An Updated Review of Porcine Deltacoronavirus in Terms of Prevalence, Pathogenicity, Pathogenesis and Antiviral Strategy

The recent experience with SARS-COV-2 has raised our alarm about the cross-species transmissibility of coronaviruses and the emergence of new coronaviruses. Knowledge of this family of viruses needs to be constantly updated. Porcine deltacoronavirus (PDCoV), a newly emerging member of the genus Deltacoronavirus in the family Coronaviridae, is a swine enteropathogen that causes diarrhea in pigs and may lead to death in severe cases. Since PDCoV diarrhea first broke out in the United States in early 2014, PDCoV has been detected in many countries, such as South Korea, Japan and China. More importantly, PDCoV can also infect species other than pigs, and infections have even been reported in children, highlighting its potential for cross-species transmission. A thorough and systematic knowledge of the epidemiology and pathogenesis of PDCoV will not only help us control PDCoV infection, but also enable us to discover the common cellular pathways and key factors of coronaviruses. In this review, we summarize the current knowledge on the prevalence, pathogenicity and infection dynamics, pathogenesis and immune evasion strategies of PDCoV. The existing anti-PDCoV strategies and corresponding mechanisms of PDCoV infection are also introduced, aiming to provide suggestions for the prevention and treatment of PDCoV and zoonotic diseases.

The Ixodes scapularis Symbiont Rickettsia buchneri Inhibits Growth of Pathogenic Rickettsiaceae in Tick Cells: Implications for Vector Competence

Ixodes scapularis is the primary vector of tick-borne pathogens in North America but notably does not transmit pathogenic Rickettsia species. This tick harbors the transovarially transmitted endosymbiont Rickettsia buchneri, which is widespread in I. scapularis populations, suggesting that it confers a selective advantage for tick survival such as providing essential nutrients. The R. buchneri genome includes genes with similarity to those involved in antibiotic synthesis. There are two gene clusters not found in other Rickettsiaceae, raising the possibility that these may be involved in excluding pathogenic bacteria from the tick. This study explored whether the R. buchneri antibiotic genes might exert antibiotic effects on pathogens associated with I. scapularis. Markedly reduced infectivity and replication of the tick-borne pathogens Anaplasma phagocytophilum, R. monacensis, and R. parkeri were observed in IRE11 tick cells hosting R. buchneri. Using a fluorescent plate reader assay to follow infection dynamics revealed that the presence of R. buchneri in tick cells, even at low infection rates, inhibited the growth of R. parkeri by 86–100% relative to R. buchneri-free cells. In contrast, presence of the low-pathogenic species R. amblyommatis or the endosymbiont R. peacockii only partially reduced the infection and replication of R. parkeri. Addition of host-cell free R. buchneri, cell lysate of R. buchneri-infected IRE11, or supernatant from R. buchneri-infected IRE11 cultures had no effect on R. parkeri infection and replication in IRE11, nor did these treatments show any antibiotic effect against non-obligate intracellular bacteria E. coli and S. aureus. However, lysate from R. buchneri-infected IRE11 challenged with R. parkeri showed some inhibitory effect on R. parkeri infection of treated IRE11, suggesting that challenge by pathogenic rickettsiae may induce the antibiotic effect of R. buchneri. This research suggests a potential role of the endosymbiont in preventing other rickettsiae from colonizing I. scapularis and/or being transmitted transovarially. The confirmation that the observed inhibition is linked to R. buchneri's antibiotic clusters requires further investigation but could have important implications for our understanding of rickettsial competition and vector competence of I. scapularis for rickettsiae.

Effect of parity segregation on Mycoplasma hyopneumoniae infection dynamics and pneumonic lesions in pigs

ABSTRACT: Gilts represent a group risk for Mycoplasma hyopneumoniae vertical transmission in swine herds. Therefore, parity segregation can be an alternative to control M. hyopneumoniae infections. The study evaluated the effect of parity segregation on M. hyopneumoniae infection dynamics and occurrence and severity of lung lesions at slaughter. For that, three multiple site herds were included in the study. Herd A consisted of the farm where gilts would have their first farrowing (parity order (PO) 1). After the first farrowing PO 1 sows were transferred to herd B (PO2-6). Herd C was a conventional herd with gilt replacement (PO1-6). Piglets born in each herd were raised in separated nursery and finishing units. Sows (n = 33 (A), 37 (B), 34 (C)) in all herds were sampled prior to farrowing and piglets (n = 54 (A), 71 (B), 66 (C)) were sampled longitudinally at 21, 63, 100, 140 days of age and at slaughter for M. hyopneumoniae detection by PCR and lung lesions scoring. M. hyopneumoniae prevalence in sows did not differ among herds. Prevalence of positive piglets was higher at weaning in the PO1 herd (A) (P < 0.05). However, prevalence of positive pigs from 100 days of age to slaughter age was higher in the PO2-6 herd (B) (P < 0.05). Lung lesion occurrence and severity were higher in herd B. The authors suggested that the lack of a proper gilt acclimation might have influenced the results, leading to sows being detected positive at farrowing, regardless of the parity.

An attempt to optimize human resources allocation based on spatial diversity of the first wave of COVID–19 in Poland

Aim. Our task was to examine the relationship between the SARS–CoV–2 arrival and the number of confi rmed COVID–19 cases in the fi rst wave (period from March 4 to May 22, 2020 (unoffi cial data)), and socio–economic variables at the powiat (county) level.Methods. We were using simple statistical techniques such as data visualisation, correlation analysis, spatial clustering and multiple linear regression.Results. We showed that immigration and the logarithm of general mobility was the best predictor of SARS–CoV–2 arrival times, while emigration, industrialisation and air quality explain most of the size of the epidemic in poviats. On the other hand, infection dynamics is driven to a lesser extent by previously postulated variables such as population size and density, income or the size of the elderly population.Conclusions. Our analyses could support Polish authorities in preparation for the second wave of infections and optimal management of resources as we have provided a proposition of optimal distribution of human resources between poviats. Although this isa retrospective analysis of the initial phase of the epidemic, similar patterns could repeat in case of new variants of SARS–CoV–2 or new respiratory disease for immunologically naive populations.

Playing dirty with virus transmission

In this issue of JEM, Fay et al. (2021. J. Exp. Med.https://doi.org/10.1084/jem.20211220) cohouse dirty pet store mice and rats with clean laboratory mice to gain insights into infection dynamics, discover new viruses, and identify relationships between viruses and the microbiome.

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

As SARS-CoV-2 becomes an endemic pathogen, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Tracking community infection dynamics of COVID-19 by monitoring SARS-CoV-2 RNA in wastewater, counting positive reactions by qPCR

Wastewater-based epidemiology has proved useful for monitoring the COVID-19 infection dynamics in communities. However, in some countries, low concentrations of SARS-CoV-2 RNA in wastewater make this difficult. Getting meaningful information from wastewater-based epidemiology in regions of low prevalence remains a key challenge. Here we used real-time reverse-transcription PCR (RT-qPCR) to monitor SARS-CoV-2 RNA in wastewater from October 2020 to February 2021 during the third wave of the COVID-19 outbreak in Japan. Viral RNA was below the limit of quantification in all samples. However, by counting the positive reactions in repeated qPCR of each sample, we found that the ratio of positive reactions to all tests in wastewater was significantly correlated with the number of clinically confirmed cases by the date of symptom onset during periods of both increasing and decreasing infection. Time-step analysis indicated that COVID-19 patients excreted large amounts of virus in their feces 2 days either side of symptom onset, which wastewater surveillance could detect. The positive count method is thus useful for tracing COVID-19 dynamics in regions of low prevalence.

Development of an In Vivo Probe to Track SARS-CoV-2 Infection in Rhesus Macaques

Infection with the novel coronavirus, SARS-CoV-2, results in pneumonia and other respiratory symptoms as well as pathologies at diverse anatomical sites. An outstanding question is whether these diverse pathologies are due to replication of the virus in these anatomical compartments and how and when the virus reaches those sites. To answer these outstanding questions and study the spatiotemporal dynamics of SARS-CoV-2 infection a method for tracking viral spread in vivo is needed. We developed a novel, fluorescently labeled, antibody-based in vivo probe system using the anti-spike monoclonal antibody CR3022 and demonstrated that it could successfully identify sites of SARS-CoV-2 infection in a rhesus macaque model of COVID-19. Our results showed that the fluorescent signal from our antibody-based probe could differentiate whole lungs of macaques infected for 9 days from those infected for 2 or 3 days. Additionally, the probe signal corroborated the frequency and density of infected cells in individual tissue blocks from infected macaques. These results provide proof of concept for the use of in vivo antibody-based probes to study SARS-CoV-2 infection dynamics in rhesus macaques.