Emergence of porcine delta-coronavirus pathogenic infections among children in Haiti through independent zoonoses and convergent evolution

Abstract

Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, coronavirus emergence in our species has been associated with zoonotic transmissions from animal reservoirs, underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae (Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gammacoronavirus), human infections reported to date have been limited to alpha and betacoronaviruses. We identify, for the first time, porcine deltacoronavirus (PDCoV) strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the nsp15 and the spike glycoprotein genes by convergent evolution. In particular, structural analysis predicts that one of the changes in the Spike S1 subunit, which contains the receptor-binding domain, may affect flexibity of the protein and binding to the host cell receptor. Our findings not only underscore the ability of deltacoronaviruses to adapt and potentially lead to human-to-human transmission, but also raise questions about the role of such transmissions in development of pre-existing immunity to other coronaviruses, such as SARS-CoV-2.

The origins of SARS-CoV-2: A critical review

“…Coronaviruses have long been known to present a high pandemic risk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the ninth documented coronavirus that infects humans and the seventh identified in the last 20 years (Lednicky et al, 2021;Vlasova et al, 2021). All previous human coronaviruses have zoonotic origins, as have the vast majority of human viruses.…”

Of bats and men: Immunomodulatory treatment options for COVID-19 guided by the immunopathology of SARS-CoV-2 infection

“…Human-to-mink transmission and vice versa has occurred (6). At least nine CoVs are known to infect humans, including three highly virulent strains [SARS-CoV-1 and SARS-CoV-2 and Middle East respiratory syndrome (MERS)-CoV], four viruses (229E, HKU1, NL63, and OC43) that elicit mild common cold symptoms (7), and two others for which cases of human transmission have been reported (8,9). Likely because of differences in their spike and nucleoproteins (7,10), SARS-CoV and MERS-CoV can precipitate severe lower respiratory tract illness, immune exhaustion, systemic hyperinflammation, cytokine storm/cytokine response syndrome (CRS), multiorgan failure, and death.…”

Construction, Characterization and Application of Recombinant Porcine Deltacoronavirus Expressing Nanoluciferase

“…Recent studies showed that PDCoV could limitedly infect mice in vivo and could be passaged in six-day-old embryonated chicken eggs (ECEs) with high viral replicative efficiency [ 26 , 27 ]. A recent study reported that PDCoV was identified in plasma samples of three Haitian children with acute undifferentiated febrile illness, demonstrating the infection of PDCoV in humans [ 28 ]. These studies suggest that PDCoV possesses the potential for cross-species transmissibility.…”