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1.
Chin Med J (Engl) ; 133(9): 1015-1024, 2020 May 05.
Article in English | MEDLINE | ID: covidwho-1722617

ABSTRACT

BACKGROUND: Human infections with zoonotic coronaviruses (CoVs), including severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV, have raised great public health concern globally. Here, we report a novel bat-origin CoV causing severe and fatal pneumonia in humans. METHODS: We collected clinical data and bronchoalveolar lavage (BAL) specimens from five patients with severe pneumonia from Wuhan Jinyintan Hospital, Hubei province, China. Nucleic acids of the BAL were extracted and subjected to next-generation sequencing. Virus isolation was carried out, and maximum-likelihood phylogenetic trees were constructed. RESULTS: Five patients hospitalized from December 18 to December 29, 2019 presented with fever, cough, and dyspnea accompanied by complications of acute respiratory distress syndrome. Chest radiography revealed diffuse opacities and consolidation. One of these patients died. Sequence results revealed the presence of a previously unknown ß-CoV strain in all five patients, with 99.8% to 99.9% nucleotide identities among the isolates. These isolates showed 79.0% nucleotide identity with the sequence of SARS-CoV (GenBank NC_004718) and 51.8% identity with the sequence of MERS-CoV (GenBank NC_019843). The virus is phylogenetically closest to a bat SARS-like CoV (SL-ZC45, GenBank MG772933) with 87.6% to 87.7% nucleotide identity, but is in a separate clade. Moreover, these viruses have a single intact open reading frame gene 8, as a further indicator of bat-origin CoVs. However, the amino acid sequence of the tentative receptor-binding domain resembles that of SARS-CoV, indicating that these viruses might use the same receptor. CONCLUSION: A novel bat-borne CoV was identified that is associated with severe and fatal respiratory disease in humans.


Subject(s)
Betacoronavirus , Coronavirus Infections/virology , Pneumonia, Viral/virology , Adult , Aged , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/therapy , Female , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/therapy , SARS-CoV-2 , Tomography, X-Ray , Treatment Outcome
2.
Acta Haematol ; 144(5): 580-584, 2021.
Article in English | MEDLINE | ID: covidwho-1194384

ABSTRACT

Recently, a significant cluster of pneumonia caused by a novel betacoronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) was described initially in China and then spread throughout the world. Like other coronaviridae, the viral transmission occurs mainly through droplets. In addition, the virus has been detected in different clinical specimens, suggesting a potential transmission by other routes, including blood transfusion. However, the potential risk of transmission of SARS-CoV-2 via blood products is still unclear. The aim of our study was to investigate the prevalence of antibodies against SARS-CoV-2 among blood donors from South-Eastern Italy. Moreover, in the seropositive donors, we searched for the presence of the virus in nasopharyngeal swabs and in plasma samples. Overall, 1,797 blood donors from the Apulia region were tested for anti-SARS-CoV-2 antibodies, using a commercially available assay. Only 18/1,797 donors (1.0%) tested positive for anti-SARS-CoV-2 antibodies; in none of them SARS-CoV-2 viral RNA was detected in nasopharyngeal swabs and in plasma samples. Our results indicate that most of the blood donors in Apulia remained uninfected during this wave of the pandemic; further, none had detectable virus both in nasopharyngeal swabs and in blood samples. The risk to carry and transmit the virus by healthy and asymptomatic blood donors is probably very low.


Subject(s)
Antibodies, Viral/blood , Blood Donors , COVID-19/pathology , SARS-CoV-2/immunology , Adolescent , Adult , Aged , COVID-19/virology , Female , Humans , Italy , Male , Middle Aged , Nasopharynx/virology , RNA, Viral/analysis , RNA, Viral/metabolism , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Viral Load , Young Adult
3.
Front Immunol ; 12: 637982, 2021.
Article in English | MEDLINE | ID: covidwho-1156123

ABSTRACT

A novel betacoronavirus (SARS-CoV-2) that causes severe pneumonia emerged through zoonosis in late 2019. The disease, referred to as COVID-19, has an alarming mortality rate and it is having a devastating effect on the global economy and public health systems. A safe, effective vaccine is urgently needed to halt this pandemic. In this study, immunogenicity of the receptor binding domain (RBD) of spike (S) glycoprotein was examined in mice. Animals were immunized with recombinant RBD antigen intraperitoneally using three different adjuvants (Zn-chitosan, Alhydrogel, and Adju-Phos), and antibody responses were followed for over 5 months. Results showed that potent neutralizing antibodies (nAbs) can be induced with 70% neutralization titer (NT70) of ~14,580 against live, infectious viruses. Although antigen-binding antibody titers decreased gradually over time, sufficiently protective levels of nAbs persisted (NT80 >2,430) over the 5-month observation period. Results also showed that adjuvants have profound effects on kinetics of nAb induction, total antibody titers, antibody avidity, antibody longevity, and B-cell epitopes targeted by the immune system. In conclusion, a recombinant subunit protein immunogen based on the RBD is a highly promising vaccine candidate. Continued evaluation of RBD immunogenicity using different adjuvants and vaccine regimens could further improve vaccine efficacy.


Subject(s)
Antibodies, Neutralizing/blood , Antibodies, Viral/blood , COVID-19 Vaccines/pharmacology , COVID-19/prevention & control , Immunization , Immunogenicity, Vaccine , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/pharmacology , Adjuvants, Immunologic/pharmacology , Animals , Antibody Affinity , COVID-19/blood , COVID-19/immunology , COVID-19/virology , COVID-19 Vaccines/immunology , Epitopes , Female , Host-Pathogen Interactions , Mice, Inbred BALB C , Protein Domains , Spike Glycoprotein, Coronavirus/immunology , Time Factors , Vaccines, Subunit/immunology , Vaccines, Subunit/pharmacology
4.
J Inflamm (Lond) ; 18(1): 3, 2021 Jan 28.
Article in English | MEDLINE | ID: covidwho-1054824

ABSTRACT

SARS-CoV-2 is a betacoronavirus causing severe inflammatory pneumonia, so that excessive inflammation is considered a risk factor for the disease. According to reports, cytokine storm is strongly responsible for death in such patients. Some of the consequences of severe inflammation and cytokine storms include acute respiratory distress syndrome, acute lung injury, and multiple organ dysfunction syndromes. Phylogenetic findings show more similarity of the SARS-CoV-2 virus with bat coronaviruses, and less with SARS-CoV. Quercetin is a carbohydrate-free flavonoid that is the most abundant flavonoid in vegetables and fruits and has been the most studied to determine the biological effects of flavonoids. Inflammasomes are cytosolic multi-protein complexes assembling in response to cytosolic PAMP and DAMPs, whose function is to generate active forms of cytokines IL-1ß and IL-18. Activation or inhibition of the NLRP3 inflammasome is affected by regulators such as TXNIP, SIRT1 and NRF2. Quercetin suppresses the NLRP3 inflammasome by affecting these regulators. Quercetin, as an anti-inflammatory, antioxidant, analgesic and inflammatory compound, is probably a potential treatment for severe inflammation and one of the main life-threatening conditions in patients with COVID-19.

5.
J Med Virol ; 92(10): 2165-2172, 2020 10.
Article in English | MEDLINE | ID: covidwho-965896

ABSTRACT

On 30th January 2020, an outbreak of atypical pneumonia caused by a novel betacoronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a public health emergency of international concern by the World Health Organization. For this reason, a detailed evolutionary analysis of SARS-CoV-2 strains currently circulating in different geographic regions of the world was performed. A compositional analysis as well as a Bayesian coalescent analysis of complete genome sequences of SARS-CoV-2 strains recently isolated in Europe, North America, South America, and Asia was performed. The results of these studies revealed a diversification of SARS-CoV-2 strains in three different genetic clades. Co-circulation of different clades in different countries, as well as different genetic lineages within different clades were observed. The time of the most recent common ancestor was established to be around 1st November 2019. A mean rate of evolution of 6.57 × 10-4 substitutions per site per year was found. A significant migration rate per genetic lineage per year from Europe to South America was also observed. The results of these studies revealed an increasing diversification of SARS-CoV-2 strains. High evolutionary rates and fast population growth characterizes the population dynamics of SARS-CoV-2 strains.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Genome, Viral , Pandemics , Polymorphism, Genetic , SARS-CoV-2/genetics , Asia/epidemiology , Bayes Theorem , COVID-19/diagnosis , COVID-19/virology , Europe/epidemiology , Evolution, Molecular , Genotype , Humans , Molecular Epidemiology , North America/epidemiology , Phylogeny , SARS-CoV-2/classification , South America/epidemiology , Travel , Virus Replication
6.
Med Chem Res ; 29(11): 1935-1955, 2020.
Article in English | MEDLINE | ID: covidwho-754695

ABSTRACT

A disease emerged in the city of Wuhan, Hubei Province, Central China in the last month of 2019. It was pneumonia caused by a newly emerged coronavirus called COVID-19, later. Coronaviruses are enveloped RNA viruses belong to the Betacoronavirus family and infected birds, humans, and other mammals. In March 2020, the World Health Organization declared the COVID-19 outbreak could be characterized as a global pandemic because the disease spread, and a large number of people were infected and died in many countries on different continents by virtue of this new virus. Now, intensive work is underway about the pathogenic mechanisms and epidemiological properties of COVID-19, and a great effort is made to develop effective specific therapeutic drugs, vaccines, and/or treatment strategies against these diseases. Herein, we have focused on all treatment options available against COVID-19 pneumonia in this text.

7.
Virus Res ; 283: 197976, 2020 07 02.
Article in English | MEDLINE | ID: covidwho-46070

ABSTRACT

An outbreak of atypical pneumonia caused by a novel Betacoronavirus (ßCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of ßCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences.


Subject(s)
Betacoronavirus/classification , Betacoronavirus/genetics , Codon Usage/genetics , Communicable Diseases, Emerging/virology , Gene Expression Regulation, Viral/genetics , Genome, Viral/genetics , Genomics , Amino Acids/genetics , Animals , Betacoronavirus/isolation & purification , China/epidemiology , Chiroptera/virology , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Coronavirus Infections/virology , Evolution, Molecular , Ferrets/virology , Humans , Mutagenesis/genetics , Open Reading Frames/genetics , SARS-CoV-2 , Viverridae/virology
8.
Infect Genet Evol ; 81: 104272, 2020 07.
Article in English | MEDLINE | ID: covidwho-4581

ABSTRACT

The seventh novel human infecting Betacoronavirus that causes pneumonia (2019 novel coronavirus, 2019-nCoV) originated in Wuhan, China. The evolutionary relationship between 2019-nCoV and the other human respiratory illness-causing coronavirus is not closely related. We sought to characterize the relationship of the translated proteins of 2019-nCoV with other species of Orthocoronavirinae. A phylogenetic tree was constructed from the genome sequences. A cluster tree was developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The combined data were used to characterize the relationship of the translated proteins of 2019-nCoV to other species of Orthocoronavirinae. Our analysis reliably suggests that 2019-nCoV is most closely related to BatCoV RaTG13 and belongs to subgenus Sarbecovirus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus. The phylogenetic profiling cluster of homolog proteins of one annotated 2019-nCoV protein against other genome sequences revealed two clades of ten 2019-nCoV proteins. Clade 1 consisted of a group of conserved proteins in Orthocoronavirinae comprising Orf1ab polyprotein, Nucleocapsid protein, Spike glycoprotein, and Membrane protein. Clade 2 comprised six proteins exclusive to Sarbecovirus and Hibecovirus. Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. Thus, we speculated that knowledge of the functional changes in the NS7b and NS8 proteins during evolution may provide important information to explore the human infective property of 2019-nCoV.


Subject(s)
Betacoronavirus/classification , Betacoronavirus/genetics , Evolution, Molecular , Phylogeny , Viral Nonstructural Proteins/genetics , Coronaviridae/classification , Coronaviridae/genetics , Coronavirus RNA-Dependent RNA Polymerase , SARS-CoV-2
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