e Recently, we reported the discovery of three novel coronaviruses, bulbul coronavirus HKU11, thrush coronavirus HKU12, and munia coronavirus HKU13, which were identified as representatives of a novel genus, Deltacoronavirus, in the subfamily Coronavirinae. In this territory-wide molecular epidemiology study involving 3,137 mammals and 3,298 birds, we discovered seven additional novel deltacoronaviruses in pigs and birds, which we named porcine coronavirus HKU15, white-eye coronavirus HKU16, sparrow coronavirus HKU17, magpie robin coronavirus HKU18, night heron coronavirus HKU19, wigeon coronavirus HKU20, and common moorhen coronavirus HKU21. Complete genome sequencing and comparative genome analysis showed that the avian and mammalian deltacoronaviruses have similar genome characteristics and structures. They all have relatively small genomes (25.421 to 26.674 kb), the smallest among all coronaviruses. They all have a single papain-like protease domain in the nsp3 gene; an accessory gene, NS6 open reading frame (ORF), located between the M and N genes; and a variable number of accessory genes (up to four) downstream of the N gene. Moreover, they all have the same putative transcription regulatory sequence of ACACCA. Molecular clock analysis showed that the most recent common ancestor of all coronaviruses was estimated at approximately 8100 BC, and those of Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus were at approximately 2400 BC, 3300 BC, 2800 BC, and 3000 BC, respectively. From our studies, it appears that bats and birds, the warm blooded flying vertebrates, are ideal hosts for the coronavirus gene source, bats for Alphacoronavirus and Betacoronavirus and birds for Gammacoronavirus and Deltacoronavirus, to fuel coronavirus evolution and dissemination.

39 On 31 st December 2019, the World Health Organization was informed of a cluster of cases of 40 pneumonia of unknown etiology in Wuhan, China. Subsequent investigations identified a novel 41 coronavirus, now named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 42 from the affected patients. Highly sensitive and specific laboratory diagnostics are important for 43 controlling the rapidly evolving SARS-CoV-2-associated Coronavirus Disease 2019 (COVID-44 19) epidemic. In this study, we developed and compared the performance of three novel real-time 45 RT-PCR assays targeting the RNA-dependent RNA polymerase (RdRp)/helicase (Hel), spike (S), 46 and nucleocapsid (N) genes of SARS-CoV-2 with that of the reported RdRp-P2 assay which is 47 used in >30 European laboratories. Among the three novel assays, the COVID-19-RdRp/Hel 48 assay had the lowest limit of detection in vitro (1.8 TCID 50 /ml with genomic RNA and 11.2 RNA 49 copies/reaction with in vitro RNA transcripts). Among 273 specimens from 15 patients with 50 laboratory-confirmed COVID-19 in Hong Kong, 77 (28.2%) were positive by both the COVID-51 19-RdRp/Hel and RdRp-P2 assays. The COVID-19-RdRp/Hel assay was positive for an 52 additional 42 RdRd-P2-negative specimens [119/273 (43.6%) vs 77/273 (28.2%), P<0.001], 53including 29/120 (24.2%) respiratory tract specimens and 13/153 (8.5%) non-respiratory tract 54 specimens. The mean viral load of these specimens was 3.21×10 4 RNA copies/ml (range, 55 2.21×10 2 to 4.71×10 5 RNA copies/ml). The COVID-19-RdRp/Hel assay did not cross-react with 56 other human-pathogenic coronaviruses and respiratory pathogens in cell culture and clinical 57 specimens, whereas the RdRp-P2 assay cross-reacted with SARS-CoV in cell culture. The highly 58 sensitive and specific COVID-19-RdRp/Hel assay may help to improve the laboratory diagnosis 59 of COVID-19. 60 61 on March 16, 2020 by guest http://jcm.asm.org/ Downloaded from 4

Our findings suggested "early" corticosteroid treatment was associated with a higher subsequent plasma viral load.

Middle East respiratory syndrome coronavirus (MERS-CoV) infection caused severe pneumonia and multiorgan dysfunction and had a higher crude fatality rate (around 50% vs. 10%) than SARS coronavirus (SARS-CoV) infection. To understand the pathogenesis, we studied viral replication, cytokine/chemokine response, and antigen presentation in MERS-CoV-infected human monocyte-derived macrophages (MDMs) versus SARS-CoV-infected MDMs. Only MERS-CoV can replicate in MDMs. Both viruses were unable to significantly stimulate the expression of antiviral cytokines (interferon α [IFN-α] and IFN-β) but induced comparable levels of tumor necrosis factor α and interleukin 6. Notably, MERS-CoV induced significantly higher expression levels of interleukin 12, IFN-γ, and chemokines (IP-10/CXCL-10, MCP-1/CCL-2, MIP-1α/CCL-3, RANTES/CCL-5, and interleukin 8) than SARS-CoV. The expression of major histocompatibility complex class I and costimulatory molecules were significantly higher in MERS-CoV-infected MDMs than in SARS-CoV-infected cells. MERS-CoV replication was validated by immunostaining of infected MDMs and ex vivo lung tissue. We conclusively showed that MERS-CoV can establish a productive infection in human macrophages. The aberrant induction of inflammatory cytokines/chemokines could be important in the disease pathogenesis.

Although human coronavirus OC43-OC43 (HCoV-OC43Coronaviruses cause infections in a wide variety of animals, resulting in respiratory, enteric, hepatic, and neurological diseases of various levels of severity. Based on genotypic and serological characterization, coronaviruses traditionally were classified into three distinct groups, groups 1, 2, and 3 (4). Recently, the Coronavirus Study Group of the International Committee for Taxonomy of Viruses has renamed the traditional group 1, 2, and 3 coronaviruses as Alphacoronavirus, Betacoronavirus, and Gammacoronavirus, respectively (http: //talk.ictvonline.org/media/p/1230.aspx).The recent severe acute respiratory syndrome (SARS) epidemic due to SARS coronavirus (SARS-CoV) and the identification of SARS-related coronaviruses (SARSr-CoVs) from Himalayan palm civets and horseshoe bats in mainland China have led to a boost in interest in the study of coronaviruses in both humans and animals (5,13,24,26,33,37,55). Before the SARS epidemic in 2003, there were only 19 known coronaviruses, including 2 human, 13 mammalian, and 4 avian coronaviruses. After the SARS epidemic, more than 20 additional novel coronaviruses have been described with complete genome sequences (9, 24-26, 31, 42, 45, 50, 53, 54, 57). These include 3 human coronaviruses, 15 mammalian coronaviruses, and 4 avian coronaviruses. For human coronaviruses, human coronavirus NL63 (HCoV-NL63) (an alphacoronavirus) and human coronavirus HKU1 (HCoV-HKU1) (a betacoronavirus) have been discovered in addition to the two previously known human coronaviruses, human coronavirus 229E (HCoV-229E) (an alphacoronavirus) and human coronavirus OC43 (HCoV-OC43) (a betacoronavirus), as well as SARSCoV (a betacoronavirus) (9,45,53,56). While HCoV-229E and HCoV-OC43 were thought to account for 5 to 30% of human respiratory tract infections, HCoV-NL63 and HCoV-HKU1 often were detected in Ͻ5% of respiratory tract samples (23,29,38). Outbreaks due to HCoV-OC43 also have been reported (3,32,44). Nevertheless, the different HCoVs often cocirculate, with one or two HCoVs being predominant depending on the geographical area and year (8,11,19,23).Coronaviruses are unique in having a high frequency of homologous RNA recombination, which is a result of random

While the novel Middle East respiratory syndrome coronavirus (MERS-CoV) is closely related to

The emerging novel human betacoronavirus 2c EMC/2012 (HCoV-EMC) was recently isolated from patients with severe pneumonia and renal failure and was associated with an unexplained high crude fatality rate of 56%. We performed a cell line susceptibility study with 28 cell lines. HCoV-EMC was found to infect the human respiratory tract (polarized airway epithelium cell line Calu-3, embryonic fibroblast cell line HFL, and lung adenocarcinoma cell line A549), kidney (embryonic kidney cell line HEK), intestinal tract (colorectal adenocarcinoma cell line Caco-2), liver cells (hepatocellular carcinoma cell line Huh-7), and histiocytes (malignant histiocytoma cell line His-1), as evident by detection of high or increasing viral load in culture supernatants, detection of viral nucleoprotein expression by immunostaining, and/or detection of cytopathic effects. Although an infected human neuronal cell line (NT2) and infected monocyte and T lymphocyte cell lines (THP-1, U937, and H9) had increased viral loads, their relatively lower viral production corroborated with absent nucleoprotein expression and cytopathic effects. This range of human tissue tropism is broader than that for all other HCoVs, including SARS coronavirus, HCoV-OC43, HCoV-HKU1, HCoV-229E, and HCoV-NL63, which may explain the high mortality associated with this disease. A recent cell line susceptibility study showed that HCoV-EMC can infect primate, porcine, and bat cells and therefore may jump interspecies barriers. We found that HCoV-EMC can also infect civet lung fibroblast and rabbit kidney cell lines. These findings have important implications for the diagnosis, pathogenesis, and transmission of HCoV-EMC.

Background The SARS-CoV-2 Omicron variant, designated as a Variant of Concern(VOC) by the World Health Organization, carries numerous spike mutations which have are known to evade neutralizing antibodies elicited by COVID-19 vaccines. A deeper understanding of the susceptibility of Omicron variant to vaccine-induced neutralizing antibodies is urgently needed for risk assessment. Methods Omicron variant strains HKU691 and HKU344-R346K were isolated from patients using TMPRSS2-overexpressing VeroE6 cells. Whole genome sequence was determined using nanopore sequencing. Neutralization susceptibility of ancestral lineage A virus and the Omicron, Delta and Beta variants to sera from 25 BNT162b2 and 25 Coronavac vaccine recipients was determined using a live virus microneutralization assay. Results The Omicron variant strain HKU344-R346K has an additional spike R346K mutation, which is present in 8.5% of strains deposited in GISAID database. Only 20% and 24% of BNT162b2 recipients had detectable neutralizing antibody against the Omicron variant HKU691 and HKU344-R346K, respectively, while none of the Coronavac recipients had detectable neutralizing antibody titer against either Omicron isolate. For BNT162b2 recipients, the geometric mean neutralization antibody titers(GMT) of the Omicron variant isolates(5.43 and 6.42) were 35.7-39.9-fold lower than that of the ancestral virus(229.4), and the GMT of both Omicron variant isolates were significantly lower than those of the Beta and Delta variants. There was no significant difference in the GMT between HKU691 and HKU344-R346K. Conclusions Omicron variant escapes neutralizing antibodies elicited by BNT162b2 or Coronavac. The additional R346K mutation did not affect the neutralization susceptibility. Our data suggest that the Omicron variant may be associated with lower COVID-19 vaccine effectiveness.