitalized patient. This virus subsequently spread to 27 countries with a total of 939 deaths and 2586 confirmed cases and now has become a serious concern globally. Camels are well known for the transmission of the virus to the human population. In this report, we have discussed the prediction, designing, and evaluation of potential siRNA targeting the ORF1ab gene for the inhibition of MERS-CoV replication. The online software, siDirect 2.0 was used to predict and design the siRNAs, their secondary structure and their target accessibility. ORF1ab gene folding was performed by RNAxs and RNAfold software. A total of twenty-one siRNAs were selected from 462 siRNAs according to their scoring and specificity. siRNAs were evaluated in vitro for their cytotoxicity and antiviral efficacy in Huh7 cell line. No significant cytotoxicity was observed for all siRNAs in Huh7 cells. The in vitro study showed the inhibition of viral replication by three siRNAs. The data generated in this study provide preliminary and encouraging information to evaluate the siRNAs separately as well as in combination against MERS-CoV replication in other cell lines. The prediction of siRNAs using online software resulted in the filtration and selection of potential siRNAs with high accuracy and strength. This computational approach resulted in three effective siRNAs that can be taken further to in vivo animal studies and can be used to develop safe and effective antiviral therapies for other prevalent disease-causing viruses.

Neutralizing antibodies for SARS-CoV-2 in stray animals from Rio de Janeiro, Brazil

The epidemic of coronavirus disease 2019 (COVID-19), caused by a novel Betacoronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a public health emergency worldwide. Few reports indicate that owned pets from households with at least one human resident that was diagnosed with COVID-19 can be infected by SARS-CoV-2. However, the exposure to SARS-CoV-2 of pets from households with no COVID-19 cases or stray animals remains less assessed. Using real-time reverse transcriptase polymerase chain reaction (RT-PCR) and plaque reduction neutralization test (PRNT90), we investigated the infection and previous exposure of dogs and cats to SARS-CoV-2 during the ongoing COVID-19 epidemic in Rio de Janeiro, Brazil. From June to August 2020, 96 animals were sampled, including 49 cats (40 owned and 9 stray) and 47 dogs (42 owned and 5 stray). Regarding owned pets, 75.6% (62/82) belonged to households with no COVID-19 cases. Samples included serum, and rectal and oropharyngeal swabs. All swabs were negative for SARS-CoV-2 RNA, but serum samples of a stray cat and a stray dog presented neutralizing antibodies for SARS-CoV-2, with PRNT90 titer of 80 and 40, respectively. Serological data presented here suggest that not only owned pets from households with COVID19 cases, but also stray animals are being exposed to SARS-CoV-2 during the COVID-19 pandemic.

Evaluation of a real-time RT-PCR panel for detection of SARS-CoV-2 in bat guano

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), which is an ongoing global health concern. The exact source of the virus has not been identified, but it is believed that this novel coronavirus originated in animals; bats in particular have been implicated as the primary reservoir of the virus. SARS-CoV-2 can also be transmitted from humans to other animals, including tigers, cats, and mink. Consequently, infected people who work directly with bats could transfer the virus to a wild North American bat, resulting in a new natural reservoir for the virus, and lead to new outbreaks of human disease. We evaluated a reverse-transcription real-time PCR panel for detection of SARS-CoV-2 in bat guano. We found the panel to be highly specific for SARS-CoV-2, and able to detect the virus in bat guano samples spiked with SARS-CoV-2 viral RNA. Our panel could be utilized by wildlife agencies to test bats in rehabilitation facilities prior to their release to the wild, minimizing the risk of spreading this virus to wild bat populations.

Risk factors for serological evidence of MERS-CoV in camels, Kenya, 2016-2017

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging viral disease and dromedary camels are known to be the source of human spill over events. A cross-sectional epidemiological surveillance study was carried out in Kenya in 2017 to, 1) estimate MERS-CoV antibody seropositivity in the camel-dense counties of Turkana, Marsabit, Isiolo, Laikipia and Nakuru to identify, and 2) determine the risk factors associated with seropositivity in camels. Blood samples were collected from a total of 1421 camels selected using a multi-stage sampling method. Data were also collected from camel owners or herders using a pre-tested structured questionnaire. The sera from camel samples were tested for the presence of circulating antibodies to MERS-CoV using the anti-MERS-CoV IgG ELISA test. Univariate and multivariable statistical analysis were used to investigate factors potentially associated with MERS-CoV seropositivity in camels. The overall seropositivity in camel sera was 62.9 %, with the highest seropositivity recorded in Isiolo County (77.7 %), and the lowest seropositivity recorded in Nakuru County (14.0 %). When risk factors for seropositivity were assessed, the "Type of camel production system" {(aOR = 5.40(95 %CI: 1.67-17.49)}, "Age between 1-2 years, 2-3 years and above 3 years" {(aOR = 1.64 (95 %CI: 1.04-2.59}", {(aOR = 3.27 (95 %CI: 3.66-5.61)}" and {(aOR = 6.12 (95 %CI: 4.04-9.30)} respectively and "Sex of camels" {(aOR = 1.75 (95 %CI: 1.27-2.41)} were identified as significant predictors of MERS-CoV seropositivity. Our studies indicate a high level of seropositivity to MERS-CoV in camels in the counties surveyed, and highlights the important risk factors associated with MERS-CoV seropositivity in camels. Given that MERS-CoV is a zoonosis, and Kenya possesses the fourth largest camel population in Africa, these findings are important to inform the development of efficient and risk-based prevention and mitigation strategies against MERS-CoV transmission to humans.

Africa's Nomadic Pastoralists and Their Animals Are an Invisible Frontier in Pandemic Surveillance

The effects of COVID-19 have gone undocumented in nomadic pastoralist communities across Africa, which are largely invisible to health surveillance systems despite the fact that they are of key significance in the setting of emerging infectious disease. We expose these landscapes as a "blind spot" in global health surveillance, elaborate on the ways in which current health surveillance infrastructure is ill-equipped to capture pastoralist populations and the animals with which they coexist, and highlight the consequential risks of inadequate surveillance among pastoralists and their livestock to global health. As a platform for further dialogue, we present concrete solutions to address this gap.