The Ecology and Evolution of SARS-CoV-2

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Virology".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 24501

Special Issue Editor


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Guest Editor
Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL 60501, USA
Interests: microbial genomics; environmental microbiology; microbial ecology; bioinformatics

Special Issue Information

Dear Colleagues,

SARS-CoV-2 is a single-stranded RNA virus causing the coronavirus disease 2019 (COVID-19) pandemic and has claimed millions of human lives all over the world. SARS-CoV-2 is about 80 nm in size, having a protein coat and an RNA genome (~30 Kb). As a microorganism, SARS-CoV-2 participates in the ecological processes in environments. Studies have demonstrated its existence in air, water, waste and surfaces, among other things. Given that it can survive for certain periods of time (from hours to several days) in environments, we have the chance to investigate the composition, diversity and distribution of the virus. Studying the effects of environmental factors—including temperature, acidity, radiations, organic matter and chemicals such as disinfectants—on the virus is helpful for the understanding of its fate and transportation in environments. The virus may also be involved in interactions with other microorganisms (viruses, bacteria or protists) in environments. The ecology of SARS-CoV-2 in environments is a newly emerging field combining virology and ecology, and it will provide useful knowledge to help better control the pandemic and reduce human deaths.

This Special Issue, entitled “The Ecology of SARS-CoV-2 in Environments”, will cover, but not be limited to, the following topics: (a) the diversity, composition and distribution of SARS-CoV-2 in environments; (b) the effects of environmental factors on the abundance of SARS-CoV-2 in environments; (c) the correlation between SARS-CoV-2 variants or between SARS-CoV-2 and other microorganisms; (d) any other topics about the ecology and evolution of SARS-CoV-2 in environments.

Dr. Renmao Tian
Guest Editor

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Keywords

  • SARS-CoV-2
  • COVID-19
  • ecology
  • evolution
  • environment

Published Papers (5 papers)

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Research

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16 pages, 3502 KiB  
Article
Organ Involvement in COVID-19: A Molecular Investigation of Autopsied Patients
by Prem Shankar, Jitendra Singh, Ankur Joshi, Anvita Gupta Malhotra, Arti Shrivas, Garima Goel, Priyal Gupta, Jayanthi Yadav, Saurabh Saigal, Sarman Singh and Shashank Purwar
Microorganisms 2022, 10(7), 1333; https://doi.org/10.3390/microorganisms10071333 - 1 Jul 2022
Cited by 7 | Viewed by 8084
Abstract
Precise reasons for severe manifestation of SARS-CoV-2 remain unanswered, and efforts have been focused on respiratory system management. Demonstration of unequivocal presence of SARS-CoV-2 in vital body organs by cadaver autopsy was the only way to prove multi-organ involvement. Hence, the primary objective [...] Read more.
Precise reasons for severe manifestation of SARS-CoV-2 remain unanswered, and efforts have been focused on respiratory system management. Demonstration of unequivocal presence of SARS-CoV-2 in vital body organs by cadaver autopsy was the only way to prove multi-organ involvement. Hence, the primary objective of the study was to determine presence of the SARS-CoV-2 in various organs of patients succumbing to SARS-CoV-2 infection. A total of 246 samples from different organs of 21 patients who died due to severe COVID-19 illness were investigated by qRT-PCR, and SARS-CoV-2 was detected in 181 (73.57%) samples and highest positivity of SARS-CoV-2 being (expectedly) found in nasopharynx (90.4%) followed by bilateral lungs (87.30%), peritoneal fluid (80%), pancreas (72.72%), bilateral kidneys (68.42%), liver (65%) and even in brain (47.2%). The deceased patients were categorized to three subgroups based upon the extent of organs in which SARS-CoV-2 was detected by qRT-PCR (high intensity ≥80%, intermediate intensity = 65–80% and low intensity ≤65% organs involvement). It was conclusively established that SARS-CoV-2 has the property of invasion beyond lungs and even crosses the blood–brain barrier, resulting in multi-system disease; this is probably the reason behind cytokine storm, though it is not clear whether organ damage is due to direct injury caused by the virus or result of inflammatory assault. Significant inverse correlation was found between the Ct value of lung samples and number of organs involved, implying that higher viral load in lungs is directly proportionate to involvement of extrapulmonary organs and patients with higher viral load in respiratory secretions should be monitored more closely for any warning signs and the treatment strategies should also address involvement of other organs for better outcome, because lungs, though the primary site of infection, are not the only organ system responsible for pathogenesis of systemic illness. Full article
(This article belongs to the Special Issue The Ecology and Evolution of SARS-CoV-2)
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9 pages, 272 KiB  
Communication
SARS-CoV-2 Serological and Biomolecular Analyses among Companion Animals in Campania Region (2020–2021)
by Lorena Cardillo, Claudio de Martinis, Sergio Brandi, Martina Levante, Loredana Cozzolino, Luisa Spadari, Federica Boccia, Carmine Carbone, Marina Pompameo and Giovanna Fusco
Microorganisms 2022, 10(2), 263; https://doi.org/10.3390/microorganisms10020263 - 24 Jan 2022
Cited by 12 | Viewed by 2639
Abstract
The first reports of SARS-CoV-2 among domestic and wild animals, together with the rapid emergence of new variants, have created serious concerns regarding a possible spillback from animal hosts, which could accelerate the evolution of new viral strains. The present study aimed to [...] Read more.
The first reports of SARS-CoV-2 among domestic and wild animals, together with the rapid emergence of new variants, have created serious concerns regarding a possible spillback from animal hosts, which could accelerate the evolution of new viral strains. The present study aimed to investigate the prevalence and the transmission of SARS-CoV-2 among both owned and stray pets. A total of 182 dogs and 313 cats were tested for SARS-CoV-2. Specimens collected among owned and stray pets were subjected to RT-PCR and serological examinations. No viral RNA was detected, while anti-N antibodies were observed in six animals (1.3%), one dog (0.8%) and five cats (1.7%). Animals’ background revealed that owned cats, living with owners with COVID-19, showed significantly different prevalence compared to stray ones (p = 0.0067), while no difference was found among dogs. Among the seropositive pets, three owned cats also showed moderate neutralizing antibody titers. Pets and other species are susceptible to SARS-CoV-2 infection because of the spike affinity towards their ACE2 cellular receptor. Nevertheless, the risk of retransmission remains unclear since pet-to-human transmission has never been described. Due to the virus’ high mutation rate, new reservoirs cannot be excluded; thus, it is reasonable to test pets, mostly if living in households affected by COVID-19. Full article
(This article belongs to the Special Issue The Ecology and Evolution of SARS-CoV-2)

Review

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18 pages, 999 KiB  
Review
SARS-CoV-2 Affects Both Humans and Animals: What Is the Potential Transmission Risk? A Literature Review
by Antonio Santaniello, Giuseppe Perruolo, Serena Cristiano, Ayewa Lawoe Agognon, Serena Cabaro, Alessia Amato, Ludovico Dipineto, Luca Borrelli, Pietro Formisano, Alessandro Fioretti and Francesco Oriente
Microorganisms 2023, 11(2), 514; https://doi.org/10.3390/microorganisms11020514 - 17 Feb 2023
Cited by 4 | Viewed by 1753
Abstract
In March 2020, the World Health Organization Department declared the coronavirus (COVID-19) outbreak a global pandemic, as a consequence of its rapid spread on all continents. The COVID-19 pandemic has been not only a health emergency but also a serious general problem as [...] Read more.
In March 2020, the World Health Organization Department declared the coronavirus (COVID-19) outbreak a global pandemic, as a consequence of its rapid spread on all continents. The COVID-19 pandemic has been not only a health emergency but also a serious general problem as fear of contagion and severe restrictions put economic and social activity on hold in many countries. Considering the close link between human and animal health, COVID-19 might infect wild and companion animals, and spawn dangerous viral mutants that could jump back and pose an ulterior threat to us. The purpose of this review is to provide an overview of the pandemic, with a particular focus on the clinical manifestations in humans and animals, the different diagnosis methods, the potential transmission risks, and their potential direct impact on the human–animal relationship. Full article
(This article belongs to the Special Issue The Ecology and Evolution of SARS-CoV-2)
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18 pages, 1552 KiB  
Review
Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era
by Cameron M. Harrison, Jayden M. Doster, Emily H. Landwehr, Nidhi P. Kumar, Ethan J. White, Dia C. Beachboard and Christopher C. Stobart
Microorganisms 2023, 11(2), 445; https://doi.org/10.3390/microorganisms11020445 - 10 Feb 2023
Cited by 6 | Viewed by 3437
Abstract
Approximately 15–30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 [...] Read more.
Approximately 15–30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 has demonstrated not only the potential for significant disease caused by emerging coronaviruses, but also the capacity of novel coronaviruses to promote pandemic spread. Largely driven by the global response to the COVID-19 pandemic, significant research in coronavirus biology has led to advances in our understanding of these viruses. In this review, we evaluate the virology, emergence, and evolution of the four endemic coronaviruses associated with the common cold, their relationship to pandemic SARS-CoV-2, and discuss the potential for future emergent human coronaviruses. Full article
(This article belongs to the Special Issue The Ecology and Evolution of SARS-CoV-2)
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7 pages, 250 KiB  
Review
Literature Review of Omicron: A Grim Reality Amidst COVID-19
by Suraj Arora, Vishakha Grover, Priyanka Saluja, Youssef Abdullah Algarni, Shahabe Abullais Saquib, Shaik Mohammed Asif, Kavita Batra, Mohammed Y. Alshahrani, Gotam Das, Rajni Jain and Anchal Ohri
Microorganisms 2022, 10(2), 451; https://doi.org/10.3390/microorganisms10020451 - 16 Feb 2022
Cited by 37 | Viewed by 7284
Abstract
Coronavirus disease 2019 (COVID-19) first emerged in Wuhan city in December 2019, and became a grave global concern due to its highly infectious nature. The Severe Acute Respiratory Coronavirus-2, with its predecessors (i.e., MERS-CoV and SARS-CoV) belong to the family of Coronaviridae. [...] Read more.
Coronavirus disease 2019 (COVID-19) first emerged in Wuhan city in December 2019, and became a grave global concern due to its highly infectious nature. The Severe Acute Respiratory Coronavirus-2, with its predecessors (i.e., MERS-CoV and SARS-CoV) belong to the family of Coronaviridae. Reportedly, COVID-19 has infected 344,710,576 people around the globe and killed nearly 5,598,511 persons in the short span of two years. On November 24, 2021, B.1.1.529 strain, later named Omicron, was classified as a Variant of Concern (VOC). SARS-CoV-2 has continuously undergone a series of unprecedented mutations and evolved to exhibit varying characteristics. These mutations have largely occurred in the spike (S) protein (site for antibody binding), which attribute high infectivity and transmissibility characteristics to the Omicron strain. Although many studies have attempted to understand this new challenge in the COVID-19 strains race, there is still a lot to be demystified. Therefore, the purpose of this review was to summarize the structural or virologic characteristics, burden, and epidemiology of the Omicron variant and its potential to evade the immune response. Full article
(This article belongs to the Special Issue The Ecology and Evolution of SARS-CoV-2)
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