Diarrhoea outbreak caused by coinfections of Cryptosporidium parvum subtype IIdA20G1 and rotavirus in pre-weaned dairy calves.

Diarrhoea is one of the most important syndromes in neonatal calves. In industrialized nations with intensive animal farming, Cryptosporidium spp. and rotavirus are primary causes of calf diarrhoea, but the role of these and other enteric pathogens is not clear in China. In November and December 2018, a diarrhoea outbreak was identified in over 150 pre-weaned calves on a dairy farm in Heilongjiang Province, northeast China and approximately 60 calves died. To determine the cause of the outbreak, we analyzed 131 faecal samples collected from pre-weaned calves (0-2 months) during (n = 114) and after the outbreak (n = 17). Initially, 10 diarrheic samples during the outbreak and 10 non-diarrheic samples after the outbreak were screened for rotavirus, coronavirus, Escherichia coli K99 and Cryptosporidium parvum by using an enzymatic immunoassay (EIA). In addition, 81 other samples were tested specifically for rotavirus by EIA, and all 131 samples were analyzed for Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi by PCR. The initial EIA analysis identified C. parvum (8/10) and rotavirus (5/10) as the dominant pathogens in calves during the outbreak, while both pathogens were detected at lower frequency after the outbreak (2/10 and 1/10, respectively). Further PCR analyses indicated that the occurrence of C. parvum infections in calves was significantly higher during the outbreak (75.4%, 86/114) than after the outbreak (11.8%, 2/17; odds ratio [OR] = 23.0), and was significantly associated with the occurrence of watery diarrhoea (OR = 15.7) and high oocyst shedding intensity. All C. parvum isolates were identified as subtype IIdA20G1. Among other pathogens analyzed, the overall prevalence of rotavirus, G. duodenalis and E. bieneusi was 19.8% (20/101), 38.9% (51/131) and 42.0% (55/131) in calves, respectively, without significant differences during and after the outbreak. Among the three pathogens, only the rotavirus infection was associated with diarrhoea in calves. More importantly, coinfections of C. parvum and rotavirus were significantly associated with the occurrence of watery diarrhoea in calves and were seen only during the outbreak. Thus, C. parvum subtype IIdA20G1 and rotavirus appeared to be responsible for this diarrhoea outbreak. Control measures should be implemented to effectively prevent the concurrent transmission of these enteric pathogens in pre-weaned dairy calves in China.

Corrigendum to "SARS-CoV-2 induced intestinal responses with a biomimetic human gut-on-chip" [Sci. Bull. (2021) 66 (8) 783-793].

[This corrects the article DOI: 10.1016/j.scib.2020.11.015.].

Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2.

Since 2002, the world has witnessed major outbreaks of acute respiratory illness by three zoonotic coronaviruses (CoVs), which differ from each other in pathogenicity. Reasons for the lower pathogenicity of SARS-CoV-2 than the other two zoonotic coronaviruses, SARS-CoV and MERS-CoV, are not well understood. We herein compared the codon usage patterns of the three zoonotic CoVs causing severe acute respiratory syndromes and four human-specific CoVs (NL63, 229E, OC43, and HKU1) causing mild diseases. We found that the seven viruses have different codon usages, with SARS-CoV-2 having the lowest effective number of codons (ENC) among the zoonotic CoVs. Human codon adaptation index (CAI) analysis revealed that the CAI value of SARS-CoV-2 is the lowest among the zoonotic CoVs. The ENC and CAI values of SARS-CoV-2 were more similar to those of the less-pathogenic human-specific CoVs. To further investigate adaptive evolution within SARS-CoV-2, we examined codon usage patterns in 3573 genomes of SARS-CoV-2 collected over the initial 4 months of the pandemic. We showed that the ENC values and the CAI values of SARS-CoV-2 were decreasing over the period. The low ENC and CAI values could be responsible for the lower pathogenicity of SARS-CoV-2. While mutational pressure appears to shape codon adaptation in the overall genomes of SARS-CoV-2 and other zoonotic CoVs, the E gene of SARS-CoV-2, which has the highest codon usage bias, appears to be under strong natural selection. Data from the study contribute to our understanding of the pathogenicity and evolution of SARS-CoV-2 in humans.

Biomimetic Human Disease Model of SARS-CoV-2-Induced Lung Injury and Immune Responses on Organ Chip System.

Coronavirus disease 2019 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The models that can accurately resemble human-relevant responses to viral infection are lacking. Here, a biomimetic human disease model on chip that allows to recapitulate lung injury and immune responses induced by SARS-CoV-2 in vitro at organ level is created. This human alveolar chip reproduce the key features of alveolar-capillary barrier by coculture of human alveolar epithelium, microvascular endothelium, and circulating immune cells under fluidic flow in normal and disease. Upon SARS-CoV-2 infection, the epithelium exhibits higher susceptibility to virus than endothelium. Transcriptional analyses show activated innate immune responses in epithelium and cytokine-dependent pathways in endothelium at day 3 post-infection, revealing the distinctive responses in different cell types. Notably, viral infection causes the immune cell recruitment, endothelium detachment, and increased inflammatory cytokines release, suggesting the crucial role of immune cells involved in alveolar barrier injury and exacerbated inflammation. Treatment with remdesivir can inhibit viral replication and alleviate barrier disruption on chip. This organ chip model can closely mirror human-relevant responses to SARS-CoV-2 infection, which is difficult to be achieved by in vitro models, providing a unique platform for COVID-19 research and drug development.

SARS-CoV-2 induced intestinal responses with a biomimetic human gut-on-chip.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic. Clinical evidence suggests that the intestine is another high-risk organ for SARS-CoV-2 infection besides the lungs. However, a model that can accurately reflect the response of the human intestine to the virus is still lacking. Here, we created an intestinal infection model on a chip that allows the recapitulation of human relevant intestinal pathophysiology induced by SARS-CoV-2 at organ level. This microengineered gut-on-chip reconstitutes the key features of the intestinal epithelium-vascular endothelium barrier through the three-dimensional (3D) co-culture of human intestinal epithelial, mucin-secreting, and vascular endothelial cells under physiological fluid flow. The intestinal epithelium showed permissiveness for viral infection and obvious morphological changes with injury of intestinal villi, dispersed distribution of mucus-secreting cells, and reduced expression of tight junction (E-cadherin), indicating the destruction of the intestinal barrier integrity caused by virus. Moreover, the vascular endothelium exhibited abnormal cell morphology, with disrupted adherent junctions. Transcriptional analysis revealed abnormal RNA and protein metabolism, as well as activated immune responses in both epithelial and endothelial cells after viral infection (e.g., upregulated cytokine genes), which may contribute to the injury of the intestinal barrier associated with gastrointestinal symptoms. This human organ system can partially mirror intestinal barrier injury and the human response to viral infection, which is not possible in existing in vitro culture models. It provides a unique and rapid platform to accelerate COVID-19 research and develop novel therapies.

Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins.

The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health1. The new coronavirus responsible for this outbreak-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG132. Although bats may be the reservoir host for a variety of coronaviruses3,4, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins-the most-trafficked mammal in the illegal wildlife trade-could represent a future threat to public health if wildlife trade is not effectively controlled.