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Hu GM, Tai YC, Chen CM. Unraveling the evolutionary patterns and phylogenomics of coronaviruses: A consensus network approach. J Med Virol 2023; 95:e29233. [PMID: 38009694 DOI: 10.1002/jmv.29233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/19/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023]
Abstract
The COVID-19 pandemic emphasizes the significance of studying coronaviruses (CoVs). This study investigates the evolutionary patterns of 350 CoVs using four structural proteins (S, E, M, and N) and introduces a consensus methodology to construct a comprehensive phylogenomic network. Our clustering of CoVs into 4 genera is consistent with the current CoV classification. Additionally, we calculate network centrality measures to identify CoV strains with significant average weighted degree and betweenness centrality values, with a specific focus on RaTG13 in the beta genus and NGA/A116E7/2006 in the gamma genus. We compare the phylogenetics of CoVs using our distance-based approach and the character-based model with IQ-TREE. Both methods yield largely consistent outcomes, indicating the reliability of our consensus approach. However, it is worth mentioning that our consensus method achieves an approximate 5000-fold increase in speed compared to IQ-TREE when analyzing the data set of 350 CoVs. This improved efficiency enhances the feasibility of conducting large-scale phylogenomic studies on CoVs.
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Affiliation(s)
- Geng-Ming Hu
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan
| | - Yu-Chen Tai
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan
| | - Chi-Ming Chen
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan
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Zhang S, Yang J, Zhou D, Yan T, Li G, Hao X, Yang Q, Cheng X, Shi H, Liu Q, Li Y, Cheng Z. Development of a DAS-ELISA for Gyrovirus Homsa1 Prevalence Survey in Chickens and Wild Birds in China. Vet Sci 2023; 10:vetsci10050312. [PMID: 37235395 DOI: 10.3390/vetsci10050312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/07/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Gyrovirus homsa1 (GyH1) is an emerging pathogenic single-stranded circular DNA virus that leads to immunosuppression, aplastic anemia, and multisystem damage in chickens. However, the prevalence of GyH1 infection in chickens and wild birds remains unknown. Here, we developed a double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) to investigate GyH1 infection in 8 chicken species and 25 wild bird species. A total of 2258 serum samples from chickens (n = 2192) in 15 provinces, and wild birds (n = 66) in Jinan Wildlife Hospital were collected from 2017 to 2021 in China. The GyH1-positive rates in chickens and wild birds were 9.3% (203/2192) and 22.7% (15/66), respectively. GyH1 was present in all flocks in 15 provinces. From 2017 to 2021, the positive rate ranged from 7.93% (18/227) to 10.67% (56/525), and the highest positive rate was present in 2019. Upon chicken age, the highest positive rate (25.5%) was present in young chickens (14-35 days old). Moreover, the GyH1-positive rate in broiler breeders (12.6%, 21/167) was significantly higher than that in layer chickens (8.9%, 14/157). This study shows that GyH1 has spread in chicken flocks and wild birds, and the higher GyH1-positive rate in wild birds indicates the risk of spillover from wild birds to chickens. Our study expanded the GyH1 epidemiological aspects and provided a theoretical basis for GyH1 prevention.
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Affiliation(s)
- Shicheng Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai 200241, China
| | - Jianhao Yang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Defang Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Tianxing Yan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Gen Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaojing Hao
- Qingdao Husbandry and Veterinary Institute, Qingdao 266199, China
| | - Qi Yang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Xiangyu Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Hengyang Shi
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Qing Liu
- Zoo Wildlife Hospital, Jinan 250032, China
| | - Yubao Li
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252059, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
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Focus on Marine Animal Safety and Marine Bioresources in Response to the SARS-CoV-2 Crisis. Int J Mol Sci 2022; 23:ijms232315136. [PMID: 36499463 PMCID: PMC9737530 DOI: 10.3390/ijms232315136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
SARS-CoV-2 as a zoonotic virus has significantly affected daily life and social behavior since its outbreak in late 2019. The concerns over its transmission through different media directly or indirectly have evoked great attention about the survival of SARS-CoV-2 virions in the environment and its potential infection of other animals. To evaluate the risk of infection by SARS-CoV-2 and to counteract the COVID-19 disease, extensive studies have been performed to understand SARS-CoV-2 biogenesis and its pathogenesis. This review mainly focuses on the molecular architecture of SARS-CoV-2, its potential for infecting marine animals, and the prospect of drug discovery using marine natural products to combat SARS-CoV-2. The main purposes of this review are to piece together progress in SARS-CoV-2 functional genomic studies and antiviral drug development, and to raise our awareness of marine animal safety on exposure to SARS-CoV-2.
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Zhigailov AV, Maltseva ER, Perfilyeva YV, Ostapchuk YO, Naizabayeva DA, Berdygulova ZA, Kuatbekova SA, Nizkorodova AS, Mashzhan A, Gavrilov AE, Abayev AZ, Akhmetollayev IA, Mamadaliyev SM, Skiba YA. Prevalence and genetic diversity of coronaviruses, astroviruses and paramyxoviruses in wild birds in southeastern Kazakhstan. Heliyon 2022; 8:e11324. [PMID: 36353173 PMCID: PMC9638769 DOI: 10.1016/j.heliyon.2022.e11324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/21/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Wild birds are natural reservoirs of many emerging viruses, including some zoonoses. Considering that the territory of Kazakhstan is crossed by several bird migration routes, it is important to know pathogenic viruses circulating in migratory birds in this region. Therefore, the aim of this study was to identify the host range, diversity and spatial distribution of avian paramyxoviruses, coronaviruses, and astroviruses in free-ranging wild birds in the southeastern region of Kazakhstan. For this purpose, we collected tracheal and cloacal swabs from 242 wild birds belonging to 51 species and screened them using conventional PCR assays. Overall, 4.1% (10/242) and 2.9% (7/242) of all examined birds tested positive for coronaviruses and astroviruses, respectively. Coronaviruses were found in the orders Pelecaniformes (30%; 3/10), Charadriiformes (30%; 3/10), Columbiformes (20%; 2/10), Anseriformes (10%; 1/10), and Passeriformes (10%; 1/10). All detected strains belonged to the genus Gammacoronavirus. Astroviruses were detected in birds representing the orders Passeriformes (57%; 4/7), Coraciiformes (14%; 1/7), Charadriiformes (14%; 1/7), and Columbiformes (14%; 1/7). Paramyxoviruses were observed in only two birds (0.8%; 2/242). Both strains were closely related to the species APMV-22, which had not been previously detected in Kazakhstan. Phylogenetic analysis of the partial RdRp gene sequences of the virus strains revealed three different clades of astroviruses, two clades of coronaviruses, and one clade of paramyxoviruses. The results of this study provide valuable information on the diversity and spatial distribution of paramyxoviruses, coronaviruses, and astroviruses in wild birds in southeastern Kazakhstan and highlight the importance of further thorough monitoring of wild birds in this region. First study on CoVs and AstroVs in wild birds in Kazakhstan. APMVs, CoVs and AstroVs are confirmed by RT-PCR and partial RdRp gene sequencing. The CoVs prevalence is higher in aquatic birds as compared to terrestrial species. The obtained CoV strains belong to the genus Gammacoronavirus Strains closely related to APMV-22 not previously detected in Kazakhstan are shown.
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Affiliation(s)
- Andrey V. Zhigailov
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Elina R. Maltseva
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
- Tethys Scientific Society, Almaty, Kazakhstan
| | - Yuliya V. Perfilyeva
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
- Corresponding author.
| | - Yekaterina O. Ostapchuk
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Dinara A. Naizabayeva
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | - Anna S. Nizkorodova
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Akzhigit Mashzhan
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | | | | | - Yuriy A. Skiba
- Almaty Branch of the National Center for Biotechnology, Almaty, Kazakhstan
- M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
- Tethys Scientific Society, Almaty, Kazakhstan
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Oladipo HJ. Dengue virus and SARS-CoV-2 Co-infection dynamics: An emerging threat among African countries. Ann Med Surg (Lond) 2022; 82:104398. [PMID: 36035770 PMCID: PMC9394095 DOI: 10.1016/j.amsu.2022.104398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 01/08/2023] Open
Abstract
The rising circulation of the vector borne disease such as dengue fever amidst the COVID-19 pandemic in African countries is on the rise, which pose a significant public health threat. In this article, we discussed the co-infection of dengue virus (DENV) (the causative agent of dengue fever) and SARS-CoV-2 (the causative agents of COVID-19) as well as the associated risk factors involved. Our review highlights that the continuous increase in the incidence and disease mortality from the co-infection of dengue Virus and SARS-CoV-2 is as result of inadequate surveillance and limited testing centers. Second, the overlapping clinical features and indistinguishable symptoms from both infections is a major challenge. Third, lack of scientific prudence among stakeholders has played a significant impact on how to contain these diseases. Therefore, there is a need to reassess research priorities in understanding the risk factors involved from the coinfection. Also, the development of accurate point-of-care diagnostics for COVID-19 and dengue fever coupled with community-based health intervention programs is highly essential for control. In Africa, the incidence and disease mortality rate from the co-infection of dengue fever and COVID- 19 is on the rise due to inadequate surveillance and limited testing centers. Overlapping clinical features and lack of scientific prudence among stakeholders have played a significant impact on how to contain these infectious diseases. Research priorities need to be reassessed with focus on understanding risk factors involved. Development of accurate point-of-care diagnostics and community-based health intervention programs for both infection is highly essential for control.
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Affiliation(s)
- Habeebullah Jayeola Oladipo
- Corresponding author. Faculty of Pharmaceutical Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria.
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Frederick C, Girard C, Wong G, Lemire M, Langwieder A, Martin MC, Legagneux P. Communicating with Northerners on the absence of SARS-CoV-2 in migratory snow geese. ECOSCIENCE 2021. [DOI: 10.1080/11956860.2021.1885803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Christina Frederick
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec (Québec), Canada
- Chaire de recherche Sentinelle Nord sur le réseau de surveillance des virus chez les oiseaux migrateurs du Grand Nord, Centre hospitalier universitaire de Québec, Université Laval, Québec (Québec), Canada
| | - Catherine Girard
- Centre d’études nordiques et Centre intersectoriel en santé durable, Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay (Québec), Canada
| | - Gary Wong
- Chaire de recherche Sentinelle Nord sur le réseau de surveillance des virus chez les oiseaux migrateurs du Grand Nord, Centre hospitalier universitaire de Québec, Université Laval, Québec (Québec), Canada
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Mélanie Lemire
- Chaire de recherche Littoral en partenariat Sentinelle Nord en approches écosystémiques de la santé, Département de médecine sociale et préventive, Centre hospitalier universitaire de Québec, Université Laval, Institut de biologie intégrative et des systèmes, Québec (Québec), Canada
| | | | - Marie-Claude Martin
- Chaire de recherche Sentinelle Nord sur l’impact des migrations animales sur les écosystèmes nordiques, Département de biologie, Centre d’études nordiques, Université Laval, Québec (Québec), Canada
| | - Pierre Legagneux
- Chaire de recherche Sentinelle Nord sur l’impact des migrations animales sur les écosystèmes nordiques, Département de biologie, Centre d’études nordiques, Université Laval, Québec (Québec), Canada
- Centre d'Études Biologiques de Chizé, UMR 7372 CNRS-La Rochelle Université, Villiers en Bois, France
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Islam A, Ferdous J, Islam S, Sayeed MA, Dutta Choudhury S, Saha O, Hassan MM, Shirin T. Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife. Viruses 2021; 13:1908. [PMID: 34696338 PMCID: PMC8537103 DOI: 10.3390/v13101908] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022] Open
Abstract
Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, VIC 3216, Australia
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Jinnat Ferdous
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Shariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Md. Abu Sayeed
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Shusmita Dutta Choudhury
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
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Rana R, Tripathi A, Kumar N, Ganguly NK. A Comprehensive Overview on COVID-19: Future Perspectives. Front Cell Infect Microbiol 2021; 11:744903. [PMID: 34595136 PMCID: PMC8476999 DOI: 10.3389/fcimb.2021.744903] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/11/2021] [Indexed: 12/16/2022] Open
Abstract
The outbreak of COVID-19 has proven to be an unprecedented disaster for the whole world. The virus has inflicted billion of lives across the globe in all aspects-physically, psychologically, as well as socially. Compared to the previous strains of β-CoV genera- MERS and SARS, SARS-CoV-2 has significantly higher transmissibility and worst post-recovery implications. A frequent mutation in the initial SARS-CoV-2 strain has been a major cause of mortalities (approx. 3 million deaths) and uncontrolled virulence (approx. 1 billion positive cases). As far as clinical manifestations are concerned, this particular virus has exhibited deleterious impacts on systems other than the respiratory system (primary target organ), such as the brain, hematological system, liver, kidneys, endocrine system, etc. with no promising curatives to date. Lack of emergency treatments and shortage of life-saving drugs has promoted the repurposing of existing therapeutics along with the emergence of vaccines with the combined efforts of scientists and industrial experts in this short span. This review summarizes every detail on COVID-19 and emphasizes undermining the future approaches to minimize its prevalence to the remaining lives.
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Domańska-Blicharz K, Miłek-Krupa J, Pikuła A. Diversity of Coronaviruses in Wild Representatives of the Aves Class in Poland. Viruses 2021; 13:v13081497. [PMID: 34452362 PMCID: PMC8402903 DOI: 10.3390/v13081497] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
The revealed prevalence of coronaviruses in wild bird populations in Poland was 4.15% and the main reservoirs were birds from orders Anseriformes and Charadriiformes, with a prevalence of 3.51% and 5.59%, respectively. Gammacoronaviruses were detected more often than deltacoronaviruses, with detection rates of 3.5% and 0.7%, respectively. Gammacoronaviruses were detected in birds belonging to six orders, including Anseriformes, Charadriiformes, Columbiformes, Galliformes, Gruiformes, and Passeriformes, indicating a relatively wide host range. Interestingly, this was the only coronavirus detected in Anseriformes (3.51%), while in Charadriiformes, the prevalence was 3.1%. The identified gammacoronaviruses belonged to the Igacovirus and Brangacovirus subgeneras. Most of these were igacoviruses and formed a common phylogenetic group with a Duck Coronavirus 2714 and two with an Avian Coronavirus/Avian Coronavirus9203, while the viruses from the pigeons formed a distinct “pigeon-like” group, not yet officially represented. The presence of deltacoronaviruses was detected in birds belonging to three orders, Charadriiformes, Galliformes, and Suliformes indicating a narrower host range. Most identified deltacoronaviruses belonged to the Buldecovirus subgenus, while only one belonged to Herdecovirus. Interestingly, the majority of buldecoviruses were identified in gulls, and they formed a distinct phylogenetic lineage not represented by any officially ratified virus species. Another separate group of buldecoviruses, also not represented by the official species, was formed by a virus identified in a common snipe. Only one identified buldecovirus (from common pheasant) formed a group with the ratified species Coronavirus HKU15. The results obtained indicate the high diversity of detected coronaviruses, and thus also the need to update their taxonomy (establishing new representative virus species). The serological studies performed revealed antibodies against an infectious bronchitis virus in the sera of white storks and mallards.
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Chu L, Huang F, Zhang M, Huang B, Wang Y. Current status of traditional Chinese medicine for the treatment of COVID-19 in China. Chin Med 2021; 16:63. [PMID: 34315521 PMCID: PMC8314260 DOI: 10.1186/s13020-021-00461-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/26/2021] [Indexed: 01/08/2023] Open
Abstract
An ongoing outbreak of severe respiratory illness and pneumonia caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2) commenced in December 2019, and the disease was named as coronavirus disease 2019 (COVID-19). Soon after, scientists identified the characteristics of SARS-CoV-2, including its genome sequence and protein structure. The clinical manifestations of COVID-19 have now been established; and nucleic acid amplification is used for the direct determination of the virus, whereas immunoassays can determine the antibodies against SARS-CoV-2. Clinical trials of several antiviral drugs are ongoing. However, there is still no specific drugs to treat COVID-19. Traditional Chinese medicine (TCM) was used in the treatment of COVID-19 during the early stages of the outbreak in China. Some ancient TCM prescriptions, which were efficacious in the treatment of severe acute respiratory syndrome (SARS) in 2002-03 and the influenza pandemic (H1N1) of 2009, have been improved by experienced TCM practitioners for the treatment of COVID-19 based on their clinical symptoms. These developed new prescriptions include Lianhua Qingwen capsules/granules, Jinhua Qinggan granules and XueBiJing injection, among others. In this review, we have summarized the presenting features of SARS-CoV-2, the clinical characteristics of COVID-19, and the progress in the treatment of COVID-19 using TCMs.
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Affiliation(s)
- Liang Chu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jie Fang Avenue, Wuhan, 430030, Hubei, China.
| | - Fang Huang
- Department of Pathology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Mengdan Zhang
- College of Life and Medicine Sciences, Zhejiang Sci-Tech University, No. 928, 2nd Street, Xiasha Higher Education Park, Hangzhou, 310018, Zhejiang, China
| | - Biao Huang
- College of Life and Medicine Sciences, Zhejiang Sci-Tech University, No. 928, 2nd Street, Xiasha Higher Education Park, Hangzhou, 310018, Zhejiang, China
| | - Yigang Wang
- College of Life and Medicine Sciences, Zhejiang Sci-Tech University, No. 928, 2nd Street, Xiasha Higher Education Park, Hangzhou, 310018, Zhejiang, China.
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Halabowski D, Rzymski P. Taking a lesson from the COVID-19 pandemic: Preventing the future outbreaks of viral zoonoses through a multi-faceted approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143723. [PMID: 33213901 PMCID: PMC7666614 DOI: 10.1016/j.scitotenv.2020.143723] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 05/22/2023]
Abstract
The pandemic of the novel coronavirus disease 2019 (COVID-19) has caused a significant burden to healthcare systems, economic crisis, and public fears. It is also a lesson to be learned and a call-to-action to minimize the risk of future viral pandemics and their associated challenges. The present paper outlines selected measures (i.e., monitoring and identification of novel viral agents in animals, limitations to wildlife trade, decreasing hunting activities, changes to mink farming and meat production), the implementation of which would decrease such a risk. The role of viral surveillance systems and research exploring the virus strains associated with different animal hosts is emphasized along with the need for stricter wild trade regulations and changes to hunting activities. Finally, the paper suggests modifications to the meat production system, particularly through the introduction of cultured meat that would not only decrease the risk of exposure to novel human viral pathogens but also strengthen food security and decrease the environmental impacts of food production.
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Affiliation(s)
- Dariusz Halabowski
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland.
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland; Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznań, Poland.
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Vlasova AN, Kenney SP, Jung K, Wang Q, Saif LJ. Deltacoronavirus Evolution and Transmission: Current Scenario and Evolutionary Perspectives. Front Vet Sci 2021; 7:626785. [PMID: 33681316 PMCID: PMC7928354 DOI: 10.3389/fvets.2020.626785] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/31/2020] [Indexed: 11/19/2022] Open
Abstract
Deltacoronavirus (DCoV)–the only coronavirus that can infect multiple species of mammals and birds–was initially identified in several avian and mammalian species, including pigs, in China in 2009–2011. Porcine DCoV has since spread worldwide and is associated with multiple outbreaks of diarrheal disease of variable severity in farmed pigs. In contrast, avian DCoV is being reported in wild birds in different countries without any evidence of disease. The DCoV transboundary nature and the recent discovery of its remarkably broad reactivity with its cellular receptor–aminopeptidase N (APN)–from different species emphasize its epidemiological relevance and necessitate additional research. Further, the ability of porcine DCoV to infect and cause disease in chicks and turkey poults and gnotobiotic calves is suggestive of its increased potential for interspecies transmission or of its avian origin. Whether, porcine DCoVs were initially acquired by one or several mammalian species from birds and whether avian and porcine DCoVs continue co-evolving with frequent spillover events remain to be major unanswered questions. In this review, we will discuss the current information on the prevalence, genetic diversity, and pathogenic potential of porcine and avian DCoVs. We will also analyze the existing evidence of the ongoing interspecies transmission of DCoVs that may provide novel insights into their complex evolution.
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Affiliation(s)
- Anastasia N Vlasova
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
| | - Scott P Kenney
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
| | - Kwonil Jung
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
| | - Qiuhong Wang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, United States
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13
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Perveen N, Muzaffar SB, Al-Deeb MA. Exploring human-animal host interactions and emergence of COVID-19: Evolutionary and ecological dynamics. Saudi J Biol Sci 2021; 28:1417-1425. [PMID: 33281479 PMCID: PMC7708805 DOI: 10.1016/j.sjbs.2020.11.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/22/2022] Open
Abstract
The novel coronavirus disease (COVID-19) that emerged in December 2019 had caused substantial morbidity and mortality at the global level within few months. It affected economies, stopped travel, and isolated individuals and populations around the world. Wildlife, especially bats, serve as reservoirs of coronaviruses from which the variant Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged that causes COVID-19. In this review, we describe the current knowledge on COVID-19 and the significance of wildlife hosts in its emergence. Mammalian and avian coronaviruses have diverse host ranges with distinct lineages of coronaviruses. Recombination and reassortments occur more frequently in mixed-animal markets where diverse viral genotypes intermingle. Human coronaviruses have evolved through gene gains and losses primarily in interfaces where wildlife and humans come in frequent contact. There is a gap in our understanding of bats as reservoirs of coronaviruses and there is a misconception that bats periodically transmit coronaviruses to humans. Future research should investigate bat viral diversity and loads at interfaces between humans and bats. Furthermore, there is an urgent need to evaluate viral strains circulating in mixed animal markets, where the coronaviruses circulated before becoming adapted to humans. We propose and discuss a management intervention plan for COVID-19 and raise questions on the suitability of current containment plans. We anticipate that more virulent coronaviruses could emerge unless proper measures are taken to limit interactions between diverse wildlife and humans in wild animal markets.
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Affiliation(s)
- Nighat Perveen
- Department of Biology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Sabir Bin Muzaffar
- Department of Biology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Mohammad Ali Al-Deeb
- Department of Biology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
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14
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Karpiński TM, Ożarowski M, Seremak-Mrozikiewicz A, Wolski H, Wlodkowic D. The 2020 race towards SARS-CoV-2 specific vaccines. Theranostics 2021; 11:1690-1702. [PMID: 33408775 PMCID: PMC7778607 DOI: 10.7150/thno.53691] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/08/2020] [Indexed: 12/13/2022] Open
Abstract
The global outbreak of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlighted a requirement for two pronged clinical interventions such as development of effective vaccines and acute therapeutic options for medium-to-severe stages of "coronavirus disease 2019" (COVID-19). Effective vaccines, if successfully developed, have been emphasized to become the most effective strategy in the global fight against the COVID-19 pandemic. Basic research advances in biotechnology and genetic engineering have already provided excellent progress and groundbreaking new discoveries in the field of the coronavirus biology and its epidemiology. In particular, for the vaccine development the advances in characterization of a capsid structure and identification of its antigens that can become targets for new vaccines. The development of the experimental vaccines requires a plethora of molecular techniques as well as strict compliance with safety procedures. The research and clinical data integrity, cross-validation of the results, and appropriated studies from the perspective of efficacy and potently side effects have recently become a hotly discussed topic. In this review, we present an update on latest advances and progress in an ongoing race to develop 52 different vaccines against SARS-CoV-2. Our analysis is focused on registered clinical trials (current as of November 04, 2020) that fulfill the international safety and efficacy criteria in the vaccine development. The requirements as well as benefits and risks of diverse types of SARS-CoV-2 vaccines are discussed including those containing whole-virus and live-attenuated vaccines, subunit vaccines, mRNA vaccines, DNA vaccines, live vector vaccines, and also plant-based vaccine formulation containing coronavirus-like particle (VLP). The challenges associated with the vaccine development as well as its distribution, safety and long-term effectiveness have also been highlighted and discussed.
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Affiliation(s)
- Tomasz M. Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego 3, 61-712 Poznań, Poland
| | - Marcin Ożarowski
- Department of Biotechnology, Institute of Natural Fibres and Medicinal Plants, Poznań, Poland
| | - Agnieszka Seremak-Mrozikiewicz
- Division of Perinatology and Women's Disease, Poznań University of Medical Sciences, Poznań, Poland
- Laboratory of Molecular Biology in Division of Perinatology and Women's Diseases, Poznań University of Medical Sciences, Poznań, Poland
- Department of Pharmacology and Phytochemistry, Institute of Natural Fibres and Medicinal Plants, Poznań, Poland
| | - Hubert Wolski
- Division of Perinatology and Women's Disease, Poznań University of Medical Sciences, Poznań, Poland
- Division of Obstetrics and Gynecology, Tytus Chałubiński's Hospital, Zakopane, Poland
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15
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Ghale-Noie ZN, Salmaninejad A, Bergquist R, Mollazadeh S, Hoseini B, Sahebkar A. Genetic Aspects and Immune Responses in Covid-19: Important Organ Involvement. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1327:3-22. [PMID: 34279825 DOI: 10.1007/978-3-030-71697-4_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the last two decades, the world has experienced outbreaks of three major coronaviruses with high morbidity and mortality rates. The most recent of these started in the form of an unusual viral pneumonia in Wuhan, China, and now the world is facing a serious pandemic. This new disease has been called COVID-19 and is caused by the SARS-CoV-2 virus. Understanding the specific genetic and phenotypic structure of SARS-CoV-2 in COVID-19 pathogenesis is vital in finding appropriate drugs and vaccines. With this in mind, this review sheds light on the virology, genetics, immune-responses, and mechanism of action of this virus.
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Affiliation(s)
- Zari Naderi Ghale-Noie
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Robert Bergquist
- Formerly UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Benyamin Hoseini
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Health Information Technology, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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16
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Poudel U, Subedi D, Pantha S, Dhakal S. Animal coronaviruses and coronavirus disease 2019: Lesson for One Health approach. Open Vet J 2020; 10:239-251. [PMID: 33282694 PMCID: PMC7703617 DOI: 10.4314/ovj.v10i3.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/06/2020] [Indexed: 02/02/2023] Open
Abstract
Coronaviruses are a group of enveloped, single-stranded, positive-sense RNA viruses that are broadly classified into alpha, beta, gamma, and delta coronavirus genera based on the viral genome. Coronavirus was not thought to be a significant problem in humans until the outbreak of severe acute respiratory syndrome in 2002, but infections in animals, including pigs, cats, dogs, and poultry, have been problematic for a long time. The outbreak of coronavirus disease 2019 in December 2019 in Wuhan, China, drew special attention towards this virus once again. The intermediate host of this novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is yet to be determined, but it has a very close genomic relationship with the bat coronavirus (Bat-CoV), RaTG13 strain, and the pangolin coronaviruses. As veterinary medicine has a long-term experience dealing with coronaviruses, this could be helpful in better understanding and detecting the origin of SARS-CoV-2 and drive human medicine towards the development of vaccines and antiviral drugs through the collaborative and transdisciplinary approaches of One Health.
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Affiliation(s)
- Uddab Poudel
- Institute of Agriculture and Animal Science (IAAS), Paklihawa Campus, Tribhuvan University, Siddharthanagar, Nepal
| | - Deepak Subedi
- Institute of Agriculture and Animal Science (IAAS), Paklihawa Campus, Tribhuvan University, Siddharthanagar, Nepal
| | - Saurav Pantha
- Institute of Agriculture and Animal Science (IAAS), Paklihawa Campus, Tribhuvan University, Siddharthanagar, Nepal
| | - Santosh Dhakal
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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17
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Rahman MM, Talukder A, Chowdhury MMH, Talukder R, Akter R. Coronaviruses in wild birds - A potential and suitable vector for global distribution. Vet Med Sci 2020; 7:264-272. [PMID: 32970935 PMCID: PMC7537155 DOI: 10.1002/vms3.360] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/18/2020] [Accepted: 09/09/2020] [Indexed: 01/08/2023] Open
Abstract
The recurrent appearance of novel coronaviruses (CoVs) and the mortality and morbidity caused by their outbreaks aroused a widespread response among the global science community. Wild birds' high biodiversity, perching and migratory activity, ability to travel long distances and possession of a special adaptive immune system may make them alarming sources of zoonotic CoV‐spreading vectors. This review gathers the available evidence on the global spread of CoVs in wild birds to date. The major wild birds associated with different types of CoVs are Anseriformes, Charadriiformes, Columbiformes, Pelecaniformes, Galliformes, Passeriformes, Psittaciformes, Accipitriformes, Ciconiiformes, Gruiformes and so on. However, the main type of CoVs found in wild birds is gammacoronavirus, followed by deltacoronavirus. Consequently, it is imperative to enable thorough research and continuous monitoring to fill the study gap in terms of understanding their role as zoonotic vectors and the frequent appearance of novel CoVs.
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Affiliation(s)
- Md Mijanur Rahman
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Asma Talukder
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Reshma Talukder
- Department of Architecture, State University of Bangladesh, Dhaka, Bangladesh
| | - Rekha Akter
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
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18
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Wille M, Holmes EC. Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses. FEMS Microbiol Rev 2020; 44:631-644. [PMID: 32672814 PMCID: PMC7454673 DOI: 10.1093/femsre/fuaa026] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
Wild birds interconnect all parts of the globe through annual cycles of migration with little respect for country or continental borders. Although wild birds are reservoir hosts for a high diversity of gamma- and deltacoronaviruses, we have little understanding of the ecology or evolution of any of these viruses. In this review, we use genome sequence and ecological data to disentangle the evolution of coronaviruses in wild birds. Specifically, we explore host range at the levels of viral genus and species, and reveal the multi-host nature of many viral species, albeit with biases to certain types of avian host. We conclude that it is currently challenging to infer viral ecology due to major sampling and technical limitations, and suggest that improved assay performance across the breadth of gamma- and deltacoronaviruses, assay standardization, as well as better sequencing approaches, will improve both the repeatability and interpretation of results. Finally, we discuss cross-species virus transmission across both the wild bird - poultry interface as well as from birds to mammals. Clarifying the ecology and diversity in the wild bird reservoir has important ramifications for our ability to respond to the likely future emergence of coronaviruses in socioeconomically important animal species or human populations.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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19
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On the Coronaviruses and Their Associations with the Aquatic Environment and Wastewater. WATER 2020. [DOI: 10.3390/w12061598] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The outbreak of Coronavirus Disease 2019 (COVID-19), a severe respiratory disease caused by betacoronavirus SARS-CoV-2, in 2019 that further developed into a pandemic has received an unprecedented response from the scientific community and sparked a general research interest into the biology and ecology of Coronaviridae, a family of positive-sense single-stranded RNA viruses. Aquatic environments, lakes, rivers and ponds, are important habitats for bats and birds, which are hosts for various coronavirus species and strains and which shed viral particles in their feces. It is therefore of high interest to fully explore the role that aquatic environments may play in coronavirus spread, including cross-species transmissions. Besides the respiratory tract, coronaviruses pathogenic to humans can also infect the digestive system and be subsequently defecated. Considering this, it is pivotal to understand whether wastewater can play a role in their dissemination, particularly in areas with poor sanitation. This review provides an overview of the taxonomy, molecular biology, natural reservoirs and pathogenicity of coronaviruses; outlines their potential to survive in aquatic environments and wastewater; and demonstrates their association with aquatic biota, mainly waterfowl. It also calls for further, interdisciplinary research in the field of aquatic virology to explore the potential hotspots of coronaviruses in the aquatic environment and the routes through which they may enter it.
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