Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection.

Among all RNA viruses, coronavirus RNA transcription is the most complex and involves a process termed "discontinuous transcription" that results in the production of a set of 3'-nested, co-terminal genomic and subgenomic RNAs during infection. While the expression of the classic canonical set of subgenomic RNAs depends on the recognition of a 6- to 7-nt transcription regulatory core sequence (TRS), here, we use deep sequence and metagenomics analysis strategies and show that the coronavirus transcriptome is even more vast and more complex than previously appreciated and involves the production of leader-containing transcripts that have canonical and noncanonical leader-body junctions. Moreover, by ribosome protection and proteomics analyses, we show that both positive- and negative-sense transcripts are translationally active. The data support the hypothesis that the coronavirus proteome is much vaster than previously noted in the literature.

1-O-Octadecyl-2-O-benzyl-sn-glyceryl-3-phospho-GS-441524 (V2043). Evaluation of Oral V2043 in a Mouse Model of SARS-CoV-2 Infection and Synthesis and Antiviral Evaluation of Additional Phospholipid Esters with Enhanced Anti-SARS-CoV-2 Activity.

Early antiviral treatments, including intravenous remdesivir (RDV), reduce hospitalization and severe disease caused by COVID-19. An orally bioavailable RDV analog may facilitate earlier treatment of non-hospitalized COVID-19 patients. Here we describe the synthesis and evaluation of alkyl glyceryl ether phosphodiesters of GS-441524 (RVn), lysophospholipid analogs which allow for oral bioavailability and stability in plasma. Oral treatment of SARS-CoV-2-infected BALB/c mice with 1-O-octadecyl-2-O-benzyl-sn-glyceryl-3-phospho-RVn (60 mg/kg orally, once daily for 5 days starting 12h after infection) reduced lung viral load by 1.5 log10 units versus vehicle at day 2 and to below the limit of detection at day 5. Structure/activity evaluation of additional analogs that have hydrophobic ethers at the sn-2 of glycerol revealed improved in vitro antiviral activity by introduction of a 3-fluoro-4-methoxy-substituted benzyl or a 3- or 4-cyano-substituted benzyl. Collectively, our data support the development of RVn phospholipid prodrugs as oral antiviral agents for prevention and treatment of SARS-CoV-2 infections.

COVID-19 and MCO-community partnerships to address enrollee social needs.

OBJECTIVES: Many Medicaid managed care organizations (MCOs) now screen enrollees and connect them to community-based organizations (CBOs) to address unmet social needs. COVID-19 has significantly disrupted health care delivery and overall economic activity in the United States. We examined how partnerships between Medicaid MCOs and CBOs to address social determinants of health have been affected by the pandemic. STUDY DESIGN: Guided by questions and recruitment strategies developed with our stakeholder advisory board, we conducted 26 interviews with representatives from all 6 of Kentucky's Medicaid MCOs. METHODS: In-depth, structured interviews for data collection and iterative content analyses to identify themes. RESULTS: Several themes emerged, including substantial increases in enrollees' unmet needs and the demand to find new ways to be responsive, changing funding patterns, disruptions to and evolving modes of communication, and shifting partner relationships. In virtually all areas of impact, COVID-19 has been associated with both negative and positive change. CONCLUSIONS: Unmet social needs associated with the pandemic placed tremendous strain on CBOs, limiting their capacity to sustain some programs and partnerships. Isolation associated with COVID-19 also had wide-ranging effects on service delivery, communication with enrollees and partners, and the ability to maintain relationships. Nonetheless, the pandemic also had some silver linings, including additional resources and flexibility for addressing unmet needs. Federal and state agencies, along with MCO leaders, should carefully evaluate what innovations have been particularly effective during the pandemic and craft new flexibilities into their policies, procedures, and regulations.

Patient Experiences With Ambulatory Telehealth in Neurology: Results of a Mixed-Methods Study.

OBJECTIVE: To assess patient experiences with rapid implementation of ambulatory telehealth during the coronavirus disease 2019 (COVID-19) pandemic. METHODS: A mixed-methods study was performed to characterize the patients' experience with neurology telehealth visits during the first 8 weeks of the COVID-19 response. Consecutive patients who completed a telehealth visit were contacted by telephone. Assenting patients completed a survey quantifying satisfaction with the visit followed by a semistructured telephone interview. Qualitative data were analyzed using the principles of thematic analysis. RESULTS: A total of 2,280 telehealth visits were performed, and 753 patients (33%) were reached for postvisit feedback. Of these, 47% of visits were by video and 53% by telephone. Satisfaction was high, with 77% of patients reporting that all needs were met, although only 51% would consider telehealth in the future. Qualitative themes were constructed, suggesting that positive patient experiences were associated not only with the elimination of commute time and associated costs but also with a positive physician interaction. Negative patient experiences were associated with the inability to complete the neurologic examination. Overall, patients tended to view telehealth as a tool that should augment, and not replace, in-person visits. CONCLUSION: In ambulatory telehealth, patients valued convenience, safety, and physician relationship. Barriers were observed but can be addressed.

Author Correction: A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A comparison of telemedicine and in-person neurology visits: what are the factors that patients consider when selecting future visit type?

OBJECTIVE: To identify factors that patients consider when choosing between future in-person, video, or telephone visits. BACKGROUND: Telemedicine has been rapidly integrated into ambulatory neurology in response to the COVID-19 pandemic. METHODS: Ambulatory neurology patients at a single center were contacted via telephone to complete: (1) a survey quantifying likelihood of scheduling a future telemedicine visit, and (2) a semi-structured qualitative interview following their visit in March 2021. Data were processed using the principles of thematic analysis. RESULTS: Of 2493 visits, 39% assented to post-visit feedback; 74% were in-person visits and 13% video and telephone. Patients with in-person visits were less likely than those with video and telephone visits to "definitely" consider a future telemedicine visit (36 vs. 59 and 62%, respectively; p < 0.001). Patients considered five key factors when scheduling future visits: "Pros of Visit Type," "Barriers to Telemedicine," "Situational Context," "Inherent Beliefs," and "Extrinsic Variables." Patients with telemedicine visits considered convenience as a pro, while those with in-person visits cited improved quality of care. Accessibility and user familiarity were considered barriers to telemedicine by patients with in-person and telephone visits, whereas system limitations were prevalent among patients with video visits. Patients agreed that stable conditions can be monitored via telemedicine, whereas physical examination warrants an in-person visit. Telemedicine was inherently considered equivalent to in-person care by patients with telephone visits. Awareness of telemedicine must be improved for patients with in-person visits. CONCLUSION: Across visit types, patients agree that telemedicine is convenient and effective in many circumstances. Future care delivery models should incorporate the patient perspective to implement hybrid models where telemedicine is an adjunct to in-person visits in ambulatory neurology.

Assessment of Kentucky's Local Health Department Cross-Jurisdictional Sharing: Strategy for Maximizing Efficiency.

OBJECTIVE: The purpose of this study was to examine patterns of cross-jurisdictional sharing across the 61 local public health jurisdictions (LHJs) in Kentucky. The opportunities to reduce the cost-of-service delivery for Kentucky's LHJs via cross-jurisdictional sharing present a mechanism to address financial instability across the state by achieving economies of scale, especially among smaller jurisdictions. DESIGN: A cross-sectional study design was used to examine patterns of cross-jurisdictional sharing across the 61 LHJs in Kentucky. The survey tool utilized was designed by the Center for Sharing Public Health Services, an initiative managed by the Kansas Health Institute with support from the Robert Wood Johnson Foundation. RESULTS: Seventy-two percent of the 61 LHJs in Kentucky responded to the survey. The majority of responding jurisdictions sharing services were rural, single-county jurisdictions, utilizing service-related informal sharing arrangements. The majority of health departments, when asked to identify which programmatic areas shared service arrangements were focused in, listed those services requiring intensive staff training such as Health Access Nurturing Development Services (HANDS) and epidemiology. Of particular interest were the services most infrequently shared such as communicable disease screening and treatment. CONCLUSIONS: This study suggests that, pre-COVID-19, a core group of primarily rural, single-county Kentucky local health departments has experience with cross-jurisdictional sharing. Among this group, engagement in informal arrangements was the form of cross-jurisdictional sharing predominantly used, with few jurisdictions reporting shared functions with joint oversight. When considering the potential benefits and efficiencies that cross-jurisdictional sharing can provide to public health departments and their communities, for some, COVID-19 may have been a catalyst to engage in sharing across health department jurisdictional lines.

A Multitrait Locus Regulates Sarbecovirus Pathogenesis.

Infectious diseases have shaped the human population genetic structure, and genetic variation influences the susceptibility to many viral diseases. However, a variety of challenges have made the implementation of traditional human Genome-wide Association Studies (GWAS) approaches to study these infectious outcomes challenging. In contrast, mouse models of infectious diseases provide an experimental control and precision, which facilitates analyses and mechanistic studies of the role of genetic variation on infection. Here we use a genetic mapping cross between two distinct Collaborative Cross mouse strains with respect to severe acute respiratory syndrome coronavirus (SARS-CoV) disease outcomes. We find several loci control differential disease outcome for a variety of traits in the context of SARS-CoV infection. Importantly, we identify a locus on mouse chromosome 9 that shows conserved synteny with a human GWAS locus for SARS-CoV-2 severe disease. We follow-up and confirm a role for this locus, and identify two candidate genes, CCR9 and CXCR6, that both play a key role in regulating the severity of SARS-CoV, SARS-CoV-2, and a distantly related bat sarbecovirus disease outcomes. As such we provide a template for using experimental mouse crosses to identify and characterize multitrait loci that regulate pathogenic infectious outcomes across species. IMPORTANCE Host genetic variation is an important determinant that predicts disease outcomes following infection. In the setting of highly pathogenic coronavirus infections genetic determinants underlying host susceptibility and mortality remain unclear. To elucidate the role of host genetic variation on sarbecovirus pathogenesis and disease outcomes, we utilized the Collaborative Cross (CC) mouse genetic reference population as a model to identify susceptibility alleles to SARS-CoV and SARS-CoV-2 infections. Our findings reveal that a multitrait loci found in chromosome 9 is an important regulator of sarbecovirus pathogenesis in mice. Within this locus, we identified and validated CCR9 and CXCR6 as important regulators of host disease outcomes. Specifically, both CCR9 and CXCR6 are protective against severe SARS-CoV, SARS-CoV-2, and SARS-related HKU3 virus disease in mice. This chromosome 9 multitrait locus may be important to help identify genes that regulate coronavirus disease outcomes in humans.

Identifying Value-Added Population Health Capabilities to Strengthen Public Health Infrastructure.

Policy Points While the coronavirus pandemic has underscored the important role of public health systems in protecting community health, it has also exposed weaknesses in the public health infrastructure that stem from chronic underfunding and fragmentation in delivery systems. The results of our study suggest that the public health system structure can be strengthened through the targeted implementation of high-value population health capabilities. Prioritizing the delivery of value-added population health capabilities can help communities efficiently use limited time and resources and identify the most effective pathways for building a stronger public health system and improving health outcomes over time. CONTEXT: While the novel coronavirus pandemic has underscored the important role of public health systems in protecting community health, it has also exposed weaknesses in the public health infrastructure that stem from chronic underfunding and fragmentation in public health delivery systems. Information about the relative value in the implementation of recommended population health capabilities can help communities prioritize their use of limited time and resources and identify the most effective pathways for building a stronger public health system. METHODS: We used a longitudinal cohort design with data from the National Longitudinal Survey of Public Health Systems to examine longitudinal and geographic trends in the delivery of population health capabilities and their impact on system strength across communities in the United States. We used linear probability models to ascertain whether the delivery of certain capabilities added value to public health system strength. FINDINGS: Those communities with the strongest classification of public health system structure in both urban and rural areas implemented the largest set of population health capabilities. Results from the linear probability model indicate that a set of population health capabilities are associated with increased public health system strength. Key activities include allocating resources based on a community health plan, surveying the community for behavioral risk factors, analyzing the data on preventive services use, and engaging community stakeholders in health improvement planning (p < 0.01). CONCLUSIONS: The results of this study suggest that public health systems can be strengthened through the targeted implementation of high-value population health capabilities. Prioritizing the delivery of value-added population health capabilities may help communities increase their public health system's capacity and improve health outcomes.

Policy Implications of the COVID-19 Pandemic on Food Insecurity in Rural America: Evidence from Appalachia.

Rural communities are disproportionally affected by food insecurity, making them vulnerable to the consequences of supply disruptions caused by the COVID-19 pandemic. While access to food was initially diminished due to food supply disruptions, little is known about the mechanisms through which federal emergency assistance programs impacted food access in rural populations. Through a series of five focus groups in spring 2021, we examined the impact of the COVID-19 pandemic on food access in a rural Appalachian community in Kentucky. Data were analyzed using a Grounded Theory Approach. Findings revealed the following four primary themes: food scarcity in grocery stores; expanded federal food assistance; expanded community food resources; and expanded home gardening. Participants provided details regarding the way increased federal assistance, especially expanded benefits within the Supplemental Nutrition Assistance Program, allowed them to purchase greater quantities of nutritious food. This study unveils the specific impacts of the COVID-19 pandemic on one rural population, including the influence of some social determinants of health on food insecurity. Policymakers and stakeholders should recognize the layered protection of multiple federal emergency assistance programs against food insecurity and the potential for long-term population health promotion in rural areas.

Rapid Implementation of Outpatient Teleneurology in Rural Appalachia: Barriers and Disparities.

OBJECTIVE: To describe rapid implementation of telehealth during the COVID-19 pandemic and assess for disparities in video visit implementation in the Appalachian region of the United States. METHODS: A retrospective cohort of consecutive patients seen in the first 4 weeks of telehealth implementation was identified from the Neurology Ambulatory Practice at a large academic medical center. Telehealth visits defaulted to video, and when unable, phone-only visits were scheduled. Patients were divided into 2 groups based on the telehealth visit type: video or phone only. Clinical variables were collected from the electronic medical record including age, sex, race, insurance status, indication for visit, and rural-urban status. Barriers to scheduling video visits were collected at the time of scheduling. Patient satisfaction was obtained by structured postvisit telephone call. RESULTS: Of 1,011 telehealth patient visits, 44% were video and 56% phone only. Patients who completed a video visit were younger (39.7 vs 48.4 years, p < 0.001), more likely to be female (63% vs 55%, p < 0.007), be White or Caucasian (p = 0.024), and not have Medicare or Medicaid insurance (p < 0.001). The most common barrier to scheduling video visits was technology limitations (46%). Although patients from rural and urban communities were equally likely to be scheduled for video visits, patients from rural communities were more likely to consider future telehealth visits (55% vs 42%, p = 0.05). CONCLUSION: Rapid implementation of ambulatory telemedicine defaulting to video visits successfully expanded video telehealth. Emerging disparities were revealed, as older, male, Black patients with Medicare or Medicaid insurance were less likely to complete video visits.

Novel modulators of p53-signaling encoded by unknown genes of emerging viruses.

The p53 transcription factor plays a key role both in cancer and in the cell-intrinsic response to infections. The ORFEOME project hypothesized that novel p53-virus interactions reside in hitherto uncharacterized, unknown, or hypothetical open reading frames (orfs) of human viruses. Hence, 172 orfs of unknown function from the emerging viruses SARS-Coronavirus, MERS-Coronavirus, influenza, Ebola, Zika (ZIKV), Chikungunya and Kaposi Sarcoma-associated herpesvirus (KSHV) were de novo synthesized, validated and tested in a functional screen of p53 signaling. This screen revealed novel mechanisms of p53 virus interactions and two viral proteins KSHV orf10 and ZIKV NS2A binding to p53. Originally identified as the target of small DNA tumor viruses, these experiments reinforce the notion that all viruses, including RNA viruses, interfere with p53 functions. These results validate this resource for analogous systems biology approaches to identify functional properties of uncharacterized viral proteins, long non-coding RNAs and micro RNAs.

SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo.

The spike aspartic acid-614 to glycine (D614G) substitution is prevalent in global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, but its effects on viral pathogenesis and transmissibility remain unclear. We engineered a SARS-CoV-2 variant containing this substitution. The variant exhibits more efficient infection, replication, and competitive fitness in primary human airway epithelial cells but maintains similar morphology and in vitro neutralization properties, compared with the ancestral wild-type virus. Infection of human angiotensin-converting enzyme 2 (ACE2) transgenic mice and Syrian hamsters with both viruses resulted in similar viral titers in respiratory tissues and pulmonary disease. However, the D614G variant transmits significantly faster and displayed increased competitive fitness than the wild-type virus in hamsters. These data show that the D614G substitution enhances SARS-CoV-2 infectivity, competitive fitness, and transmission in primary human cells and animal models.

The Current and Future State of Vaccines, Antivirals and Gene Therapies Against Emerging Coronaviruses.

Emerging coronaviruses (CoV) are constant global public health threats to society. Multiple ongoing clinical trials for vaccines and antivirals against CoVs showcase the availability of medical interventions to both prevent and treat the future emergence of highly pathogenic CoVs in human. However, given the diverse nature of CoVs and our close interactions with wild, domestic and companion animals, the next epidemic zoonotic CoV could resist the existing vaccines and antivirals developed, which are primarily focused on Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS CoV). In late 2019, the novel CoV (SARS-CoV-2) emerged in Wuhan, China, causing global public health concern. In this review, we will summarize the key advancements of current vaccines and antivirals against SARS-CoV and MERS-CoV as well as discuss the challenge and opportunity in the current SARS-CoV-2 crisis. At the end, we advocate the development of a "plug-and-play" platform technologies that could allow quick manufacturing and administration of broad-spectrum countermeasures in an outbreak setting. We will discuss the potential of AAV-based gene therapy technology for in vivo therapeutic antibody delivery to combat SARS-CoV-2 outbreak and the future emergence of severe CoVs.

Swine acute diarrhea syndrome coronavirus replication in primary human cells reveals potential susceptibility to infection.

Zoonotic coronaviruses represent an ongoing threat, yet the myriads of circulating animal viruses complicate the identification of higher-risk isolates that threaten human health. Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a newly discovered, highly pathogenic virus that likely evolved from closely related HKU2 bat coronaviruses, circulating in Rhinolophus spp. bats in China and elsewhere. As coronaviruses cause severe economic losses in the pork industry and swine are key intermediate hosts of human disease outbreaks, we synthetically resurrected a recombinant virus (rSADS-CoV) as well as a derivative encoding tomato red fluorescent protein (tRFP) in place of ORF3. rSADS-CoV replicated efficiently in a variety of continuous animal and primate cell lines, including human liver and rectal carcinoma cell lines. Of concern, rSADS-CoV also replicated efficiently in several different primary human lung cell types, as well as primary human intestinal cells. rSADS-CoV did not use human coronavirus ACE-2, DPP4, or CD13 receptors for docking and entry. Contemporary human donor sera neutralized the group I human coronavirus NL63, but not rSADS-CoV, suggesting limited human group I coronavirus cross protective herd immunity. Importantly, remdesivir, a broad-spectrum nucleoside analog that is effective against other group 1 and 2 coronaviruses, efficiently blocked rSADS-CoV replication in vitro. rSADS-CoV demonstrated little, if any, replicative capacity in either immune-competent or immunodeficient mice, indicating a critical need for improved animal models. Efficient growth in primary human lung and intestinal cells implicate SADS-CoV as a potential higher-risk emerging coronavirus pathogen that could negatively impact the global economy and human health.

Remdesivir Inhibits SARS-CoV-2 in Human Lung Cells and Chimeric SARS-CoV Expressing the SARS-CoV-2 RNA Polymerase in Mice.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the novel viral disease COVID-19. With no approved therapies, this pandemic illustrates the urgent need for broad-spectrum antiviral countermeasures against SARS-CoV-2 and future emerging CoVs. We report that remdesivir (RDV) potently inhibits SARS-CoV-2 replication in human lung cells and primary human airway epithelial cultures (EC50 = 0.01 µM). Weaker activity is observed in Vero E6 cells (EC50 = 1.65 µM) because of their low capacity to metabolize RDV. To rapidly evaluate in vivo efficacy, we engineered a chimeric SARS-CoV encoding the viral target of RDV, the RNA-dependent RNA polymerase of SARS-CoV-2. In mice infected with the chimeric virus, therapeutic RDV administration diminishes lung viral load and improves pulmonary function compared with vehicle-treated animals. These data demonstrate that RDV is potently active against SARS-CoV-2 in vitro and in vivo, supporting its further clinical testing for treatment of COVID-19.

SARS-CoV-2: Combating Coronavirus Emergence.

The emergence and rapid global spread of SARS-CoV-2 mark the third such identification of a novel coronavirus capable of causing severe, potentially fatal disease in humans in the 21st century. As noted by Andersen et al. (Nature Medicine), the sequencing of proximal zoonotic ancestors to SARS-CoV-2 has aided in the identification of alleles that may contribute to the virus' virulence in humans.

An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice.

Coronaviruses (CoVs) traffic frequently between species resulting in novel disease outbreaks, most recently exemplified by the newly emerged SARS-CoV-2, the causative agent of COVID-19. Here, we show that the ribonucleoside analog ß-d-N4-hydroxycytidine (NHC; EIDD-1931) has broad-spectrum antiviral activity against SARS-CoV-2, MERS-CoV, SARS-CoV, and related zoonotic group 2b or 2c bat-CoVs, as well as increased potency against a CoV bearing resistance mutations to the nucleoside analog inhibitor remdesivir. In mice infected with SARS-CoV or MERS-CoV, both prophylactic and therapeutic administration of EIDD-2801, an orally bioavailable NHC prodrug (ß-d-N4-hydroxycytidine-5'-isopropyl ester), improved pulmonary function and reduced virus titer and body weight loss. Decreased MERS-CoV yields in vitro and in vivo were associated with increased transition mutation frequency in viral, but not host cell RNA, supporting a mechanism of lethal mutagenesis in CoV. The potency of NHC/EIDD-2801 against multiple CoVs and oral bioavailability highlights its potential utility as an effective antiviral against SARS-CoV-2 and other future zoonotic CoVs.

Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus.

Recently, a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by severe acute respiratory syndrome coronavirus (SARS-CoV). Since the SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between the SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here, we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV and may help epidemic surveillance and preventive measures against 2019-nCoV.IMPORTANCE The recent emergence of Wuhan coronavirus (2019-nCoV) puts the world on alert. 2019-nCoV is reminiscent of the SARS-CoV outbreak in 2002 to 2003. Our decade-long structural studies on the receptor recognition by SARS-CoV have identified key interactions between SARS-CoV spike protein and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. One of the goals of SARS-CoV research was to build an atomic-level iterative framework of virus-receptor interactions to facilitate epidemic surveillance, predict species-specific receptor usage, and identify potential animal hosts and animal models of viruses. Based on the sequence of 2019-nCoV spike protein, we apply this predictive framework to provide novel insights into the receptor usage and likely host range of 2019-nCoV. This study provides a robust test of this reiterative framework, providing the basic, translational, and public health research communities with predictive insights that may help study and battle this novel 2019-nCoV.

Trypsin Treatment Unlocks Barrier for Zoonotic Bat Coronavirus Infection.

Traditionally, the emergence of coronaviruses (CoVs) has been attributed to a gain in receptor binding in a new host. Our previous work with severe acute respiratory syndrome (SARS)-like viruses argued that bats already harbor CoVs with the ability to infect humans without adaptation. These results suggested that additional barriers limit the emergence of zoonotic CoV. In this work, we describe overcoming host restriction of two Middle East respiratory syndrome (MERS)-like bat CoVs using exogenous protease treatment. We found that the spike protein of PDF2180-CoV, a MERS-like virus found in a Ugandan bat, could mediate infection of Vero and human cells in the presence of exogenous trypsin. We subsequently show that the bat virus spike can mediate the infection of human gut cells but is unable to infect human lung cells. Using receptor-blocking antibodies, we show that infection with the PDF2180 spike does not require MERS-CoV receptor DPP4 and antibodies developed against the MERS spike receptor-binding domain and S2 portion are ineffective in neutralizing the PDF2180 chimera. Finally, we found that the addition of exogenous trypsin also rescues HKU5-CoV, a second bat group 2c CoV. Together, these results indicate that proteolytic cleavage of the spike, not receptor binding, is the primary infection barrier for these two group 2c CoVs. Coupled with receptor binding, proteolytic activation offers a new parameter to evaluate the emergence potential of bat CoVs and offers a means to recover previously unrecoverable zoonotic CoV strains.IMPORTANCE Overall, our studies demonstrate that proteolytic cleavage is the primary barrier to infection for a subset of zoonotic coronaviruses. Moving forward, the results argue that both receptor binding and proteolytic cleavage of the spike are critical factors that must be considered for evaluating the emergence potential and risk posed by zoonotic coronaviruses. In addition, the findings also offer a novel means to recover previously uncultivable zoonotic coronavirus strains and argue that other tissues, including the digestive tract, could be a site for future coronavirus emergence events in humans.