Heart-nosed #bat #alphacoronaviruses use #human CEACAM6 to enter #cells

 

Abstract

Identifying viruses with zoonotic potential on the basis of their ability to enter human cells is a critical component of pandemic prediction, prevention and preparedness. Here using a computational approach that retains maximum phylogenetic diversity, we selected an optimal subset of alphacoronavirus spike proteins to screen against broad coronavirus receptor libraries. Most of the selected spike proteins did not use any of the established coronavirus receptors. However, the pseudotyped spike protein of Cardioderma cor (heart-nosed bat) coronavirus KY43 (CcCoV-KY43) could enter human cells. Using a recombinant CcCoV receptor-binding domain (RBD) and a human receptor screening platform, we identified direct interactions with the human CEACAM proteins CEACAM3, CEACAM5 and CEACAM6. Overexpression of human CEACAM6—a protein widely expressed in the human lung—conferred permissivity to otherwise refractory human cells. A crystal structure showed that the RBD binds the amino-terminal IgV-like domain of human CEACAM6. Immune surveillance studies using sera of individuals from the Taveta region of Kenya, where CcCoV-KY43 was identified, did not show significant evidence of recent spillover. Wider characterization of alphacoronaviruses related to CcCoV-KY43 showed that human CEACAM6 is used by two other CcCoVs collected in Kenya. Moreover, there was more restricted nonhuman CEACAM6 tropism for viruses isolated from Rhinolophus bats from Russia and China. Thus, alphacoronaviruses that use CEACAM6 are probably geographically widespread, and viruses from East Africa show potential for transmission to humans.

Source: 

Link: https://www.nature.com/articles/s41586-026-10394-x

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Uncomplicated #malaria as a #risk factor for #COVID19 duration and severity in western #Kenya and #Burkina Faso (MALCOV): a prospective cohort study

 

Summary

Background

The relationship between malaria and COVID-19 varies across different clinical scenarios; historical malaria exposure might protect against severe COVID-19, whereas co-infection in hospitalised patients with severe disease might increase mortality. Interactions between non-severe malaria and COVID-19 remain poorly understood. We conducted a cohort study among COVID-19 patients of all ages in western Kenya and Burkina Faso to assess the effects of acute, uncomplicated Plasmodium falciparum malaria co-infection on COVID-19 outcomes in ambulatory patients.

Methods

Participants with laboratory-confirmed SARS-CoV-2 infection (positive rapid antigen test or reverse transcription quantitative real-time PCR [RT-qPCR]) were tested for malaria by rapid antigen tests with confirmatory microscopy. Patients with COVID-19 and malaria co-infection received artemether–lumefantrine or pyronaridine–artesunate. COVID-19 symptom course was assessed daily using FLU-PRO Plus (a validated patient-reported outcome instrument) until day 14. Viral load was measured by RT-qPCR on days 0, 3, 7, 14, and 28. The primary endpoint was time to symptom resolution on the FLU-PRO Plus. Analyses were adjusted for country, age, disease severity, and viral load.

Findings

Between Jan 8, 2021 and Jan 24, 2022, we screened 5161 participants and recruited 756 with COVID-19. 742 participants with valid malaria tests were enrolled, of which 151 (20%) had malaria co-infection and the remaining 591 (80%) did not have malaria. Patients with malaria were younger (49 [32%] aged <15 years) than those without malaria (35 [6%]; p<0·0001). Time to symptom resolution was similar between those with malaria (median 9 days [IQR 5–13]) and those without (10 days [IQR 6–13]; adjusted hazard ratio [aHR] 1·14 [95% CI 0·91–1·42]; p=0·26). Three (2%) patients with malaria and nine (2%) without malaria were hospitalised; two (1%) with malaria and three (1%) without malaria died, four from acute respiratory distress syndrome and one (in the no malaria group) from perforated peptic ulcer complicated by anaemia. Participants with malaria more frequently reported moderate-to-severe symptoms at enrolment (68% vs 60%; p=0·074), but overall symptom duration was similar (adjusted incidence rate ratio 0·95 [95% CI 0·86–1·05]; p=0·31). Previous malaria exposure significantly modified outcomes, with patients with malaria co-infection and previous exposure having faster symptom clearance than those without previous exposure (pinteraction=0·042). SARS-CoV-2 clearance was slower in the malaria group by day 7 (aHR 0·69 [95% CI 0·51–0·94]; p=0·017) but was similar between groups by day 28 (adjusted risk ratio 0·99 [95% CI 0·79–1·24]; p=0·95).

Interpretation

This study shows that acute uncomplicated malaria co-infection does not adversely affect COVID-19 progression when appropriately treated. Moreover, serological evidence confirms that previous lifelong malaria exposure might provide some protection, with exposed individuals having faster symptom resolution.

Funding

Gates Foundation.

Translation

For the French translation of the abstract see Supplementary Materials section.

Source: 

Link: https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(25)00541-8/fulltext

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Detection and genetic characterization of #alphacoronaviruses in co-roosting #bat species, southeastern #Kenya

 

Abstract

Bats are associated with some of the most significant and virulent emerging zoonoses globally, yet research and surveillance of bat pathogens remains limited across parts of the world. We surveyed the prevalence and genetic diversity of coronaviruses from bats in Taita Hills, southeastern Kenya, as part of ongoing surveillance efforts in this remote part of eastern Africa. We collected fecal and intestinal samples in May 2018 and March 2019 from 16 bat species. We detected one genus of coronavirus (alphacoronavirus), with an overall RNA prevalence of 6.5% (30/463). The prevalence of coronavirus RNA was 3.8% (9/235) and 11.6% (21/181) for the two most captured free-tailed bat species, Mops condylurus and M. pumilus respectively, with no detections from other bat species (0/90). Phylogenetic analyses based on the partial RNA-dependent RNA polymerase gene and whole genome sequences revealed that the sequences clustered together and were closely related to alphacoronavirus detected in free tailed bats in Eswatini, Nigeria and Rhinolophus simulator bats in South Africa. The sequences were more distantly related to alphacoronavirus isolated from Chaerophon plicatus bat species in Yunnan province, China and Ozimops species from southwestern Australia. These findings highlight coronavirus transmission among bats that share habitats with humans and livestock, posing a potential risk of exposure. Future research should investigate whether coronaviruses detected in these bats have the potential to spillover to other hosts.

Author summary

Bats are known to carry several zoonotic pathogens with potential to cause serious illnesses and death in humans. Yet, surveillance on the pathogens they carry remains limited in much of the world. We studied the prevalence and diversity of coronaviruses from bats in Taita Hills, southeastern Kenya to better understand the circulation of these viruses and inform disease preparedness. We detected alphacoronaviruses in urban Mops condylurus and M. pumilus bat species. The bat alpha coronaviruses we detected were closely related to alphacoronaviruses that have been previously detected in bats elsewhere in Africa and distantly related to alphacoronavirus detected from Chaerophon plicatus bat species in Yunnan province, China and Ozimops species from southwestern Australia. This work demonstrates coronavirus circulation among bats that share habitats with people and livestock providing conditions that can lead to spillover. Identifying whether coronaviruses detected in these bats have the potential to infect other hosts is critical for developing countermeasures and mitigating potential outbreaks.

Source: PLoS Neglected Tropical Diseases, https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0012805

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Low #Prevalence of #MERS #Coronavirus #Infection in #Camel-Exposed #Patients Presenting with Respiratory Symptoms in Northern #Kenya

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus that causes acute respiratory disease after transmission via close contact with camels. In contrast to the incidence of MERS-CoV human infections in the Middle East, MERS-CoV infections in the Horn of Africa have been rarely reported despite the high number of camels and common camel–human interactions in the area. Whether passive cross-sectional sampling misses active human cases is a significant gap in our understanding of MERS-CoV epidemiology and its impact in the Horn of Africa. To address this gap, we conducted a prospective cross-sectional study at Laisamis Catholic Hospital in northern Kenya’s camel pastoralist community. A total of 942 patients with acute respiratory symptoms were enrolled over 18 months (August 2022–February 2024); 54% of these individuals reported frequent contact with camels and consumption of camel products. Testing via reverse transcriptase – polymerase chain reaction (RT-PCR) revealed that all patients (N = 942) had negative results for MERS-CoV RNA on either nasopharyngeal or oropharyngeal swabs at the time of presentation. Because polymerase chain reaction testing may only detect active cases with higher levels of viral shedding, serology was also performed on a randomly selected subset of 297 individuals from the total sample pool to detect IgG antibodies. Only eight individuals (2.7%) exhibited positive results by serology; accounting for the test specificity of 99.8%, the 95% CI for true MERS-CoV seropositivity was 0.72–4.27%. Despite frequent camel interactions, MERS-CoV seroprevalence was low, suggesting limited zoonotic transmission in this setting and highlighting the need for more comprehensive diagnostics to identify prevalent causes of acute respiratory illness in pastoralist communities.

Source: American Journal of Tropical Medicine and Hygiene, https://www.ajtmh.org/view/journals/tpmd/aop/article-10.4269-ajtmh.25-0098/article-10.4269-ajtmh.25-0098.xml

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A Novel #Nobecovirus in an Epomophorus wahlbergi #Bat from #Nairobi, #Kenya

Abstract

Most human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, we obtained fecal swabs from two fruit bat species—Eidolon helvum (n = 6) and Epomophorus wahlbergi (n = 43) (family Pteropodidae)—in peridomestic habitats in Nairobi, Kenya, and used metagenome sequencing to detect microorganisms. A near-complete genome of a novel virus assigned taxonomically to the Coronaviridae family Betacoronavirus genus and Nobecovirus subclade was characterized from E. wahlbergi. Phylogenetic analysis indicates this unique Nobecovirus clade shares a common ancestor with Eidolon/Rousettus Nobecovirus subclades isolated from Madagascar, Kenya, and Cameroon. Recombination was detected across open reading frames, except the spike protein, in all BOOTSCAN analyses, indicating intra-host coinfection and genetic exchange between genome regions. Although Nobecoviruses are currently bat-specific and are not known to be zoonotic, the propensity of coronaviruses to undergo frequent recombination events and the location of the virus alongside high human and livestock densities in one of East Africa’s most rapidly developing cities justifies continued surveillance of animal viruses in high-risk urban landscapes.

Source: Viruses, https://www.mdpi.com/1999-4915/17/4/557

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