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Viruses
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Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination
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Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Coronaviruses".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 3960

Special Issue Editor

Prof. Dr. Maged Gomaa Hemida

E-Mail Website
Guest Editor
College of Veterinary Medicine, Long Island University, Brooklyn, NY, USA
Interests: molecular biology of coronaviruses; coronavirus/host interaction; One Health; roles of small RNA molecules in viral pathogenesis; development of novel vaccines against coronaviruses of livestock and avian species
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The COVID-19 pandemic made the global scientific community continuously monitor various coronaviruses at the genome level. The occurrence of mutations, the possibility of recombination between different coronaviruses strains and variants, and the possibilities of new host adaptation and species jump paved the way for the emergence of novel coronaviruses that affect humans and different species of animals and birds. Many research gaps hamper our understanding of the molecular biology of coronaviruses. The antigenic shift and drift of influenza viruses, as well as their ability to recombine, also substantially contributed to the emergence of new variants/strains and to their adaptation to new species. Thus, active research is needed to tackle several research objectives in the context of coronaviruses/influenza viruses, their hosts, and their interactions with the environment, including studies on (1) the molecular biology of coronaviruses/influenza viruses; (2) molecular evolution; (3) inter-species transmission; (4) virus/host interaction; the development of novel vaccines from some newly emerging strains/variants of coronaviruses infecting mammals and birds；(5) the development of novel diagnostic assays that keep up with the dynamic changes of coronaviruses at the genomic level, which hamper the success of certain recently developed diagnostic assays and vaccines. These strategies will help reduce the potential threats of an upcoming coronavirus pandemic.

Prof. Dr. Maged Gomaa Hemida
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • coronaviruses
  • influenza viruses
  • highly pathogenic influenza viruses
  • species jump
  • avian coronaviruses
  • porcine coronaviruses
  • vaccines
  • diagnostic assays
  • one health
  • virus/host interaction.

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Published Papers (4 papers)

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12 pages, 2610 KiB  
Communication
Novel Minimal Absent Words Detected in Influenza A Virus
by Elif Zülal Bigiş, Elif Yıldız, Anna Tagka, Athanasia Pavlopoulou, George P. Chrousos and Styliani Geronikolou
Viruses 2025, 17(5), 659; https://doi.org/10.3390/v17050659 (registering DOI) - 30 Apr 2025
Abstract
Influenza is a communicable disease caused by RNA viruses. Strains A (affecting animals, humans), B (affecting humans), C (affecting rarely humans and pigs), and D (affecting cattle) comprise a variety of substrains each. Influenza A strain, affecting both humans and animals, is considered [...] Read more.
Influenza is a communicable disease caused by RNA viruses. Strains A (affecting animals, humans), B (affecting humans), C (affecting rarely humans and pigs), and D (affecting cattle) comprise a variety of substrains each. Influenza A strain, affecting both humans and animals, is considered the most infectious, causing pandemics. There is an emerging need for the accurate classification of the different influenza A virus (IAV) subtypes, elucidating their mode of infection, as well as their fast and accurate diagnosis. Notably, in recent years, oligomeric sequences (words) that are present in the pathogen genomes and entirely absent from the host human genome were suggested to provide robust biomarkers for virus classification and rapid detection. To this end, we performed updated phylogenetic analyses of the IAV hemagglutinin genes, focusing on the sub H1N1 and H5N1. More importantly, we applied in silico methods to identify minimum length “words” that exist consistently in the IAV genomes and are entirely absent from the human genome; these sequences identified in our current analysis may represent minimal signatures that can be utilized to distinguish IAV from other influenza viruses, as well as to perform rapid diagnostic tests. Full article
(This article belongs to the Special Issue Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination)
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22 pages, 13356 KiB  
Article
Comparative Genome Sequencing Analysis of Some Novel Feline Infectious Peritonitis Viruses Isolated from Some Feral Cats in Long Island
by Abid Ullah Shah, Blanca Esparza, Oscar Illanes and Maged Gomaa Hemida
Viruses 2025, 17(2), 209; https://doi.org/10.3390/v17020209 - 31 Jan 2025
Viewed by 1040
Abstract
Feline infectious peritonitis virus (FIPV) remains as one of the leading causes of morbidity and mortality in young cats from shelters and catteries worldwide. Since little is known about the molecular characteristics of currently circulating FIPV strains in Long Island, New York, samples [...] Read more.
Feline infectious peritonitis virus (FIPV) remains as one of the leading causes of morbidity and mortality in young cats from shelters and catteries worldwide. Since little is known about the molecular characteristics of currently circulating FIPV strains in Long Island, New York, samples from two shelter cats submitted to the Pathology Diagnostic Services of the Long Island University College of Veterinary Medicine, with gross and microscopic lesions consistent with those of FIP were processed for virus isolation, molecular characterization and full-length genome decoding. The younger shelter cat, a 1-year-old male (A15) was found dead without previous signs of illness. Postmortem examination revealed gross and microscopic lesions characterized by vasculitis, necrosis, hemorrhage, and pyogranulomatous inflammation confined to the colon and associated lymph nodes. The second cat, a 7-year-old spayed female (A37) had an identical clinical history and similar but widespread lesions, including fibrinous peritoneal effusion, cecal, colonic, renal, and hepatic involvement. The gross and microscopic diagnosis of FIP in these cats was confirmed by immunohistochemistry (IHC) demonstration of feline coronavirus antigen using mouse anti-FIPV3-70 monoclonal antibody. Virus isolation from saved frozen kidney and colon tissue was performed through several subsequent blind passages in MDCK and Vero cell lines. Confirmation of the FIPV isolation was done through qRT-PCR, IFA, western blot using N protein antibodies, and NGS of the full-length genome sequencing. The full-length genome sequences of the virus isolate from the two cats were decoded using next-generation sequencing (NGS) and deposited in the GenBank as accession numbers PQ192636 and PQ202302. The genome size of these isolates was (29355 and 29321) nucleotides (nt) in length, respectively. While their genome organization was consistent with other FIPV genomes as follows (5’UTR-ORF1ab-S-3abc-M-E-7b-3’UTR-3’), marked differential mutations were observed in the ORF1a/b, S, 3Abc, and 7b protein genes of the two FIPV isolates. One notable deletion of 34 nucleotides was observed in the 7b genes of one of these isolates but was absent in the other. We confirmed the potential recombination events during the evolution of those two FIPV field isolates with the potential parent virus as FECoV-US isolated in 1970 and the potential minor parent as the Canine coronavirus. Our results provide a comprehensive molecular analysis of two novel FIPV isolates causing fatal disease in shelter cats from Long Island. Diagnostic surveillance with molecular characterization and sequencing analysis of circulating FIPV strains within animal shelters may help early detect unique emerging clinical and pathological manifestations of the disease and develop more targeted prophylactic and therapeutic approaches to control it. Full article
(This article belongs to the Special Issue Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination)
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24 pages, 3828 KiB  
Article
Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63
by Tamila Musaeva, Artem Fadeev, Maria Pisareva, Veronika Eder, Andrey Ksenafontov, Margarita Korzhanova, Valery Tsvetkov, Alexander Perederiy, Irina Kiseleva, Daria Danilenko, Dmitry Lioznov and Andrey Komissarov
Viruses 2025, 17(1), 13; https://doi.org/10.3390/v17010013 - 25 Dec 2024
Viewed by 1034
Abstract
Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In [...] Read more.
Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900–1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with >70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses. Full article
(This article belongs to the Special Issue Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination)
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9 pages, 699 KiB  
Brief Report
Novel Rodent Coronavirus-like Virus Detected Among Beef Cattle with Respiratory Disease in Mexico
by Ismaila Shittu, Judith U. Oguzie, Gustavo Hernández-Vidal, Gustavo Moreno-Degollado, Diego B. Silva, Lyudmyla V. Marushchak, Claudia M. Trujillo-Vargas, John A. Lednicky and Gregory C. Gray
Viruses 2025, 17(3), 433; https://doi.org/10.3390/v17030433 - 18 Mar 2025
Viewed by 1248
Abstract
In February 2024, while conducting surveillance for novel respiratory viruses, we studied four beef cattle farms near Monterrey, Mexico. Nasal swabs were collected from sick and healthy beef cattle along with 3 h aerosol samples. None of the samples had molecular evidence of [...] Read more.
In February 2024, while conducting surveillance for novel respiratory viruses, we studied four beef cattle farms near Monterrey, Mexico. Nasal swabs were collected from sick and healthy beef cattle along with 3 h aerosol samples. None of the samples had molecular evidence of influenza A viruses. Three (8%) of thirty-six nasal swabs collected from the four farms and four (33.3%) of the twelve bioaerosol specimens had molecular evidence of influenza D virus. Five sick cow nasal swabs and one bioaerosol sample on a single farm had molecular evidence of rodent coronavirus-like (RCoV), an alphacoronavirus. Three (60%) of the five RCoV-positive cattle nasal swabs also had molecular evidence of influenza D. Attempts to isolate the RCoV in Vero-E6, LLC-MK2, MDBK, and L-2 cells were unsuccessful. However, we were able to assemble ~60% of the RCoV genome using next-generation sequencing. The six RCoV-positive samples clustered with RCoV strains identified in China in 2021. During the last 12 months, we have studied an estimated 478 dairy and beef cattle nasal swabs on 11 farms in the US and Mexico, and these RCoV detections are the first we have encountered. While feed contamination cannot be ruled out, given the propensity of CoVs to jump species and that we detected RCoV only in the noses of sick cows on this one farm, we are concerned that these findings could represent an isolated RCoV spillover event. With this report, we are alerting veterinarians and cattle farm owners of our observations that RCoV may be a new cause of bovine respiratory disease. Full article
(This article belongs to the Special Issue Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination)
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