Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning

The COVID-19 pandemic has demonstrated the serious potential for novel zoonotic coronaviruses to emerge and cause major outbreaks. The immediate animal origin of the causative virus, SARS-CoV-2, remains unknown, a notoriously challenging task for emerging disease investigations. Coevolution with hosts leads to specific evolutionary signatures within viral genomes that can inform likely animal origins. We obtained a set of 650 spike protein and 511 whole genome nucleotide sequences from 222 and 185 viruses belonging to the family Coronaviridae, respectively. We then trained random forest models independently on genome composition biases of spike protein and whole genome sequences, including dinucleotide and codon usage biases in order to predict animal host (of nine possible categories, including human). In hold-one-out cross-validation, predictive accuracy on unseen coronaviruses consistently reached ~73%, indicating evolutionary signal in spike proteins to be just as informative as whole genome sequences. However, different composition biases were informative in each case. Applying optimised random forest models to classify human sequences of MERS-CoV and SARS-CoV revealed evolutionary signatures consistent with their recognised intermediate hosts (camelids, carnivores), while human sequences of SARS-CoV-2 were predicted as having bat hosts (suborder Yinpterochiroptera), supporting bats as the suspected origins of the current pandemic. In addition to phylogeny, variation in genome composition can act as an informative approach to predict emerging virus traits as soon as sequences are available. More widely, this work demonstrates the potential in combining genetic resources with machine learning algorithms to address long-standing challenges in emerging infectious diseases.

Interferon lambda 4 signals via the IFNλ receptor to regulate antiviral activity against HCV and coronaviruses

The IFNL4 gene is a recently discovered type III interferon, which in a significant fraction of the human population harbours a frameshift mutation abolishing the IFNλ4 ORF. The expression of IFNλ4 is correlated with both poor spontaneous clearance of hepatitis C virus (HCV) and poor response to treatment with type I interferon. Here, we show that the IFNL4 gene encodes an active type III interferon, named IFNλ4, which signals through the IFNλR1 and IL-10R2 receptor chains. Recombinant IFNλ4 is antiviral against both HCV and coronaviruses at levels comparable to IFNλ3. However, the secretion of IFNλ4 is impaired compared to that of IFNλ3, and this impairment is not due to a weak signal peptide, which was previously believed. We found that IFNλ4 gets N-linked glycosylated and that this glycosylation is required for secretion. Nevertheless, this glycosylation is not required for activity. Together, these findings result in the paradox that IFNλ4 is strongly antiviral but a disadvantage during HCV infection.

Decreased activity of brush border membrane-bound digestive enzymes in small intestines from pigs experimentally infected with porcine epidemic diarrhea virus

Brush border membrane-bound digestive enzymes such as disaccharidases (lactase, sucrase, and maltase), leucine aminopeptidase N, and alkaline phosphatase were measured in jejunum from pigs experimentally infected with porcine epidemic diarrhea virus (PEDV). Three piglets from the infected and control groups were euthanized by electrocution and subjected to necropsy at 24, 36, 48, 60, and 72 hours post-inoculation (hpi). The infection of PEDV to jejunum resulted in significant decreases in brush border membrane-bound digestive enzymes such as disaccharidases (lactase, sucrase, and maltase), leucine aminopeptidase N, and alkaline phosphatase. PEDV replication results in massive destruction of villous enterocytes leading to a marked reduction of intestinal epithelial surface and brush border membrane-bound digestive enzyme activity. Reduced enzymatic activity and villous atrophy in the small intestine is thought to result in a maldigestive and malabsorptive diarrhea.

Determination of lactose and xylose malabsorption in preruminant diarrheic calves

In preliminary studies feeding the poorly absorbed carbohydrate sorbitol at 2.3 g/kg body weight as an indication of maximal fermentative capacity failed to produce the expected large increase in breath hydrogen excretion but did produce a transient diarrhea in five out of six control calves. Twelve healthy control and eighteen diarrheic calves were fed lactose or D-xylose on consecutive days at 1.15 g/kg body weight and a concentration of 46 g/L. Breath and blood samples were collected at 1 h intervals from 0 to 7 h. After administration of lactose, there was a significant increase in breath hydrogen excretion in diarrheic versus control calves. The increase in plasma glucose concentrations was delayed in diarrheic calves but the area under the absorption curve was similar in control and diarrheic calves. After administration of D-xylose, breath hydrogen excretion did not increase significantly but plasma D-xylose concentrations were significantly reduced in diarrheic calves. The pathogens commonly isolated from the feces were Cryptosporidium species, rotavirus and coronavirus. The number of pathogens and the severity of the calves' acid-base deficit were not related to the severity of carbohydrate malabsorption. Decreased absorption of lactose and D-xylose may be the result of intestinal villous atrophy caused by viral or parasite infection. It was concluded that carbohydrate malabsorption rather than a specific lactose maldigestion is a significant problem in diarrheic calves. Diarrheic calves appear to digest and absorb lactose when fed in small amounts.

Bovine coronavirus uses N-acetyl-9-O-acetylneuraminic acid as a receptor determinant to initiate the infection of cultured cells

The importance of N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2) as a receptor determinant for bovine coronavirus (BCV) on cultured cells was analysed. Pretreatment of MDCK I (Madin Darby canine kidney) cells with neuraminidase or acetylesterase rendered the cells resistant to infection by BCV. The receptors on a human (CaCo-2) and a porcine (LLC-PK1) epithelial cell line were also found to be sensitive to neuraminidase treatment. The susceptibility to infection by BCV was restored after resialylation of asialo-MDCK I cells with Neu5,9Ac2. Transfer of sialic acid lacking a 9-O-acetyl group was ineffective in this respect. These results demonstrate that 9-O-acetylated sialic acid is used as a receptor determinant by BCV to infect cultured cells. The possibility is discussed that the initiation of a BCV infection involves the recognition of different types of receptors, a first receptor for primary attachment and a second receptor to mediate the fusion between the viral envelope and the cellular membrane.

Epithelia-damaging virus infections affect vitamin A status in chickens

The effect of infection with infectious bronchitis virus (IBV) and reovirus (RV) on vitamin A status was investigated in chickens with a normal or marginal intake of vitamin A. At the age of 4 wk, chickens were infected with either IBV or RV, primarily affecting the respiratory or intestinal tract, respectively. Both viruses lowered plasma retinol levels significantly. The effect was more pronounced in chickens fed a diet marginally deficient in vitamin A than in those fed a diet adequate in vitamin A. Concentrations of retinol-binding protein, transthyretin and albumin in RV-infected chickens were also significantly lower than in noninfected chickens fed the same diets; in chickens infected with IBV, there was no effect. These results suggest that the reduced vitamin A status of IBV-infected chickens could be attributed to increased rate of utilization by tissues. In RV infection, this mechanism could be involved but impaired absorption of nutrients (including vitamin A) and direct loss of nutrients via the intestinal tract could also be important.

Redistribution and reduction of interphotoreceptor retinoid-binding protein during ocular coronavirus infection

Inoculation of the neurotropic coronavirus mouse hepatitis virus strain JHM intravitreally or into the anterior chamber causes acute infection of the retinal pigment epithelium (RPE) and neural retina. Weeks later, many retinas have foci of moderate to severe atrophy. The effect of coronavirus infection (after intravitreal inoculation) was examined on interphotoreceptor retinoid-binding protein (IRBP), the glycolipoprotein in the interphotoreceptor matrix (IPM) thought to transport retinoids between the photoreceptors and the RPE. Changes in IRBP distribution accompanied virus-associated retinal pathology, including photoreceptor loss and RPE abnormalities. Immunohistochemistry on days 3 and 6 showed that IRBP had diffused into the neural retina away from the IPM. The IRBP became localized abnormally in the same areas as virus-induced lesions, shown by staining adjacent sections with a monoclonal antibody specific for the viral nucleocapsid protein. Moreover, the level of IRBP in isolated retinas, measured in an immunoslot-blot assay, decreased significantly by day 3 and remained low through day 23. This decrease was confirmed in eyecups isolated on day 6. It may be caused in part by loss of photoreceptors and diffusion of IRBP through the retina into the vitreous. These studies show that a virus may induce an acute, limited infection in the retina that can be cleared by the host. However, the infection initiated a series of events resulting in long-term reduction and redistribution of a critical photoreceptor protein.

Modulation of coronavirus-mediated cell fusion by homeostatic control of cholesterol and fatty acid metabolism

Cellular susceptibility to fusion mediated by murine coronavirus (mouse hepatitis virus, MHV strain A59) was separated into lipid-dependent and lipid-independent mechanisms with the use of subclones and selected mutants of mouse L-2 fibroblasts. Fusion-resistant L-2 cell mutants had similar cholesterol and fatty acid composition as did their fusion-susceptible parent subclone, and were presumably deficient in a genetically mutable non-lipid, host cell factor (e.g., fusion protein receptor). On the other hand, cellular sensitivity to virus fusion, which is known to be influenced by cell cholesterol content [Daya et al., 1988], was shown further to be modulated by homeostatic alterations in fatty acid metabolism. Cholesterol supplementation of mouse L-2 fibroblasts or of peritoneal macrophages from MHV-susceptible mice elevated susceptibility to viral fusion. Increased fusion susceptibility occurred in cholesterol-supplemented L-2 cells in the absence of any detectable alterations in host cell fatty acid composition, thus demonstrating fusion enhancement by cholesterol alone. L-2 cells cloned by limiting dilution in normal (not cholesterol-supplemented) medium were found to be heterogeneous in cholesterol content. Interestingly, high cholesterol-containing subclones had increased levels of C-18:0, C-18:2, C-20:4, and C-22:6 and markedly reduced levels of C-18:1 fatty acids when compared to low cholesterol-containing subclones. High cholesterol-containing subclones did not show enhanced susceptibility to viral fusion, suggesting that homeostatic alteration of fatty acid metabolism compensated for the increased cholesterol levels and countered the normally fusion-enhancing effect of cholesterol alone.(ABSTRACT TRUNCATED AT 250 WORDS)

Neurovirulence of six different murine coronavirus JHMV variants for rats

Six variant viruses of the JHMV strain of murine coronavirus with large (cl-2, CNSV, DL and DS) or small (sp-4 and JHM-X) S proteins were compared in terms of their relative neurovirulence in weanling Lewis rats. Inoculation of various doses of the variants revealed that the cl-2 and CNSV were highly virulent and DL and DS were low-virulent, while sp-4 and JHM-X were avirulent. Pathological examination of rats infected with variants cl-2, DL and sp-4 showed that the cl-2 and DL induced severe and mild acute encephalomyelitis, respectively, while no lesions were observed in the central nervous system of rats infected with sp-4. Virus growth and distribution of antigen in rat brains correlated strongly with neurovirulence. These results suggest that S protein plays a role in neurovirulence in rats. In addition, these variant viruses were shown to be useful tools for further analysis of JHMV neurovirulence in animals as well as in cultured cells.

Effect of interferon or Propionibacterium acnes on the course of experimentally induced feline infectious peritonitis in specific-pathogen-free and random-source cats

Seventy-four cats (52 treated and 22 untreated) were evaluated in efficacy studies of interferon (IFN), Propionibacterium acnes, or a combination of these drugs against experimentally induced feline infectious peritonitis (FIP). Cats were given doses of recombinant human leukocyte (alpha) IFN (rHuIFN-alpha), feline fibroblastic (beta) IFN (FIFN-beta) or P acnes at regular intervals before and after inoculation of virulent FIP virus (FIPV). Prophylactic and therapeutic administration of high doses (10(6) U/kg of body weight) or moderate doses (10(4) U/kg) of rHuIFN-alpha, FIFN-beta (10(3) u/kg), or P acnes (0.4 or 4 mg) did not significantly reduce mortality in treated vs untreated cats. However, the mean survival time in cats treated with 10(6) U of rHuIFN-alpha-/kg alone or combined with doses of P acnes was significantly (P = 0.03) increased after inoculation of highly lethal amounts (200 LD100) of FIPV vs survival time in untreated cats. Although P acnes alone was ineffective, there was some indication that a combination of P acnes and high doses of rHuIFN-alpha was more effective than rHuIFN-alpha alone. Seemingly, the efficacy of rHuIFn-alpha treatment was improved in cats challenge-exposed with less FIPV; in 1 trial, 4 of 5 cats (80%) treated with high doses of rHuIFN-alpha survived after inoculation of minimal lethal amounts (0.6 LD100) of FIPV, whereas only 2 of 5 untreated cats (40%) survived. Pretreatment of cats with 10(6) U of rHuIFN-alpha/kg resulted in detectable serum IFN activity 24 hours later; serum IFN activity was not detected in cats pretreated with P acnes, FIFN-beta, or 10(4) U of rHuIFn-alpha/kg.(ABSTRACT TRUNCATED AT 250 WORDS)

Expression of viral and myelin gene transcripts in a murine CNS demyelinating disease caused by a coronavirus

C57BI/6N mice develop a CNS demyelinating disease when inoculated intracranially at 4 weeks of age with the A59 strain of mouse hepatitis virus (MHV-A59). In order to explore the virus-host interactions, the histological features of the demyelinating disease were correlated with the spatial and temporal distribution of viral transcripts and the expression of oligodendrocyte-specific genes (myelin basic protein, proteolipid protein, myelin-associated glycoprotein, and 2',3' cyclic nucleotide 3'-phosphohydrolase) in the spinal cord of diseased mice. Three distinct phases in the disease were identified. In the first phase, 1 week postinfection (1 WPI), virus replication was widespread in both gray and white matter but was preferentially occurring in glial cells. In the ventral and dorsal root zones where viral transcripts were most abundant, all myelin gene transcripts were decreased before demyelination was seen. During the second phase of the disease (2-3 WPI), viral transcripts decreased in abundance and became restricted to the white matter. Numerous demyelinating lesions were observed and were characterized by inflammatory cells, paucity of oligodendrocytes, and a profound decrease of all myelin gene transcripts. In the third phase of the disease (4-6 WPI) no viral transcripts were detected, and remyelination began. In the lesions and the tissue surrounding them, transcripts of all myelin genes increased to levels above normal. The increased expression of myelin gene transcripts occurred in a synchronized manner and with a cellular distribution reminiscent of that seen in developmental myelination. These molecular events correlated with efficient remyelination and clinical recovery in this murine demyelinating disease.

Effect of Gray strain infectious bronchitis virus and high dietary calcium on renal function of Single Comb White Leghorn pullets at 6, 10, and 18 weeks of age

Experiments were designed to evaluate the effects of Gray strain infectious bronchitis virus (IBV) and high dietary calcium (Ca), alone and in combination, on renal function in pullets. Eight hundred female Single Comb White Leghorn chicks were raised on starter ration. Five hundred chicks were inoculated intravenously with Gray strain IBV at 4 wk of age; the remaining chicks were not exposed to IBV. At 6 wk of age, IBV-inoculated and uninoculated chicks were randomly divided into two diet treatment groups. Half the chicks were fed commercial grower ration (approximately 1.0% Ca, .6% available P) and half were fed commercial layer ration (approximately 3.25% Ca, .5% available P). Birds remained on their respective diets until 18 wk of age. Kidney function studies were conducted on anesthetized birds at 6 wk of age prior to initiation of the diet treatments, at 10 wk of age, and at 18 wk of age. The layer ration increased Ca excretion, decreased inorganic phosphate excretion, and decreased urine hydrogen ion concentration in 10-wk-old pullets in comparison with the grower ration. These diet effects on kidney function were attenuated when the pullets reached 18 wk of age. The layer ration also caused an 11.5% incidence of urolithiasis, and significantly increased kidney asymmetry in 18-wk-old pullets relative to the effects of the grower ration. Gray strain IBV exposure significantly increased kidney asymmetry in 18-wk-old pullets, but had no gross effect on kidney function clearly related to the etiology of urolithiasis. Gray strain IBV did not enhance the incidence of urolithiasis in any of the age groups.

Inhibition of phagocytosis and interleukin-1 production in pulmonary macrophages from rats with sialodacryoadenitis virus infection

To test whether or not sialodacryoadenitis virus (SDAV) infection in rats affects pulmonary macrophage function, we intranasally inoculated pathogen-free F344 rats with SDAV and collected alveolar and interstitial macrophages 5 d later. We assessed Fc receptor-mediated attachment and phagocytosis by phase-contrast microscopic examination of monolayers of alveolar and interstitial macrophages incubated with zymosan, nonopsonized sheep erythrocytes, or erythrocytes opsonized with rabbit antisheep-erythrocyte IgG. Alveolar macrophages from virus-infected rats had significantly (P less than or equal to .05) lower indices of attachment and phagocytosis of opsonized erythrocytes than control macrophages, but there was no difference in attachment of zymosan particles. Interstitial macrophages were not affected. Alveolar macrophages from SDAV-infected rats produced significantly less interleukin-1 than those from control rats, as assessed by testing supernatants from lipopolysaccharide-stimulated macrophage cultures for induction of mouse thymocytes to take up tritiated thymidine. Effects of SDAV infection on lung macrophages could increase host susceptibility to other pathogens or complicate studies of respiratory tract immunity.

Depletion of salivary gland epidermal growth factor by sialodacryoadenitis virus infection in the Wistar rat

Male and female Wistar rats 2 to 15 months of age were inoculated intranasally with sialoda-cryoadenitis (SDA) virus and killed at 8 to 21 days post-inoculation (PI). Submandibular glands were evaluated by light and electron microscopy, and levels of salivary gland epidermal growth factor (EGF) were quantitated by cytochemistry and competitive radioreceptor assay. Apical granules in the epithelial cells of the granular convoluted tubules (GCT) were selectively depleted during the acute and convalescent stages of the disease. In addition, levels of immunoreactive EGF were reduced in affected submandibular glands, especially at 8 to 14 days PI with SDA virus, but some evidence of EGF depletion was seen at up to 3 weeks PI. A corresponding transient depletion of EGF receptor reactive salivary EGF was seen between 1 and 3 weeks after experimental SDA infection. These studies suggest that a clinical (or subclinical) infection with SDA virus could have significant effects on experimental studies on EGF-dependent functions, including reproductive physiology and carcinogenesis.

Altered metabolism, acute shock, and therapeutic response in a calf with severe coronavirus-induced diarrhea

Acute shock and metabolic failure appeared in a diarrheic calf being studied intensively to determine kinetics of glucose and lactate metabolism. Intravenous therapy significantly improved its condition. During metabolic failure, the rapid increase in blood lactate and concomitant decrease in glucose were due to inhibited gluconeogenesis, as glucose entry and lactate oxidation were not modified. Therapy restored metabolic activity and decreased the severe hyperkalemia.