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20 pages, 2952 KiB

Open AccessArticle

Low Pathogenicity H7N3 Avian Influenza Viruses Have Higher Within-Host Genetic Diversity Than a Closely Related High Pathogenicity H7N3 Virus in Infected Turkeys and Chickens

by Christina M. Leyson, Miriã F. Criado, Sungsu Youk and Mary J. Pantin-Jackwood

Viruses 2022, 14(3), 554; https://doi.org/10.3390/v14030554 - 08 Mar 2022

Cited by 1 | Viewed by 2506

Abstract

Within-host viral diversity offers a view into the early stages of viral evolution occurring after a virus infects a host. In recent years, advances in deep sequencing have allowed for routine identification of low-frequency variants, which are important sources of viral genetic diversity [...] Read more.

Within-host viral diversity offers a view into the early stages of viral evolution occurring after a virus infects a host. In recent years, advances in deep sequencing have allowed for routine identification of low-frequency variants, which are important sources of viral genetic diversity and can potentially emerge as a major virus population under certain conditions. We examined within-host viral diversity in turkeys and chickens experimentally infected with closely related H7N3 avian influenza viruses (AIVs), specifically one high pathogenicity AIV (HPAIV) and two low pathogenicity AIV (LPAIVs) with different neuraminidase protein stalk lengths. Consistent with the high mutation rates of AIVs, an abundance of intra-host single nucleotide variants (iSNVs) at low frequencies of 2–10% was observed in all samples collected. Furthermore, a small number of common iSNVs were observed between turkeys and chickens, and between directly inoculated and contact-exposed birds. Notably, the LPAIVs have significantly higher iSNV diversities and frequencies of nonsynonymous changes than the HPAIV in both turkeys and chickens. These findings highlight the dynamics of AIV populations within hosts and the potential impact of genetic changes, including mutations in the hemagglutinin gene that confers the high pathogenicity pathotype, on AIV virus populations and evolution. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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14 pages, 2019 KiB

Open AccessArticle

Spatiotemporal Dynamics, Evolutionary History and Zoonotic Potential of Moroccan H9N2 Avian Influenza Viruses from 2016 to 2021

by Fatiha El Mellouli, Mohamed Mouahid, Alice Fusaro, Bianca Zecchin, Hasnae Zekhnini, Abderrazak El Khantour, Edoardo Giussani, Elisa Palumbo, Hamid Rguibi Idrissi, Isabella Monne and Abdelaziz Benhoussa

Viruses 2022, 14(3), 509; https://doi.org/10.3390/v14030509 - 01 Mar 2022

Cited by 7 | Viewed by 3135

Abstract

The H9N2 virus continues to spread in wild birds and poultry worldwide. At the beginning of 2016, the H9N2 Avian influenza virus (AIV) was detected in Morocco for the first time; despite the implementation of vaccination strategies to control the disease, the virus [...] Read more.

The H9N2 virus continues to spread in wild birds and poultry worldwide. At the beginning of 2016, the H9N2 Avian influenza virus (AIV) was detected in Morocco for the first time; despite the implementation of vaccination strategies to control the disease, the virus has become endemic in poultry in the country. The present study was carried out to investigate the origins, zoonotic potential, as well as the impact of vaccination on the molecular evolution of Moroccan H9N2 viruses. Twenty-eight (28) H9N2 viruses collected from 2016 to 2021 in Moroccan poultry flocks were isolated and their whole genomes sequenced. Phylogenetic and evolutionary analyses showed that Moroccan H9N2 viruses belong to the G1-like lineage and are closely related to viruses isolated in Africa and the Middle East. A high similarity among all the 2016–2017 hemagglutinin sequences was observed, while the viruses identified in 2018–2019 and 2020–2021 were separated from their 2016–2017 ancestors by long branches. Mutations in the HA protein associated with antigenic drift and increased zoonotic potential were also found. The Bayesian phylogeographic analyses revealed the Middle East as being the region where the Moroccan H9N2 virus may have originated, before spreading to the other African countries. Our study is the first comprehensive analysis of the evolutionary history of the H9N2 viruses in the country, highlighting their zoonotic potential and pointing out the importance of implementing effective monitoring systems. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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17 pages, 2726 KiB

Open AccessArticle

Genetic Variability among Swine Influenza Viruses in Italy: Data Analysis of the Period 2017–2020

by Chiara Chiapponi, Alice Prosperi, Ana Moreno, Laura Baioni, Silvia Faccini, Roberta Manfredi, Irene Zanni, Valentina Gabbi, Irene Calanchi, Alice Fusaro, Maria Serena Beato, Lara Cavicchio, Camilla Torreggiani, Giovanni Loris Alborali and Andrea Luppi

Viruses 2022, 14(1), 47; https://doi.org/10.3390/v14010047 - 28 Dec 2021

Cited by 7 | Viewed by 2034

Abstract

Swine play an important role in the ecology of influenza A viruses (IAVs), acting as mixing vessels. Swine (sw) IAVs of H1N1 (including H1N1pdm09), H3N2, and H1N2 subtypes are enzootic in pigs globally, with different geographic distributions. This study investigated the genetic diversity [...] Read more.

Swine play an important role in the ecology of influenza A viruses (IAVs), acting as mixing vessels. Swine (sw) IAVs of H1N1 (including H1N1pdm09), H3N2, and H1N2 subtypes are enzootic in pigs globally, with different geographic distributions. This study investigated the genetic diversity of swIAVs detected during passive surveillance of pig farms in Northern Italy between 2017 and 2020. A total of 672 samples, IAV-positive according to RT-PCR, were subtyped by multiplex RT-PCR. A selection of strains was fully sequenced. High genotypic diversity was detected among the H1N1 and H1N2 strains, while the H3N2 strains showed a stable genetic pattern. The hemagglutinin of the H1Nx swIAVs belonged to HA-1A, HA-1B, and HA-1C lineages. Increasing variability was found in HA-1C strains with the circulation of HA-1C.2, HA-1C.2.1 and HA-1C.2.2 sublineages. Amino acid deletions in the HA-1C receptor binding site were observed and antigenic drift was confirmed. HA-1B strains were mostly represented by the Δ146-147 Italian lineage HA-1B.1.2.2, in combination with the 1990s human-derived NA gene. One antigenic variant cluster in HA-1A strains was identified in 2020. SwIAV circulation in pigs must be monitored continuously since the IAVs’ evolution could generate strains with zoonotic potential. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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18 pages, 2603 KiB

Open AccessEditor’s ChoiceArticle

Heterogeneity of Early Host Response to Infection with Four Low-Pathogenic H7 Viruses with a Different Evolutionary History in the Field

by Gianpiero Zamperin, Alice Bianco, Jacqueline Smith, Alessio Bortolami, Lonneke Vervelde, Alessia Schivo, Andrea Fortin, Sabrina Marciano, Valentina Panzarin, Eva Mazzetto, Adelaide Milani, Yohannes Berhane, Paul Digard, Francesco Bonfante and Isabella Monne

Viruses 2021, 13(11), 2323; https://doi.org/10.3390/v13112323 - 21 Nov 2021

Cited by 5 | Viewed by 10799

Abstract

Once low-pathogenic avian influenza viruses (LPAIVs) of the H5 and H7 subtypes from wild birds enter into poultry species, there is the possibility of them mutating into highly pathogenic avian influenza viruses (HPAIVs), resulting in severe epizootics with up to 100% mortality. This [...] Read more.

Once low-pathogenic avian influenza viruses (LPAIVs) of the H5 and H7 subtypes from wild birds enter into poultry species, there is the possibility of them mutating into highly pathogenic avian influenza viruses (HPAIVs), resulting in severe epizootics with up to 100% mortality. This mutation from a LPAIV to HPAIV strain is the main cause of an AIV’s major economic impact on poultry production. Although AIVs are inextricably linked to their hosts in their evolutionary history, the contribution of host-related factors in the emergence of HPAI viruses has only been marginally explored so far. In this study, transcriptomic sequencing of tracheal tissue from chickens infected with four distinct LP H7 viruses, characterized by a different history of pathogenicity evolution in the field, was implemented. Despite the inoculation of a normalized infectious dose of viruses belonging to the same subtype (H7) and pathotype (LPAI), the use of animals of the same age, sex and species as well as the identification of a comparable viral load in the target samples, the analyses revealed a heterogeneity in the gene expression profile in response to infection with each of the H7 viruses administered. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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11 pages, 1409 KiB

Open AccessArticle

Evolutionary Dynamics of H5 Highly Pathogenic Avian Influenza Viruses (Clade 2.3.4.4B) Circulating in Bulgaria in 2019–2021

by Bianca Zecchin, Gabriela Goujgoulova, Isabella Monne, Annalisa Salviato, Alessia Schivo, Iskra Slavcheva, Ambra Pastori, Ian H. Brown, Nicola S. Lewis, Calogero Terregino and Alice Fusaro

Viruses 2021, 13(10), 2086; https://doi.org/10.3390/v13102086 - 16 Oct 2021

Cited by 10 | Viewed by 2735

Abstract

The first detection of a Highly Pathogenic Avian Influenza (HPAI) H5N8 virus in Bulgaria dates back to December 2016. Since then, many outbreaks caused by HPAI H5 viruses from clade 2.3.4.4B have been reported in both domestic and wild birds in different regions [...] Read more.

The first detection of a Highly Pathogenic Avian Influenza (HPAI) H5N8 virus in Bulgaria dates back to December 2016. Since then, many outbreaks caused by HPAI H5 viruses from clade 2.3.4.4B have been reported in both domestic and wild birds in different regions of the country. In this study, we characterized the complete genome of sixteen H5 viruses collected in Bulgaria between 2019 and 2021. Phylogenetic analyses revealed a persistent circulation of the H5N8 strain for four consecutive years (December 2016–June 2020) and the emergence in 2020 of a novel reassortant H5N2 subtype, likely in a duck farm. Estimation of the time to the most recent common ancestor indicates that this reassortment event may have occurred between May 2019 and January 2020. At the beginning of 2021, Bulgaria experienced a new virus introduction in the poultry sector, namely a HPAI H5N8 that had been circulating in Europe since October 2020. The periodical identification in domestic birds of H5 viruses related to the 2016 epidemic as well as a reassortant strain might indicate undetected circulation of the virus in resident wild birds or in the poultry sector. To avoid the concealed circulation and evolution of viruses, and the risk of emergence of strains with pandemic potential, the implementation of control measures is of utmost importance, particularly in duck farms where birds display no clinical signs. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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8 pages, 713 KiB

Open AccessCommunication

Live Bird Markets in Nigeria: A Potential Reservoir for H9N2 Avian Influenza Viruses

by Lanre Sulaiman, Ismaila Shittu, Alice Fusaro, Bitrus Inuwa, Bianca Zecchin, Dorcas Gado, Alessia Schivo, Alice Bianco, Agnes Laleye, Federica Gobbo, Columba Vakuru, Tony Joannis, Isabella Monne and Clement Meseko

Viruses 2021, 13(8), 1445; https://doi.org/10.3390/v13081445 - 24 Jul 2021

Cited by 9 | Viewed by 2582

Abstract

Since 2006, multiple outbreaks of avian influenza (AI) have been reported in Nigeria involving different subtypes. Surveillance and molecular epidemiology have revealed the vital role of live bird markets (LBMs) in the dissemination of AI virus to commercial poultry farms. To better understand [...] Read more.

Since 2006, multiple outbreaks of avian influenza (AI) have been reported in Nigeria involving different subtypes. Surveillance and molecular epidemiology have revealed the vital role of live bird markets (LBMs) in the dissemination of AI virus to commercial poultry farms. To better understand the ecology and epidemiology of AI in Nigeria, we performed whole-genome sequencing of nineteen H9N2 viruses recovered, from apparently healthy poultry species, during active surveillance conducted in nine LBMs across Nigeria in 2019. Analyses of the HA gene segment of these viruses showed that the H9N2 strains belong to the G1 lineage, which has zoonotic potential, and are clustered with contemporary H9N2 identified in Africa between 2016 and 2020. We observed two distinct clusters of H9N2 viruses in Nigeria, suggesting different introductions into the country. In view of the zoonotic potential of H9N2 and the co-circulation of multiple subtypes of AI virus in Nigeria, continuous monitoring of the LBMs across the country and molecular characterization of AIVs identified is advocated to mitigate economic losses and public health threats. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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11 pages, 3029 KiB

Open AccessCommunication

Multiple Reassortants of H5N8 Clade 2.3.4.4b Highly Pathogenic Avian Influenza Viruses Detected in South Korea during the Winter of 2020–2021

by Yoon-Gi Baek, Yu-Na Lee, Dong-Hun Lee, Jae-in Shin, Ji-Ho Lee, David H. Chung, Eun-Kyoung Lee, Gyeong-Beom Heo, Mingeun Sagong, Soo-Jeong Kye, Kwang-Nyeong Lee, Myoung-Heon Lee and Youn-Jeong Lee

Viruses 2021, 13(3), 490; https://doi.org/10.3390/v13030490 - 16 Mar 2021

Cited by 47 | Viewed by 4189

Abstract

During October 2020–January 2021, we isolated a total of 67 highly pathogenic avian influenza (HPAI) H5N8 viruses from wild birds and outbreaks in poultry in South Korea. We sequenced the isolates and performed phylogenetic analysis of complete genome sequences to determine the origin, [...] Read more.

During October 2020–January 2021, we isolated a total of 67 highly pathogenic avian influenza (HPAI) H5N8 viruses from wild birds and outbreaks in poultry in South Korea. We sequenced the isolates and performed phylogenetic analysis of complete genome sequences to determine the origin, evolution, and spread patterns of these viruses. Phylogenetic analysis of the hemagglutinin (HA) gene showed that all the isolates belong to H5 clade 2.3.4.4 subgroup B (2.3.4.4b) and form two distinct genetic clusters, G1 and G2. The cluster G1 was closely related to the 2.3.4.4b H5N8 HPAI viruses detected in Europe in early 2020, while the cluster G2 had a close genetic relationship with the 2.3.4.4b H5N8 viruses that circulated in Europe in late 2020. A total of seven distinct genotypes were identified, including five novel reassortants carrying internal genes of low pathogenic avian influenza viruses. Our Bayesian discrete trait phylodynamic analysis between host types suggests that the viruses initially disseminated from migratory waterfowl to domestic duck farms in South Korea. Subsequently, domestic duck farms most likely contributed to the transmission of HPAI viruses to chicken and minor poultry farms, highlighting the need for enhanced, high levels of biosecurity measures at domestic duck farms to effectively prevent the introduction and spread of HPAI. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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13 pages, 1868 KiB

Open AccessArticle

Spatiotemporal Dynamics of Highly Pathogenic Avian Influenza Subtype H5N8 in Poultry Farms, South Korea

by Woo-Hyun Kim, Sun Hak Bae and Seongbeom Cho

Viruses 2021, 13(2), 274; https://doi.org/10.3390/v13020274 - 10 Feb 2021

Cited by 9 | Viewed by 2823

Abstract

Highly pathogenic avian influenza (HPAI), a zoonotic disease, is a major threat to humans and poultry health worldwide. In January 2014, HPAI virus subtype H5N8 first infected poultry farms in South Korea, and 393 outbreaks, overall, were reported with enormous economic damage in [...] Read more.

Highly pathogenic avian influenza (HPAI), a zoonotic disease, is a major threat to humans and poultry health worldwide. In January 2014, HPAI virus subtype H5N8 first infected poultry farms in South Korea, and 393 outbreaks, overall, were reported with enormous economic damage in the poultry industry. We analyzed the spatiotemporal distribution of HPAI H5N8 outbreaks in poultry farms using the global and local spatiotemporal interaction analyses in the first (January to July 2014) and second (September 2014 to June 2015) outbreak waves. The space–time K-function analyses revealed significant interactions within three days and in an over-40 km space–time window between the two study periods. The excess risk attributable value (D₀) was maintained despite the distance in the case of HPAI H5N8 in South Korea. Eleven spatiotemporal clusters were identified, and the results showed that the HPAI introduction was from the southwestern region, and spread to the middle region, in South Korea. This spatiotemporal interaction indicates that the HPAI epidemic in South Korea was mostly characterized by short period transmission, regardless of the distance. This finding supports strict control strategies such as preemptive depopulation, and poultry movement tracking. Further studies are needed to understand HPAI disease transmission patterns. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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11 pages, 1900 KiB

Open AccessArticle

A New Variant among Newcastle Disease Viruses Isolated in the Democratic Republic of the Congo in 2018 and 2019

by Augustin T. Twabela, Lam Thanh Nguyen, Justin Masumu, Patrick Mpoyo, Serge Mpiana, Julienne Sumbu, Masatoshi Okamatsu, Keita Matsuno, Norikazu Isoda, Bianca Zecchin, Isabella Monne and Yoshihiro Sakoda

Viruses 2021, 13(2), 151; https://doi.org/10.3390/v13020151 - 20 Jan 2021

Cited by 9 | Viewed by 2083

Abstract

Newcastle disease (ND) is a highly transmissible and devastating disease that affects poultry and wild birds worldwide. Comprehensive knowledge regarding the characteristics and epidemiological factors of the ND virus (NDV) is critical for the control and prevention of ND. Effective vaccinations can prevent [...] Read more.

Newcastle disease (ND) is a highly transmissible and devastating disease that affects poultry and wild birds worldwide. Comprehensive knowledge regarding the characteristics and epidemiological factors of the ND virus (NDV) is critical for the control and prevention of ND. Effective vaccinations can prevent and control the spread of the NDV in poultry populations. For decades, the Democratic Republic of the Congo (DRC) has reported the impacts of ND on commercial and traditional poultry farming systems. The reports were preliminary clinical observations, and few cases were confirmed in the laboratory. However, data on the phylogenetic, genetic, and virological characteristics of NDVs circulating in the DRC are not available. In this study, the whole-genome sequences of three NDV isolates obtained using the next-generation sequencing method revealed two isolates that were a new variant of NDV, and one isolate that was clustered in the subgenotype VII.2. All DRC isolates were velogenic and were antigenically closely related to the vaccine strains. Our findings reveal that despite the circulation of the new variant, ND can be controlled in the DRC using the current vaccine. However, epidemiological studies should be conducted to elucidate the endemicity of the disease so that better control strategies can be implemented. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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13 pages, 1211 KiB

Open AccessArticle

Can Coronaviruses Steal Genes from the Host as Evidenced in Western European Hedgehogs by EriCoV Genetic Characterization?

by Luca De Sabato, Ilaria Di Bartolo, Maria Alessandra De Marco, Ana Moreno, Davide Lelli, Claudia Cotti, Mauro Delogu and Gabriele Vaccari

Viruses 2020, 12(12), 1471; https://doi.org/10.3390/v12121471 - 20 Dec 2020

Cited by 5 | Viewed by 5488

Abstract

Due to their need for living cells, viruses have developed adaptive evolutionary strategies to survive and perpetuate in reservoir hosts that play a crucial role in the ecology of emerging pathogens. Pathogenic and potentially pandemic betacoronaviruses arose in humans in 2002 (SARS-CoV, disappeared [...] Read more.

Due to their need for living cells, viruses have developed adaptive evolutionary strategies to survive and perpetuate in reservoir hosts that play a crucial role in the ecology of emerging pathogens. Pathogenic and potentially pandemic betacoronaviruses arose in humans in 2002 (SARS-CoV, disappeared in July 2003), 2012 (MERS-CoV, still circulating in Middle East areas), and 2019 (SARS-CoV-2, causing the current global pandemic). As universally recognized, bats host ancestors of the above-mentioned zoonotic viruses. However, hedgehogs have been recently identified in Europe and Asia as possible reservoirs of MERS-CoV-like strains classified as Erinaceus coronavirus (EriCoV). To elucidate the evolution and genetics of EriCoVs, NGS (next generation sequencing) and Sanger sequencing were used to examine fecal samples collected in Northern Italy in 2018/2019 from 12 hedgehogs previously found EriCoV-positive by RT-PCR. By sequence analysis, eight complete EriCoV genomes, obtained by NGS, showed a high phylogenetic correlation with EriCoV strains previously reported in Eurasia. Interestingly, eight viral strains presented an additional ORF encoding for the CD200 ortholog located between the genes encoding for the Spike and the ORF3a proteins. The CD200 ortholog sequences were closely similar to the host CD200 protein but varying among EriCoVs. The result, confirmed by Sanger sequencing, demonstrates for the first time that CoVs can acquire host genes potentially involved in the immune-modulatory cascade and possibly enabling the virus to escape the host defence. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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7 pages, 600 KiB

Open AccessCommunication

Highly Pathogenic Avian Influenza Clade 2.3.4.4b Subtype H5N8 Virus Isolated from Mandarin Duck in South Korea, 2020

by Sol Jeong, Dong-Hun Lee, Jung-Hoon Kwon, Yu-Jin Kim, Sun-Hak Lee, Andrew Y. Cho, Tae-Hyeon Kim, Jung-Eun Park, Song-I Lee and Chang-Seon Song

Viruses 2020, 12(12), 1389; https://doi.org/10.3390/v12121389 - 04 Dec 2020

Cited by 30 | Viewed by 3639

Abstract

In October 2020, a highly pathogenic avian influenza (HPAI) subtype H5N8 virus was identified from a fecal sample of a wild mandarin duck (Aix galericulata) in South Korea. We sequenced all eight genome segments of the virus, designated as A/Mandarin duck/Korea/K20-551-4/2020(H5N8), [...] Read more.

In October 2020, a highly pathogenic avian influenza (HPAI) subtype H5N8 virus was identified from a fecal sample of a wild mandarin duck (Aix galericulata) in South Korea. We sequenced all eight genome segments of the virus, designated as A/Mandarin duck/Korea/K20-551-4/2020(H5N8), and conducted genetic characterization and comparative phylogenetic analysis to track its origin. Genome sequencing and phylogenetic analysis show that the hemagglutinin gene belongs to H5 clade 2.3.4.4 subgroup B. All genes share high levels of nucleotide identity with H5N8 HPAI viruses identified from Europe during early 2020. Enhanced active surveillance in wild and domestic birds is needed to monitor the introduction and spread of HPAI via wild birds and to inform the design of improved prevention and control strategies. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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17 pages, 2998 KiB

Open AccessArticle

Bovine Coronavirus: Variability, Evolution, and Dispersal Patterns of a No Longer Neglected Betacoronavirus

by Giovanni Franzo, Michele Drigo, Matteo Legnardi, Laura Grassi, Daniela Pasotto, Maria Luisa Menandro, Mattia Cecchinato and Claudia Maria Tucciarone

Viruses 2020, 12(11), 1285; https://doi.org/10.3390/v12111285 - 10 Nov 2020

Cited by 13 | Viewed by 3018

Abstract

Bovine coronavirus (BoCV) is an important pathogen of cattle, causing severe enteric disease and playing a role in the bovine respiratory disease complex. Similar to other coronaviruses, a remarkable variability characterizes both its genome and biology. Despite their potential relevance, different aspects of [...] Read more.

Bovine coronavirus (BoCV) is an important pathogen of cattle, causing severe enteric disease and playing a role in the bovine respiratory disease complex. Similar to other coronaviruses, a remarkable variability characterizes both its genome and biology. Despite their potential relevance, different aspects of the evolution of BoCV remain elusive. The present study reconstructs the history and evolution of BoCV using a phylodynamic approach based on complete genome and spike protein sequences. The results demonstrate high mutation and recombination rates affecting different parts of the viral genome. In the spike gene, this variability undergoes significant selective pressures—particularly episodic pressure—located mainly on the protein surface, suggesting an immune-induced selective pressure. The occurrence of compensatory mutations was also identified. On the contrary, no strong evidence in favor of host and/or tissue tropism affecting viral evolution has been proven. The well-known plasticity is thus ascribable to the innate broad viral tropism rather than mid- or long-term adaptation. The evaluation of the geographic spreading pattern clearly evidenced two clusters: a European cluster and an American–Asian cluster. While a relatively dense and quick migration network was identified in the former, the latter was dominated by the primary role of the United States (US) as a viral exportation source. Since the viral spreading pattern strongly mirrored the cattle trade, the need for more intense monitoring and preventive measures cannot be underestimated as well as the need to enforce the vaccination of young animals before international trade, to reduce not only the clinical impact but also the transferal and mixing of BoCV strains. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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20 pages, 3275 KiB

Open AccessArticle

Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada

by Victor Palomino-Tapia, Darko Mitevski, Tom Inglis, Frank van der Meer, Emily Martin, Marina Brash, Chantale Provost, Carl A. Gagnon and Mohamed Faizal Abdul-Careem

Viruses 2020, 12(10), 1096; https://doi.org/10.3390/v12101096 - 28 Sep 2020

Cited by 20 | Viewed by 3400

Abstract

In this study, we aimed to molecularly characterize 14 whole genome sequences of chicken astrovirus (CAstV) isolated from samples obtained from white chick syndrome (WCS) outbreaks in Western Canada during the period of 2014–2019. Genome sequence comparisons showed all these sequences correspond to [...] Read more.

In this study, we aimed to molecularly characterize 14 whole genome sequences of chicken astrovirus (CAstV) isolated from samples obtained from white chick syndrome (WCS) outbreaks in Western Canada during the period of 2014–2019. Genome sequence comparisons showed all these sequences correspond to the novel Biv group from which no confirmed representatives were published in GenBank. Molecular recombination analyses using recombination detection software (i.e., RDP5 and SimPlot) and phylogenetic analyses suggest multiple past recombination events in open reading frame (ORF)1a, ORF1b, and ORF2. Our findings suggest that recombination events and the accumulation of point mutations may have contributed to the substantial genetic variation observed in CAstV and evidenced by the current seven antigenic sub-clusters hitherto described. This is the first paper that describes recombination events in CAstV following analysis of complete CAstV sequences originated in Canada. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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7 pages, 6437 KiB

Open AccessBrief Report

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021

by Dong-Hun Lee, Zeinab H. Helal, Junwon Kim, Amelia Hunt, Alyza Barbieri, Natalie Tocco, Salvatore Frasca, Jr., Kirklyn Kerr, Ji-Yeon Hyeon, David H. Chung and Guillermo Risatti

Viruses 2021, 13(11), 2141; https://doi.org/10.3390/v13112141 - 23 Oct 2021

Cited by 5 | Viewed by 3020

Abstract

We report the first detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a 3-month-old dog in Connecticut that died suddenly and was submitted to the state veterinary diagnostic laboratory for postmortem examination. Viral RNA was detected in multiple organs of the [...] Read more.

We report the first detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a 3-month-old dog in Connecticut that died suddenly and was submitted to the state veterinary diagnostic laboratory for postmortem examination. Viral RNA was detected in multiple organs of the dog by reverse transcription real time-PCR (RT-qPCR). Negative and positive sense strands of viral RNA were visualized by in situ hybridization using RNAscope technology. Complete genome sequencing and phylogenetic analysis of the hCoV-19/USA/CT-CVMDL-Dog-1/2021 (CT_Dog/2021) virus were conducted to identify the origin and lineage of the virus. The CT_Dog/2021 virus belonged to the GH/B1.2. genetic lineage and was genetically similar to SARS-CoV-2 identified in humans in the U.S. during the winter of 2020–2021. However, it was not related to other SARS-CoV-2 variants identified from companion animals in the U.S. It contained both the D614G in spike and P323L in nsp12 substitutions, which have become the dominant mutations in the United States. The continued sporadic detections of SARS-CoV-2 in companion animals warrant public health concerns about the zoonotic potential of SARS-CoV-2 and enhance our collective understanding of the epidemiology of the virus. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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9 pages, 2214 KiB

Open AccessBrief Report

Genetic Diversity of Rift Valley Fever Strains Circulating in Namibia in 2010 and 2011

by Gian Mario Cosseddu, Kudakwashe Magwedere, Umberto Molini, Chiara Pinoni, Sigfried Khaiseb, Massimo Scacchia, Maurilia Marcacci, Andrea Capobianco Dondona, Fabrizia Valleriani, Andrea Polci and Federica Monaco

Viruses 2020, 12(12), 1453; https://doi.org/10.3390/v12121453 - 16 Dec 2020

Cited by 4 | Viewed by 2360

Abstract

Outbreaks of Rift Valley fever (RVF) occurred in Namibia in 2010 and 2011. Complete genome characterization was obtained from virus isolates collected during disease outbreaks in southern Namibia in 2010 and from wildlife in Etosha National Park in 2011, close to the area [...] Read more.

Outbreaks of Rift Valley fever (RVF) occurred in Namibia in 2010 and 2011. Complete genome characterization was obtained from virus isolates collected during disease outbreaks in southern Namibia in 2010 and from wildlife in Etosha National Park in 2011, close to the area where RVF outbreaks occurred in domestic livestock. The virus strains were sequenced using Sanger sequencing (Namibia_2010) or next generation sequencing (Namibia_2011). A sequence-independent, single-primer amplification (SISPA) protocol was used in combination with the Illumina Next 500 sequencer. Phylogenetic analysis of the sequences of the small (S), medium (M), and large (L) genome segments of RVF virus (RVFV) provided evidence that two distinct RVFV strains circulated in the country. The strain collected in Namibia in 2010 is genetically similar to RVFV strains circulating in South Africa in 2009 and 2010, confirming that the outbreaks reported in the southern part of Namibia in 2010 were caused by possible dissemination of the infection from South Africa. Isolates collected in 2011 were close to RVFV isolates from 2010 collected in humans in Sudan and which belong to the large lineage containing RVFV strains that caused an outbreak in 2006–2008 in eastern Africa. This investigation showed that the RVFV strains circulating in Namibia in 2010 and 2011 were from two different introductions and that RVFV has the ability to move across regions. This supports the need for risk-based surveillance and monitoring. Full article

(This article belongs to the Special Issue Drivers of Evolution of Animal RNA Viruses)

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