Arruda, Luciana de Barros

Campos, Fabrício Souza

Silva, Maite Vaslin de Freitas

Viruses

English

Lume 5.8

Citation: Vaslin, M.F.S.; Arruda,L.d.B.; Campos, F.S. Surveillance,Prevention, Evolution and Control ofEmerging Viruses: A 2022 EditorialUpdate. Viruses 2023, 15, 2098.https://doi.org/10.3390/v15102098Received: 13 September 2023Revised: 12 October 2023Accepted: 13 October 2023Published: 17 October 2023Copyright: © 2023 by the authors.Licensee MDPI, Basel, Switzerland.This article is an open access articledistributed under the terms andconditions of the Creative CommonsAttribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).virusesEditorialSurveillance, Prevention, Evolution and Control of EmergingViruses: A 2022 Editorial UpdateMaite Freitas Silva Vaslin 1,*, Luciana de Barros Arruda 1,* and Fabricio Souza Campos 2,*1 Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Riode Janeiro, Rio de Janeiro 21941-902, RJ, Brazil2 Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de CiênciasBásicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre CEP 90035-003, RS, Brazil* Correspondence: maite@micro.ufrj.br.com (M.F.S.V.); arruda@micro.ufrj.br (L.d.B.A.);camposvet@gmail.com (F.S.C.)The Special Issue “Emerging Viruses: Surveillance, Prevention, Evolution and Control”has been published annually by Viruses, since 2019, highlighting the increasing effort ofthe scientific community for the surveillance and further research of new emerging or re-emerging viruses. As organisms with the fastest evolutionary rates, viruses pose challengesfor many research areas relevant to human health, agricultural practices, and the worldeconomy. The SI 2022 reflects the insights of virologists around the globe about relevantand potentially threatening new viruses, especially those arising in the edge betweenrural and forest biomes. Indeed, the emergence of new virus species and/or isolatesinfecting wild animals from the interface between forest/rural/metropolitan areas andanimals from growing farms were the most prevalent issues in this SI. New arteriviruses,hepinaviruses, coronaviruses, and astroviruses were identified in rodent, vole, and goslingspecies, respectively [1–4]. Also, new isolates of high pathogenic H5N1 influenza virus,epizootic hemorrhagic disease virus strain (EHDV), and Lumpy skin disease virus (LSDV)were reported in wild birds and poultry, cattle, and yaks [5–7].Human–animal interface in the Amazonian metropolitan area represents a constantopportunity for the emergence of new viruses. In an effort to identify viral communitiesin wild animals from this region, Da Paz and collaborators [1] conducted expeditionsbetween 2014 and 2015, in the Belém metropolitan mesoregion of Pará State, Brazil, andcollected serum and tissues from 39 mammals, comprising 18 marsupials, 12 rodents, and9 chiropterans. Metagenomic analyses from pooled tissue samples obtained from rodents,morphologically identified as Oecomys sp., unveiled a new arterivirus, classified in theVariarterivirinae clade. Using a similar approach, the same group also identified a newhepinidavirus-like in the marsupials Marmosa demerarae, opossums, adjacent to a ruralmunicipality of Peixe-Boi, Pará State, Brazil [2]. Henipavirus is a Paramyxoviridae genusthat comprises some emerging viruses of serious public health concern. The novel viruscalled the Peixe-Boi virus (PBV) corroborates the circulation of henipa-like viruses far fromAfrica, Asia, and Australia. It was the first description of henipa-like viruses in marsupialsworldwide, indicating the importance of including these animals in surveillance studies.The vulnerability of deforested environments such as those at the study site, where wildhabitats overlap with rural areas, resembles the conditions in which Hendra henipavirus(HeV) and Nipah henipavirus (NiV) outbreaks arose previously [8].In another effort, using next-generation sequencing, but primer-targeted to coronavirusspike, a new Betacoronavirus species designed as Grimsö virus was found in bank voles(Myodes glareolus) in Grimsö, Sweden [3]. Bank voles are among the most common rodentspecies in Europe and are known reservoirs for several zoonotic pathogens, such as Puumalaorthohantavirus and Francisella tularensis. The study analyzed vole communities for 3 years,and the Grimsö virus was detected during this time. The phylogenetic analysis of ORF1b,Viruses 2023, 15, 2098. https://doi.org/10.3390/v15102098 https://www.mdpi.com/journal/virusesViruses 2023, 15, 2098 2 of 4S, and N genes, as well as a partial RdRp gene, suggested a relatively broad geographicdistribution of CoVs in bank voles in Europe, which is indicative of possible long-termhost–virus association [3].In 2016, an outbreak of a novel gout disease affecting goslings emerged in China. Anovel goose astrovirus (GoAstV) was associated with the disease, and successive outbreaksresulted in serious economic loss. In the study by Fu et al. [4], GoAstV was detected inmultiple tissue samples from animals with clinical signs of gout in different goose farms insouthern China. The authors reported the genomes of six GoAstV strains, which could bedivided into two distinct clades, GoAstV-1 and GoAstV-2. GoAstV-2 is responsible for goutoutbreaks in goslings and could be classified into Avastrovirus 3 (AAstV-3), while GoAstV-1belongs to Avastrovirus 1 (AAstV-1).Sghaier et al. reported the re-emergence and spread of the epizootic hemorrhagicdisease virus strain 8 (EHDV-8), causing epizootic hemorrhagic disease in cattle in Tunisiain 2021 [5]. The EHDV-8 strain had not been detected since 1982. The EHDV-8 strainidentified in this outbreak represents a new isolate, and it was only the second time thatthis strain was reported. Also in Africa, this time in Botswana, a high pathogenic avianinfluenza virus H5N1 emerged in 2021, infecting wild birds and poultry. After activesurveillance by public departments, together with the initiation of a public awarenesscampaign, Letsholo et al. [6] could collect data and carcasses from infected, dying, or deadbirds, and fecal material from wild birds around water bodies and farms nationwide. Theauthors described the clinical signs observed in different species and studied the carcassesof the affected birds for the detection of influenza A. The gull genomes of four identifiedvirus samples from distinct locations along the country were described. High-pathogenicavian influenza (HPAI) always represents a concern in wild birds and poultry, regardlessof the location from which it originates. The fast identification and control of diseaseoutbreaks in this case helped to limit epizootic spread and deleterious effects in the wildbird population and especially in the poultry industry. The absence of densely populatedpoultry farms in the country helped to limit the spread of this outbreak. However, thereal impact on the Okavango Delta ecosystem could be to a greater extent, and only afuture census will help to define the true impact on 25 threatened species that reside at theOkavango River.In October 2021, an outbreak of suspected Lumpy skin disease virus (LSDV) occurredon a mixed yak and cattle farms in Sichuan Province, China. The outbreak resultedin high morbidity and mortality rates in yaks. Li et al. [7] detected a novel vaccine-associated recombinant LSDV infecting yaks and cattle. The recombinant strain, namedChina/LSDV/SiC/2021, presents at least 18 recombination events. Virus DNA was alsofound in Culex tritaeniorhynchus Giles (Diptera: Culicidae), indicating that it could be avector of the virus.Three human-infecting viruses were discussed in this SI, including the genomic surveil-lance of Chikungunya virus (CHIKV) in a Brazilian state [9] and the proposal of a modelfor broader control of pandemic viruses, based on influenza A-H1N1 and SARS-CoV-2data [10]. CHIKV is an arbovirus from the Togaviridae family. Human transmission ismediated by Aedes spp. The virus was introduced in Brazil in 2014; however, there isstill limited information about the genomic epidemiology of CHIKV from surveillancestudies. Souza et al. [9] reported the recovery of 27 newly complete genome sequencesfrom the Tocantins State in Brazil. Their study also provided a preliminary overview ofthe introduction and circulation of the virus within the state, with a focus on its interplaywith other Brazilian states. Notably, their research highlighted the significant role of highlypopulated regions like the State of Rio de Janeiro, serving as an amplifier for the CHIKVand a source of dissemination to other parts of Brazil.In a different approach, Lim and colleagues [10] developed a modeling study consid-ering the typical viral load reported and the relative transmission rate of influenza A-H1N1and SARS-CoV-2. Post-pandemic economic recovery drastically depends on efficient bordercontrol for safe cross-border movement. The authors refined a previously described modelViruses 2023, 15, 2098 3 of 4and predicted the relative transmission risk (TR) posed by incoming infected travelersunder given measures. They observed that viruses with high typical viral loads and lowtransmission risk given low viral loads, such as SARS-CoV-2, are effectively controlledwith moderate-sensitivity tests (ARTs) and modest quarantine periods. In contrast, viruseswith low typical viral loads and substantial transmission risk at low viral loads, such asinfluenza A-H1N1, require high-sensitivity tests (such as polymerase chain reaction (PCR))and longer quarantine periods.In an interesting paper, Juma et al. [11] reported the development of a new ampliconmultiplex PCR-based method for the genome surveillance of segmented RNA viruses. Theuse of this alternative method can help the faster identification of virus outbreaks, leadingto faster responses without the need for virus cell culture enrichment. Using 74 primer pairsmatching the three genomic segments of the entire Rift Valley fever virus (RVFV) (genusPhlebovirus, family Phenuiviridae) genome, they obtained around 80–90% of the genomecovering of the virus from not enriched samples. The proposed amPCR method achievessufficient sequence coverage for genotyping and other genomic epidemiological studiessuch as transmission dynamics.Finally, Keck and collaborators [12] tested and compared different kinds of biosamplecollection cards to assess the risks of virus transmission during transport. These types ofcollection cards are inexpensive and useful alternatives to transport virus samples betweencollection sites and the laboratories used for processing. Virus inactivation and nucleic acidstabilization were analyzed at different time points for a wide variety of viruses: bluetonguevirus (BTV), family Reoviridae, a double-stranded RNA genome with no envelope; foot-and-mouth disease virus (FMDV), family Picornaviridae, a single-stranded RNA genome withpositive polarity; small ruminant morbillivirus, family Paramyxoviridae, a single-strandedRNA genome with negative polarity and lipid envelope; and lumpy skin disease virus(LSDV), family Poxviridae, a double-stranded DNA genome with lipid envelope. Thegeneral conclusion was that cards are safe if samples are appropriately applied. The reportalso described which card showed the best nucleic acid recovery.In summary, the manuscripts featured in this Special Issue encompass studies ona wide range of viral species, offering invaluable insights into their origin, evolution,transmission patterns, and potential outcomes. These studies underscore the significanceof comprehensive research not only to enhance our understanding of these novel virusesbut also to enable effective strategies for their surveillance and control.Acknowledgments: We thank the Brazilian Society for Virology for the support during the organiza-tion and divulgation of this Special Issue. F.S.C. and L.B.A. are CNPq research fellows. L.B.A. is aFAPERJ fellow.Conflicts of Interest: The authors declare no conflict of interest.References1. da Paz, T.; Hernández, L.; Silva, S.; Silva, F.; Barros, B.; Casseb, L.; Guimarães, R.; Vasconcelos, P.; Cruz, A. Novel RodentArterivirus Detected in the Brazilian Amazon. Viruses 2023, 15, 1150. [CrossRef] [PubMed]2. Hernández, L.; da Paz, T.; Silva, S.; Silva, F.; Barros, B.; Nunes, B.; Casseb, L.; Medeiros, D.; Vasconcelos, P.; Cruz, A. First GenomicEvidence of a Henipa-like Virus in Brazil. Viruses 2022, 14, 2167. [CrossRef] [PubMed]3. Wasberg, A.; Raghwani, J.; Li, J.; Pettersson, J.; Lindahl, J.; Lundkvist, Å.; Ling, J. Discovery of a Novel Coronavirus in SwedishBank Voles (Myodes glareolus). Viruses 2022, 14, 1205. [CrossRef] [PubMed]4. Fu, X.; Hou, Z.; Liu, W.; Cao, N.; Liang, Y.; Li, B.; Jiang, D.; Li, W.; Xu, D.; Tian, Y.; et al. Insight into the Epidemiologyand Evolutionary History of Novel Goose Astrovirus-Associated Gout in Goslings in Southern China. Viruses 2022, 14, 1306.[CrossRef] [PubMed]5. Sghaier, S.; Sailleau, C.; Marcacci, M.; Thabet, S.; Curini, V.; Ben Hassine, T.; Teodori, L.; Portanti, O.; Hammami, S.; Jurisic, L.;et al. Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses 2023, 15, 16. [CrossRef] [PubMed]6. Letsholo, S.; James, J.; Meyer, S.; Byrne, A.; Reid, S.; Settypalli, T.; Datta, S.; Oarabile, L.; Kemolatlhe, O.; Pebe, K.; et al. Emergenceof High Pathogenicity Avian Influenza Virus H5N1 Clade 2.3.4.4b in Wild Birds and Poultry in Botswana. Viruses 2022, 14, 2601.[CrossRef]Viruses 2023, 15, 2098 4 of 47. Li, Y.; Zeng, Z.; Li, K.; Rehman, M.; Nawaz, S.; Kulyar, M.; Hu, M.; Zhang, W.; Zhang, Z.; An, M.; et al. Detection of Culextritaeniorhynchus Giles and Novel Recombinant Strain of Lumpy Skin Disease Virus Causes High Mortality in Yaks. Viruses 2023,15, 880. [CrossRef] [PubMed]8. Thibault, P.A.; Watkinson, R.E.; Moreira-Soto, A.; Drexler, J.F.; Lee, B. Zoonotic potential of emerging paramyxoviruses: Knowsand unknows. Adv. Virus Res. 2017, 98, 1–55.9. Souza, U.; Santos, R.; Giovanetti, M.; Alcantara, L.; Galvão, J.; Cardoso, F.; Brito, F.; Franco, A.; Roehe, P.; Ribeiro, B.; et al.Genomic Epidemiology Reveals the Circulation of the Chikungunya Virus East/Central/South African Lineage in TocantinsState, North Brazil. Viruses 2022, 14, 2311. [CrossRef] [PubMed]10. Lim, N.; Lim, J.; Dickens, B. Border Control for Infectious Respiratory Disease Pandemics: A Modelling Study for H1N1 and FourStrains of SARS-CoV-2. Viruses 2023, 15, 978. [CrossRef]11. Juma, J.; Konongoi, S.; Nsengimana, I.; Mwangi, R.; Akoko, J.; Nyamota, R.; Muli, C.; Dobi, P.; Kiritu, E.; Osiany, S.; et al. UsingMultiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for GenomicSurveillance. Viruses 2023, 15, 477. [CrossRef]12. Keck, H.; Eschbaumer, M.; Beer, M.; Hoffmann, B. Comparison of Biosafety and Diagnostic Utility of Biosample Collection Cards.Viruses 2022, 14, 2392. [CrossRef]Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individualauthor(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury topeople or property resulting from any ideas, methods, instructions or products referred to in the content.

Surveillance, prevention, evolution and control of emerging viruses : a 2022 editorial update

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Surveillance, prevention, evolution and control of emerging viruses : a 2022 editorial update

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