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Genomic Epidemiology of Viral Infections

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

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 45204

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Dr. Krisztián Bányai

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Guest Editor

Veterinary Medical Research Institute, Budapest, Hungary
Interests: virus discovery; metagenomics; genomic epidemiology
Special Issues, Collections and Topics in MDPI journals

Dr. István Kiss

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Guest Editor

Scientific Support and Investigation Unit, Ceva-Phylaxia Co., Ltd., Budapest, Hungary
Interests: viral diseases, diagnostics

Dr. György Lengyel

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Guest Editor

Laboratory of Epidemiological Virology, Hungarian Military Medical Centre, Budapest, Hungary
Interests: clinical virology; genomic epidemiology; infectology

Special Issue Information

Dear Colleagues,

The genomic epidemiology of virus infections is a fairly new research area that connects epidemiological data with viral genomics and sophisticated bioinformatics tools. This research area has benefited from new developments in laboratory tools designed to collect large amounts of genetic sequence data (i.e., high-throughput next-generation sequencers). Genomic epidemiology has been helpful to understand novel routes and modes of disease transmission, and has provided plausible scenarios for the origin of pathogens on an evolutionary time scale. For example, viral genomic data together with epidemiological and ecological data have helped to identify the origin of outbreaks or sites of pathogen incursion in recently emerged viral diseases, including Ebola in Africa, Zika virus infection in South America, subtype H5 avian influenza in circumpolar regions of the northern hemisphere, as well as SARS-CoV-2, the etiologic agent of the ongoing pandemic.

In this Thematic Issue of the journal Viruses, the Guest Editors wish to invite researchers to contribute new data related to the genome-sequence-based molecular epidemiology of viral infections. The Guest Editors hope that the collection of papers in this Thematic Issue will help promote molecular epidemiological studies to be placed on a new fundament. Viral diseases causing significant veterinary and/or public health burden are equally welcome.

Dr. Krisztián Bányai
Dr. István Kiss
Dr. György Lengyel
Guest Editors

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Published Papers (10 papers)

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11 pages, 2665 KiB

Open AccessCommunication

High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses

by Nikhil S. Sahajpal, Ashis K. Mondal, Allan Njau, Zachary Petty, Jiani Chen, Sudha Ananth, Pankaj Ahluwalia, Colin Williams, Ted M. Ross, Alka Chaubey, Grace DeSantis, Gary P. Schroth, Justin Bahl and Ravindra Kolhe

Viruses 2021, 13(10), 2063; https://doi.org/10.3390/v13102063 - 14 Oct 2021

Cited by 10 | Viewed by 4193

Abstract

Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. The isolates from the same county formed paraphyletic groups, indicating virus transmission between counties. The study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats and models that provide insights into viral transmission patterns and predict transmission/resurgence of regional outbreaks as well as providing critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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12 pages, 1277 KiB

Open AccessArticle

Genomic Characterisation of a Highly Divergent Siadenovirus (Psittacine Siadenovirus F) from the Critically Endangered Orange-Bellied Parrot (Neophema chrysogaster)

by Ajani Athukorala, David N. Phalen, Ashutosh Das, Karla J. Helbig, Jade K. Forwood and Subir Sarker

Viruses 2021, 13(9), 1714; https://doi.org/10.3390/v13091714 - 28 Aug 2021

Cited by 26 | Viewed by 4154

Abstract

Siadenoviruses have been detected in wild and captive birds worldwide. Only nine siadenoviruses have been fully sequenced; however, partial sequences for 30 others, many of these from wild Australian birds, are also described. Some siadenoviruses, e.g., the turkey siadenovirus A, can cause disease; however, most cause subclinical infections. An example of a siadenovirus causing predominately subclinical infections is psittacine siadenovirus 2, proposed name psittacine siadenovirus F (PsSiAdV-F), which is enzootic in the captive breeding population of the critically endangered orange-bellied parrot (OBP, Neophema chrysogaster). Here, we have fully characterised PsSiAdV-F from an OBP. The PsSiAdV-F genome is 25,392 bp in length and contained 25 putative genes. The genome architecture of PsSiAdV-F exhibited characteristics similar to members within the genus Siadenovirus; however, the novel PsSiAdV-F genome was highly divergent, showing highest and lowest sequence similarity to skua siadenovirus A (57.1%) and psittacine siadenovirus D (31.1%), respectively. Subsequent phylogenetic analyses of the novel PsSiAdV-F genome positioned the virus into a phylogenetically distinct sub-clade with all other siadenoviruses and did not show any obvious close evolutionary relationship. Importantly, the resulted tress continually demonstrated that novel PsSiAdV-F evolved prior to all known members except the frog siadenovirus A in the evolution and possibly the ancestor of the avian siadenoviruses. To date, PsSiAdV-F has not been detected in wild parrots, so further studies screening PsSiAdV-F in wild Australian parrots and generating whole genome sequences of siadenoviruses of Australian native passerine species is recommended to fill the siadenovirus evolutionary gaps. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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12 pages, 1353 KiB

Open AccessArticle

Molecular Characterization of Highly Pathogenic Avian Influenza Viruses H5N6 Detected in Denmark in 2018–2019

by Yuan Liang, Jesper Schak Krog, Pia Ryt-Hansen, Anders Gorm Pedersen, Lise Kirstine Kvisgaard, Elisabeth Holm, Pernille Dahl Nielsen, Anne Sofie Hammer, Jesper Johannes Madsen, Kasper Thorup, Lars Erik Larsen and Charlotte Kristiane Hjulsager

Viruses 2021, 13(6), 1052; https://doi.org/10.3390/v13061052 - 2 Jun 2021

Cited by 14 | Viewed by 3793

Abstract

Beginning in late 2017, highly pathogenic avian influenza (HPAI) H5N6 viruses caused outbreaks in wild birds and poultry in several European countries. H5N6 viruses were detected in 43 wild birds found dead throughout Denmark. Most of the Danish virus-positive dead birds were found in the period from February to April 2018. However, unlike the rest of Europe, sporadic HPAI H5N6-positive dead wild birds were detected in Denmark in July, August, September, and December 2018, with the last positive bird being found in January 2019. HPAI viruses were not detected in active surveillance of apparently healthy wild birds. In this study, we use full genome sequencing and phylogenetic analysis to investigate the wild bird HPAI H5N6 viruses found in Denmark. The Danish viruses were found to be closely related to those of contemporary HPAI H5N6 viruses detected in Europe. Their sequences formed two clusters indicating that at least two or more introductions of H5N6 into Denmark occurred. Notably, all viruses detected in the latter half of 2018 and in 2019 grouped into the same cluster. The H5N6 viruses appeared to have been maintained undetected in the autumn 2018. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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11 pages, 2363 KiB

Open AccessArticle

Genetic Insights into Feline Parvovirus: Evaluation of Viral Evolutionary Patterns and Association between Phylogeny and Clinical Variables

by Claudia Maria Tucciarone, Giovanni Franzo, Matteo Legnardi, Elena Lazzaro, Andrea Zoia, Matteo Petini, Tommaso Furlanello, Marco Caldin, Mattia Cecchinato and Michele Drigo

Viruses 2021, 13(6), 1033; https://doi.org/10.3390/v13061033 - 30 May 2021

Cited by 14 | Viewed by 3308

Abstract

Feline panleukopenia is a severe disease of cats caused by feline parvovirus (FPV), and marginally canine parvovirus (CPV). Despite being less rapid than CPV, FPV evolution deserves attention, especially since outbreaks of particular severity are currently reported. This apparently different virulence needs monitoring from genetic and clinical points of view. This manuscript explored FPV molecular epidemiology at both Italian and international levels and the possible association between viral phylogeny and disease severity. Sequences from clinical cases of feline panleukopenia in Italy were obtained from 2011 to 2019, and the etiological agent was characterized, distinguishing FPV from CPV. Phylogenetic and phylodynamic analyses were conducted on Italian and international sequences. Moreover, the association between the viral sequence and clinical variables was evaluated on a group of highly characterized patients. After its origin in the 1920s, FPV showed a constant population size until a more recent expansion since 2000. Few long-distance introduction events characterized FPV spreading, however, most of its evolution occurred locally. Although without a strong statistical association, several clinical variables appeared influenced by viral phylogeny, suggesting a differential virulence potentially characterizing FPV strains. These results stress the importance of the continuous study of viral evolution and its repercussions on the disease clinical aspects. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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13 pages, 1903 KiB

Open AccessArticle

An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India

by Pragya D. Yadav, Dimpal A. Nyayanit, Triparna Majumdar, Savita Patil, Harmanmeet Kaur, Nivedita Gupta, Anita M. Shete, Priyanka Pandit, Abhinendra Kumar, Neeraj Aggarwal, Jitendra Narayan, Neetu Vijay, Usha Kalawat, Attayur P. Sugunan, Ashok Munivenkatappa, Tara Sharma, Sulochna Devi, Tapan Majumdar, Subhash Jaryal, Rupinder Bakshi, Yash Joshi, Rima Sahay, Jayanti Shastri, Mini Singh, Manoj Kumar, Vinita Rawat, Shanta Dutta, Sarita Yadav, Kaveri Krishnasamy, Sharmila Raut, Debasis Biswas, Biswajyoti Borkakoty, Santwana Verma, Sudha Rani, Hirawati Deval, Disha Patel, Jyotirmayee Turuk, Bharti Malhotra, Bashir Fomda, Vijaylakshmi Nag, Amita Jain, Anudita Bhargava, Varsha Potdar, Sarah Cherian, Priya Abraham, Anjani Gopal, Samiran Panda and Balram Bhargava Show full author list Hide full author list

Viruses 2021, 13(5), 925; https://doi.org/10.3390/v13050925 - 17 May 2021

Cited by 27 | Viewed by 6404

Abstract

The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the ‘GH’ clade, whereas the southern part reported the ‘GR’, with a few exceptions. These sequences also revealed the presence of single independent mutations—E484Q and N440K—from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January–August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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13 pages, 2987 KiB

Open AccessArticle

Recombination Events Shape the Genomic Evolution of Infectious Bronchitis Virus in Europe

by Krisztina Bali, Ádám Bálint, Attila Farsang, Szilvia Marton, Borbála Nagy, Eszter Kaszab, Sándor Belák, Vilmos Palya and Krisztián Bányai

Viruses 2021, 13(4), 535; https://doi.org/10.3390/v13040535 - 24 Mar 2021

Cited by 22 | Viewed by 3603

Abstract

Infectious bronchitis of chicken is a high morbidity and mortality viral disease affecting the poultry industry worldwide; therefore, a better understanding of this pathogen is of utmost importance. The primary aim of this study was to obtain a deeper insight into the genomic diversity of field infectious bronchitis virus (IBV) strains using phylogenetic and recombination analysis. We sequenced the genome of 20 randomly selected strains from seven European countries. After sequencing, we created a genome sequence data set that contained 36 European origin field isolates and 33 vaccine strains. When analyzing these 69 IBV genome sequences, we identified 215 recombination events highlighting that some strains had multiple recombination breaking points. Recombination hot spots were identified mostly in the regions coding for non-structural proteins, and multiple recombination hot spots were identified in the nsp2, nsp3, nsp8, and nsp12 coding regions. Recombination occurred among different IBV genotypes and involved both field and vaccine IBV strains. Ninety percent of field strains and nearly half of vaccine strains showed evidence of recombination. Despite the low number and the scattered geographical and temporal origin of whole-genome sequence data collected from European Gammacoronaviruses, this study underlines the importance of recombination as a major evolutionary mechanism of IBVs. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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21 pages, 6417 KiB

Open AccessArticle

The Novel Genetic Background of Infectious Bursal Disease Virus Strains Emerging from the Action of Positive Selection

by Anna Pikuła, Anna Lisowska, Agnieszka Jasik and Lester J. Perez

Viruses 2021, 13(3), 396; https://doi.org/10.3390/v13030396 - 2 Mar 2021

Cited by 11 | Viewed by 2838

Abstract

The circulation in Europe of novel reassortant strains of infectious bursal disease virus (IBDV), containing a unique genetic background composition, represents a serious problem for animal health. Since the emergence of this novel IBDV mosaic was first described in Poland, this scenario has become particularly attractive to uncover the evolutionary forces driving the genetic diversity of IBDV populations. This study additionally addressed the phenotypic characterization of these emergent strains, as well as the main features affecting the viral fitness during the competition process of IBDV lineages in the field. Our results showed how different evolutionary mechanisms modulate the genetic diversity of co-existent IBDV lineages, leading to the error catastrophe effect, Muller ratchet effect, or prevalence, depending on their genetic compositions. We also determined that the action of the positive selection pressure, depending on the genomic segment on which it is acting, can drive two main phenotypes for IBDV: immune-escaping strains from the selection on segment A or strains with functional advantages from the selection on segment B. This last group seems to possess an increased fitness landscape in the viral quasispecies composition, presenting better adaptability to dissimilar environmental conditions and likely becoming the dominant population. The reassortant strains also exhibited a lower mortality rate compared with the well-known vvIBDV strains, which can facilitate their spreading. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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10 pages, 1378 KiB

Open AccessArticle

Multiple SARS-CoV-2 Introductions Shaped the Early Outbreak in Central Eastern Europe: Comparing Hungarian Data to a Worldwide Sequence Data-Matrix

by Gábor Kemenesi, Safia Zeghbib, Balázs A Somogyi, Gábor Endre Tóth, Krisztián Bányai, Norbert Solymosi, Peter M Szabo, István Szabó, Ádám Bálint, Péter Urbán, Róbert Herczeg, Attila Gyenesei, Ágnes Nagy, Csaba István Pereszlényi, Gergely Csaba Babinszky, Gábor Dudás, Gabriella Terhes, Viktor Zöldi, Róbert Lovas, Szabolcs Tenczer, László Kornya and Ferenc Jakab Show full author list Hide full author list

Viruses 2020, 12(12), 1401; https://doi.org/10.3390/v12121401 - 6 Dec 2020

Cited by 7 | Viewed by 4562

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 is the third highly pathogenic human coronavirus in history. Since the emergence in Hubei province, China, during late 2019, the situation evolved to pandemic level. Following China, Europe was the second epicenter of the pandemic. To better comprehend the detailed founder mechanisms of the epidemic evolution in Central-Eastern Europe, particularly in Hungary, we determined the full-length SARS-CoV-2 genomes from 32 clinical samples collected from laboratory confirmed COVID-19 patients over the first month of disease in Hungary. We applied a haplotype network analysis on all available complete genomic sequences of SARS-CoV-2 from GISAID database as of 21 April 2020. We performed additional phylogenetic and phylogeographic analyses to achieve the recognition of multiple and parallel introductory events into our region. Here, we present a publicly available network imaging of the worldwide haplotype relations of SARS-CoV-2 sequences and conclude the founder mechanisms of the outbreak in Central-Eastern Europe. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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11 pages, 1852 KiB

Open AccessBrief Report

Genomic Epidemiology and Evolution of Duck Hepatitis A Virus

by Enikő Fehér, Szilvia Jakab, Krisztina Bali, Eszter Kaszab, Borbála Nagy, Katalin Ihász, Ádám Bálint, Vilmos Palya and Krisztián Bányai

Viruses 2021, 13(8), 1592; https://doi.org/10.3390/v13081592 - 11 Aug 2021

Cited by 7 | Viewed by 6758

Abstract

Duck hepatitis A virus (DHAV), an avian picornavirus, causes high-mortality acute disease in ducklings. Among the three serotypes, DHAV-1 is globally distributed, whereas DHAV-2 and DHAV-3 serotypes are chiefly restricted to Southeast Asia. In this study, we analyzed the genomic evolution of DHAV-1 strains using extant GenBank records and genomic sequences of 10 DHAV-1 strains originating from a large disease outbreak in 2004–2005, in Hungary. Recombination analysis revealed intragenotype recombination within DHAV-1 as well as intergenotype recombination events involving DHAV-1 and DHAV-3 strains. The intergenotype recombination occurred in the VP0 region. Diversifying selection seems to act at sites of certain genomic regions. Calculations estimated slightly lower rates of evolution of DHAV-1 (mean rates for individual protein coding regions, 5.6286 × 10⁻⁴ to 1.1147 × 10⁻³ substitutions per site per year) compared to other picornaviruses. The observed evolutionary mechanisms indicate that whole-genome-based analysis of DHAV strains is needed to better understand the emergence of novel strains and their geographical dispersal. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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9 pages, 2004 KiB

Open AccessBrief Report

Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster

by Nicole Pedro, Veronica Fernandes, Bruno Cavadas, João Tiago Guimarães, Henrique Barros, Margarida Tavares and Luisa Pereira

Viruses 2021, 13(6), 1116; https://doi.org/10.3390/v13061116 - 10 Jun 2021

Cited by 3 | Viewed by 3560

Abstract

Field epidemiology and viral sequencing provide a comprehensive characterization of transmission chains and allow a better identification of superspreading events. However, very few examples have been presented to date during the COVID-19 pandemic. We studied the first COVID-19 cluster detected in Portugal (59 individuals involved amongst extended family and work environments), following the return of four related individuals from work trips to Italy. The first patient to introduce the virus would be misidentified following the traditional field inquiry alone, as shown by the viral sequencing in isolates from 23 individuals. The results also pointed out family, and not work environment, as the primary mode of transmission. Full article

(This article belongs to the Special Issue Genomic Epidemiology of Viral Infections)

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