Cross-species Transmission Research Articles

Influenza A as a True Zoonotic Pathogen: Transmission through Reservoir Hosts

Influenza A virus (IAV) represents a considerable global health threat due to its rapid mutation rates and broad host range, facilitating cross-species transmission and enabling the virus to evade immune defenses. This review explores the molecular mechanisms underlying IAV's pathogenicity, focusing on its zoonotic potential through reservoir hosts, such as wild birds and swine. The virus's ability to undergo antigenic shift and drift allows it to continually adapt to new hosts and environments, posing challenges for control and treatment. Current antiviral therapies are limited by the emergence of resistant strains, underscoring the necessity for innovative vaccine development and treatment strategies. By examining IAV's molecular evolution, immune evasion tactics, and transmission dynamics, this review highlights the critical need for enhanced surveillance, improved therapeutic options, and international cooperation to mitigate future outbreaks. A deeper understanding of these processes is essential to inform public health efforts and combat the persistent threat of IAV.

Emergence of highly virulent and multidrug-resistant Escherichia coli in breeding sheep with pneumonia, Hainan Province, China

BackgroundSheep are a rarely raised livestock in Hainan Island, China, because of the unfavorable tropical marine climate. Here, this article reports a severe pneumonia in the sheep breeding and domestication facility caused acute mortality during the winter 2021–2022.MethodsSix sheep were clinically dissected and histopathologically observed. The bacteria were isolated and cultured by traditional methods and identified by 16S rRNA sequencing. The genotypes, serotypes, virulence genes and antimicrobial resistance genes were analyzed by PCR and whole genome sequencing. The pubMLST website was used for phylogenetic analysis of related strains. Kirby-Bauer disk diffusion method was used for antimicrobial susceptibility test. The antimicrobial susceptibility test standard was referred to the Clinical and Laboratory Standards Institute (CLSI). The virulence of bacteria was detected by mouse infection model.ResultsEtiology and histopathology examination of the pneumonia reveled pulmonary abscess and alveolar neutrophilia and pulmonary fibrinous exudates. Escherichia coli was the only bacterial species isolated, primarily from the lungs and blood of the six dead or moribund sheep, a total of 29 E. coli strains were isolated. Antimicrobial resistance profiling shows that all the isolates were resistant to six agents (penicillin, ampicillin, cephalothin, neomycin, erythromycin, and vancomycin) belonging to five classes of antibiotics, classifying them as multi drug resistant (MDR). Furthermore, genotyping analysis revealed all strains were common with 11–17 virulence factors indicating high pathogenicity. The lab mice infection model shows that all strains severely affect the health status particularly weight loss, lethargy, pneumonia and shortly lead to death. The molecular epidemiological analysis indicated most strains share the same genotype as previously reported strains in humans and other farmed animals this suggests a high possibility of cross-species transmission (CST) of virulent and MDR isolates. This CST could be from sheep to humans and other farmed animals or from humans and other farmed animals to sheep.ConclusionTherefore, this study indicates that E. coli is an emerging threat that causes sheep pneumonia in Hainan, and the quarantine of contacts is important to control the spread of virulent E. coli and the transmission of acquired resistance genes between humans and farmed animals such as sheep.

Endogenous nege-like viral elements in arthropod genomes reveal virus-host coevolution and ancient history of two plant virus families.

Although negevirus is phylogenetically related to plant virus, the evolutionary history of negevirus-host and its relationship with plant virus remain largely unknown. In this study, we used endogenous nege-like viral elements (ENVEs) as the molecular fossil records to investigate the history of nege-like viral infection in arthropod hosts and the evolution of two related plant virus families (Virgaviridae and Kitaviridae). Our results showed the infection of nege-like viruses for over 60 My during the arthropod evolution. ENVEs highly homologous to viral sequences in Virgaviridae and Kitaviridae were present in a wide range of arthropod genomes but were absent in plant genomes, indicating that plant viruses in these two families possibly evolved from the nege-like virus ancestor through cross-species horizontal virus transmission. Our findings provide a new perspective on the virus-host coevolution and the origins of plant viruses.

Serological analysis in humans in Malaysian Borneo suggests prior exposure to H5 avian influenza near migratory shorebird habitats

Cases of H5 highly pathogenic avian influenzas (HPAI) are on the rise. Although mammalian spillover events are rare, H5N1 viruses have an estimated mortality rate in humans of 60%. No human cases of H5 infection have been reported in Malaysian Borneo, but HPAI has circulated in poultry and migratory avian species transiting through the region. Recent deforestation in coastal habitats in Malaysian Borneo may increase the proximity between humans and migratory birds. We hypothesise that higher rates of human-animal contact, caused by this habitat destruction, will increase the likelihood of potential zoonotic spillover events. In 2015, an environmentally stratified cross-sectional survey was conducted collecting geolocated questionnaire data in 10,100 individuals. A serological survey of these individuals reveals evidence of H5 neutralisation that persisted following depletion of seasonal H1/H3 HA binding antibodies from the plasma. The presence of these antibodies suggests that some individuals living near migratory sites may have been exposed to H5 HA. There is a spatial and environmental overlap between individuals displaying high H5 HA binding and the distribution of migratory birds. We have developed a novel surveillance approach including both spatial and serological data to detect potential spillover events, highlighting the urgent need to study cross-species pathogen transmission in migratory zones.

Birds as reservoirs: unraveling the global spread of Gamma- and Deltacoronaviruses.

Avian migration is a global phenomenon that transcends geographical boundaries. These migratory birds serve as unwitting carriers of diverse Gammacoronaviruses (γ-CoVs) and Deltacoronaviruses (δ-CoVs). While recombination events have been documented among γ-CoVs in avian species and β-CoVs in mammals, evidence for recombination between CoVs of distinct genera remains limited. This minireview examines the prevalence of CoVs in both domestic waterfowl (ducks and geese) and wild bird populations inhabiting various regions. We investigate the dissemination patterns of γ-CoVs and δ-CoVs among these populations, highlighting their shared characteristics. Furthermore, the review explores the intricate web of cross-species transmission of δ-CoVs from wild birds to mammals, with a particular focus on pigs. Understanding the distinct features of CoVs harbored by waterfowl and wild birds and their potential for cross-species transmission is crucial for preparedness and response to future CoV epidemics.

Molecular Screening and Characterization of Enteric Protozoan Parasites and Microsporidia in Wild Ducks from Portugal.

Enteric parasites pose significant threats to both human and veterinary health, ranking among the top causes of mortality worldwide. Wild migratory waterfowl, such as ducks, may serve as hosts and vectors for these parasites, facilitating their transmission across ecosystems. This study conducted a molecular screening of enteric parasites in three species of wild ducks of the genus Anas (A. acuta, A. platyrhynchos and A. crecca) from Portugal, targeting Blastocystis sp., Balantioides coli, Cryptosporidium spp., Encephalitozoon spp., and Enterocytozoon bieneusi. Fecal samples from 71 ducks were analyzed using PCR and sequencing techniques. The results revealed a 2.82% occurrence of Blastocystis sp. subtype 7 and Cryptosporidium baileyi, marking the first molecular detection of these pathogens in wild ducks in Portugal. While previous studies have documented these parasites in Anas spp. in other regions, this study contributes novel data specific to the Portuguese context. No evidence of Balantioides coli, Encephalitozoon spp. or Enterocytozoon bieneusi was found. These findings highlight the potential role of migratory ducks as vectors for zoonotic protozoa, emphasizing the need for enhanced surveillance of avian populations to mitigate cross-species transmission risks. Further research is warranted to understand the global public health implications associated with migratory waterfowl.

Cross-Species Susceptibility of Emerging Variants of SARS-CoV-2 Spike.

The continuous evolution of SARS-CoV-2 and the emergence of novel variants with numerous mutations have heightened concerns surrounding the possibility of cross-species transmission and the establishment of natural animal reservoirs for the virus, but the host range of emerging SARS-CoV-2 variants has not been fully explored yet. We employed an in vitro model comprising VSV∆G* pseudotyped viruses bearing SARS-CoV-2 spike proteins to explore the plausible host range of SARS-CoV-2 emerging variants. The overall host tropism of emerging SARS-CoV-2 variants are consistent with that of the SARS-CoV-2 wuhan-hu-1 strain with minor difference. Pseudotyped viruses bearing spike protein from RaTG13 and RmYN02 can enter cell cultures from a broad range of mammalian species, revealing that mink and hamsters may act as potential intermediate hosts. We further investigated 95 potential site-specific mutations in the SARS-CoV-2 spike protein that could impact viral infectivity across different species. The results showed that 13 of these mutations notably increased the transduction rates by more than two-fold when compared to the wild-type spike protein. Further examination of these 13 mutations within cell cultures from 31 different species revealed heightened sensitivity in cells derived from palm civets, minks, and Chinese horseshoe bats to the VSV∆G*-SARS2-S mutants. Specific mutations, such as L24F, R158G, and L212I, were seen to significantly enhance the capacity for SARS-CoV-2 of cross-species transmission. This study offers critical insights for the ongoing surveillance and monitoring efforts of SARS-CoV-2 evolution, emphasizing the need for the vigilant monitoring of specific mutations in both human and animal populations.

Species barrier as molecular basis for adaptation of synthetic prions with N-terminally truncated PrP.

Mammalian prions are neurotropic pathogens formed from PrPSc assemblies, a misfolded variant of the host-encoded prion protein PrPC. Multiple PrPSc conformations or strains self-propagate in host populations or mouse models of prion diseases, exhibiting distinct biological and biochemical phenotypes. Constrained interactions between PrPSc and PrPC conformations confer species specificity and regulate cross-species transmission. The pathogenicity of fibrillar assemblies derived from bacterially expressed recombinant PrP (rPrP) has been instrumental in demonstrating the protein-only nature of prions. Yet, their ability to encode different strains and transmit between species remains poorly studied, hampering their use in exploring structure-to-strain relationships. Fibrillar assemblies from rPrP with hamster, mouse, human, and bovine primary structures were generated and tested for transmission and adaptation in tg7 transgenic mice expressing hamster PrPC. All assemblies, except the bovine ones, were fully pathogenic on the primary passage, causing clinical disease, PrPSc brain deposition, and spongiform degeneration. They exhibited divergent adaptation processes and strain properties upon subsequent passage. Assemblies of hamster origin propagated without apparent need for adaptation, those of mouse origin adapted abruptly, and those of human origin required serial passages for optimal fitness. Molecular analyses revealed the presence of endogenously truncated PrPSc species in the resulting synthetic strains that lack the 90-140 amino acid region considered crucial for infectivity. In conclusion, rPrP assemblies provide a facile means of generating novel prion strains with adaptative/evolutive properties mimicking genuine prions. The PrP amino acid backbone is sufficient to encode different strains with specific adaptative properties, offering insights into prion transmission and strain diversity.

Identification and genetic characterization of five novel bat coronaviruses from Yunnan, China

BackgroundCoronaviruses (CoVs) represent a serious threat to human health and have become a major transmissible, endemic, and causative pathogen in humans; they represent a major health concern, given their ability to cause infectious diseases. Bats are natural hosts for diverse viruses. Many transmission events of CoVs and identification of multiple novel CoVs in bats has increased attention towards their capacity to serve as hosts for zoonotic viruses.ResultsIn this study, 61 bats from Yunnan Province were analyzed, identifying seven CoVs, including three α- and two β-CoVs with full-genome sequences. Among the five identified alpha-CoVs, four belong to the Decacovirus subgenus and one to the Minunacovirus subgenus. Two beta-CoVs were also identified, both belonging to the Sarbecovirus subgenus.The genetic structures revealed similarities to known strains such as HKU10 and SARS-CoV-2, along with novel findings such as the Minunacovirus subgenus CoV YJ3c/f and unique ORF patterns. Our results demonstrated that strain JCC9 has a unique recombination pattern and shows a higher binding affinity to civet and pangolin ACE2 receptors, then the HpJC8xc strain transmits and recombines between hosts (bats), indicating a potential risk of crossing the interspecies barrier and infecting other animals.ConclusionsThe CoVs detected in the bats studied in this research exhibit high diversity. Genomic analysis revealed that CoVs in bats undergo frequent recombination events. Furthermore, recombination patterns and evolutionary analyses suggest that alpha-CoVs are more prone to cross-species transmission across different bat families/genera, whereas beta-CoVs demonstrate host specificity and tend to co-evolve with their bat hosts.Our finding suggest that bats, as hosts of CoVs, be constantly monitored to prevent outbreaks of new infections caused by viruses passing across interspecies barriers, and consequently, viral diseases in humans or livestock.

Assessment of PPMV-1 Genotype VI Virulence in Pigeons and Chickens and Protective Effectiveness of Paramyxovirus Vaccines in Pigeons.

Pigeon paramyxovirus serotype 1 (PPMV-1), an antigenic and host variant of avian paramyxovirus Newcastle disease virus (NDV), primarily originating from racing pigeons, has become a global panzootic. Egypt uses both inactivated PPMV-1 and conventional NDV vaccines to protect pigeons from disease and mortality. However, the impact of prevalent strains and the effectiveness of available vaccines in pigeons in Egypt are unclear. This study investigates the virulence of PPMV-1 (Pigeon/Egypt/Sharkia-19/2015/KX580988) and evaluates available paramyxovirus vaccines in protecting pigeons against a PPMV-1 challenge. Ten-day-old specific-pathogen-free (SPF) embryonated chicken eggs infected with this strain exhibited a mean death time (MDT) of 86.4 ± 5.88 h. The intracerebral pathogenicity index (ICPI) in day-old chickens was 0.8, while pigeons experienced an ICPI of 0.96 and an intravenous pathogenicity index (IVPI) of 2.11. These findings classify the strain as virulent and velogenic. Experimental infection of pigeons with this PPMV-1 strain at 106 EID50/0.1 mL resulted in a 62.5% mortality rate, displaying nervous and enteric distress. The virus caused extensive lesions in visceral organs, with strong immunohistochemistry signals in all examined organs, indicating the systemic spread of the virus concurrent to its neurotropic and viscerotropic tropism. Furthermore, vaccination using an inactivated PPMV-1 and live NDV LaSota vaccine regimen protected 100% of pigeons against mortality, while with a single NDV LaSota vaccine, it was 62.5%. The PPMV alone or combined with NDV LaSota induced protective levels of haemagglutination inhibition (HI) antibody titres and reduced virus shedding from buccal and cloacal cavities. Based on generalised linear gamma model analysis, both PPMV-1 and NDV LaSota are antigenically comparable by HI. These findings suggest that using both inactivated PPMV-1 (G-VI) and live attenuated NDV (LaSota) vaccines is an effective prophylactic regimen for preventing and controlling PPMV-1 and NDV in pigeons, thereby reducing the risk of interspecies transmission.

Phosphorylation of Ser711 residue in the hypervariable region of zoonotic genotype 3 hepatitis E virus is important for virus replication.

Hepatitis E virus (HEV) is distinct from other hepatotropic viruses because it is zoonotic. HEV-1 and HEV-2 exclusively infect humans, whereas HEV-3 and HEV-4 are zoonotic. However, the viral and/or host factors responsible for cross-species HEV transmission remain elusive. The hypervariable region (HVR) in HEV is extremely heterogenetic and is implicated in HEV adaptation. Here, we investigated the potential role of Serine phosphorylation in the HVR in HEV replication. We first analyzed HVR sequences across different HEV genotypes and identified a unique region at the N-terminus of the HVR, which is variable in the human-exclusive HEV genotypes but relatively conserved in zoonotic HEV genotypes. Using predictive tools, we identified four potential phosphorylation sites that are highly conserved in zoonotic HEV-3 and HEV-4 genomes but absent in human-exclusive HEV-1 strains. To explore the functional significance of these putative phosphorylation sites, we introduced mutations into the HEV-3 infectious clone and indicator replicon, replacing each Serine residue individually with alanine or aspartic acid, and assessed the impact of these substitutions on HEV-3 replication. We found that the phospho-blatant S711A mutant significantly reduced virus replication, whereas the phospho-mimetic S711D mutant modestly reduced virus replication. Conversely, mutations in the other three Serine residues did not significantly affect HEV-3 replication. Furthermore, we demonstrated that Ser711 phosphorylation did not alter host cell tropism of zoonotic HEV-3. In conclusion, our results showed that potential phosphorylation of the Ser711 residue significantly affects HEV-3 replication in vitro, providing new insights into the potential mechanisms of zoonotic HEV transmission.IMPORTANCEHEV is an important zoonotic pathogen, causing both acute and chronic hepatitis E and extrahepatic manifestation of diseases, such as neurological sequelae. The zoonotic HEV-3 is linked to chronic infection and neurological diseases. The specific viral and/or host factors facilitating cross-species HEV infection are unknown. The intrinsically disordered HVR in ORF1 is crucial for viral fitness and adaptation, both in vitro and in vivo. We hypothesized that phosphorylation of Serine residues in the HVR of zoonotic HEV by unknown host cellular kinases is associated with cross-species HEV transmission. In this study, we identified a conserved region within the HVR of zoonotic HEV strains but absent in the human-exclusive HEV-1 and HEV-2. We elucidated the important role of phosphorylation at the Ser711 residue in zoonotic HEV-3 replication, without altering the host cell tropism. These findings contribute to our understanding the mechanisms of cross-species HEV transmission.

Assessment of genetic diversity, tissue tropism, and antigenic properties of Grimsö betacoronavirus in Swedish bank voles (Clethrionomys glareolus)

Zoonotic coronaviruses can transmit over species barriers and infect humans. To understand the zoonotic potential of a betacoronavirus, Grimsö virus (GRIV), we investigated the geographic distribution and tissue tropism of GRIV in Swedish bank voles (Clethrionomys glareolus), and the antigenicity of the nucleocapsid (N) protein. We screened the lung tissues from animals collected in the southern Sweden by RT-PCR with primers targeting the spike gene. Seven out of 74 animals were found to be positive. They are genetically close to GRIV from Grimsö, central Sweden. Positive rodents were studied for the tissue distribution of GRIV and GRIV RNA was mainly found in the respiratory tract. After three attempts of virus isolation were failed, we successfully established a Vero E6 cell line that stably expressed GRIV N protein, which has no cross-reactivity with patient serum containing antibodies against SARS-CoV-2, or with MERS-CoV. However, a low level of cross-reactivity to common cold coronaviruses was found, likely HCoV-OC43 or HCoV-HKU1, probably due to shared linear epitopes. With the high prevalence and the suggested respiratory transmission route, GRIV may have a high potential for spillover and cross-species transmission, and future serological screening of GRIV infections in domestic animals or humans will be needed.

Modulation of human-to-swine influenza a virus adaptation by the neuraminidase low-affinity calcium-binding pocket

Frequent interspecies transmission of human influenza A viruses (FLUAV) to pigs contrasts with the limited subset that establishes in swine. While hemagglutinin mutations are recognized for their role in cross-species transmission, the contribution of neuraminidase remains understudied. Here, the NA’s role in FLUAV adaptation was investigated using a swine-adapted H3N2 reassortant virus with human-derived HA and NA segments. Adaptation in pigs resulted in mutations in both HA (A138S) and NA (D113A). The D113A mutation abolished calcium (Ca2+) binding in the low-affinity Ca2+-binding pocket of NA, enhancing enzymatic activity and thermostability under Ca2+-depleted conditions, mirroring swine-origin FLUAV NA behavior. Structural analysis predicts that swine-adapted H3N2 viruses lack Ca2+ binding in this pocket. Further, residue 93 in NA (G93 in human, N93 in swine) also influences Ca2+ binding and impacts NA activity and thermostability, even when D113 is present. These findings demonstrate that mutations in influenza A virus surface proteins alter evolutionary trajectories following interspecies transmission and reveal distinct mechanisms modulating NA activity during FLUAV adaptation, highlighting the importance of Ca2+ binding in the low-affinity calcium-binding pocket.

Unusual G3P[10] bat-like rotavirus strains detected in children with acute gastroenteritis in Thailand.

Rotavirus A (RVA) is the main cause of acute gastroenteritis among children under the age of five globally. The unusual bat-like human RVA strains G3P[10] (RVA/Human-wt/THA/CMH079/05/2005/G3P[10] and RVA/Human-wt/THA/CMH-S015-19/2019/G3P[10]) were detected in children with acute gastroenteritis in 2005 and 2019, respectively, in the same geographical area of Northern Thailand. To elucidate the genetic backgrounds of these unusual or bat-like human RVA strains, the complete genome of these RVA strains was sequenced and phylogenetically analyzed. All eleven genome segments of these G3P[10] strains were genotyped as G3-P[10]-I8-R3-C3-M3-A9-N3-T3-E3-H6, which is closely related to bat G3P[10] RVA strain (RVA/Bat-tc/CHN/MYAS33/2013/G3P[10]) and bat-like human RVA strain (RVA/Human-wt/THA/MS2015-1-0001/2015/G3P[10]). The findings indicate that human G3P[10] RVA strains detected in this study (RVA/Human-wt/THA/CMH079/05/2005/G3P[10] and RVA/Human-wt/THA/CMH-S015-19/2019/G3P[10]) contained all eleven genome segments similar to those of bat RVA strains and appeared to be human RVA strains of bat origin. Phylogenetic analysis revealed that several genome segments of these two RVA strains were also closely related with those of other species in addition to bats and had a zoonotic transmission history. The results of this study supported the roles of interspecies transmission of RVA strains among bats and humans in the natural environment and provided convincing evidence that the evolution of human RVAs was closely interrelated with those of animal RVAs. Continuing surveillance of RVAs in humans and animals is imperative to gain a better understanding of the origin and the evolution of these viruses.

CHALLENGES IN DEVELOPING VACCINE FOR CANINE DISTEMPER

The Canine Distemper Virus (CDV) represents a considerable risk to domestic and wild carnivore populations globally, notwithstanding the existence of vaccinations. This study examines the significant obstacles in creating successful CDV vaccines, especially regarding virus evolution, immune evasion, cross-species transmission, and vaccine reluctance. This review aims to consolidate existing research on CDV vaccine development, emphasizing emerging technologies, such as nanoparticle and DNA vaccines, and their capacity to address present challenges in immunogenicity and cross-species protection. Through the analysis of recent findings, this review delineates significant gaps in the comprehension of CDV's genetic variety of CDVs, the sustainability of wildlife reservoirs, and the obstacles to attaining extensive vaccination coverage. This review evaluates the influence of public health infrastructure and socioeconomic factors on vaccination distribution and uptake constraints, particularly in developing areas. These findings highlight the significance of a One Health approach, which amalgamates veterinary, wildlife, and public health viewpoints to address CDV epidemics more efficiently. Future research should focus on augmenting vaccine efficacy in non-domestic species, increasing public awareness of immunization initiatives, and creating thermostable vaccines for improved distribution accessibility. This review offers critical insights into the intricacies of the CDV vaccination and presents a framework for enhancing worldwide initiatives to combat this destructive virus.

Epidemiology and genetic diversity of bocavirus in wild rodents in urban areas of Guangzhou, Southern China

Members of the genus Bocaparvovirus have a significant impact on human health and can infect a wide range of hosts, increasing the likelihood of crossing species barriers. Among the various mammalian hosts, rodents are widely recognized as important reservoirs for emerging and zoonotic viruses. However, despite recent reports of bocavirus infections in rodents, our current understanding of rat bocavirus (RBoV) genetic diversity and evolution is limited. In this study, rodent samples were collected from the urban areas of Guangzhou city, Southern China, to investigate the presence and genetic diversity of RBoV. Through PCR-based screening of 296 rodent spleens, 54 samples were determined to be positive for RBoV infection, and 12 nearly complete genome sequences of RBoV were recovered. Phylogenetic analysis revealed distinct lineages and sub-lineages of RBoV, and six recombination events with strong statistical support were identified, with five of these events involving sequences obtained from this study. These results highlight the genetic diversity of RBoV circulating in rodents in Guangzhou city and emphasize the importance of extensive surveillance to gain a better understanding of RBoV epidemiology, evolutionary characteristics, and potential for cross-species transmission.

Whole Genome Sequences of the Wildtype AU-1 Rotavirus A Strain: The Prototype of the AU-1-like Genotype Constellation.

Most human rotaviruses belong to the Wa-like, DS-1-like, or AU-1-like genotype constellation. The AU-1-like constellation, albeit minor, captured attention because its prototype strain AU-1 originated from feline rotavirus, leading to the concept of interspecies transmission of rotavirus. The AU-1 genome sequence determined by various laboratories over the years has documented two conflicting VP7 sequences in the GenBank. As culture-adaptation may introduce changes in the viral genome, the original fecal (wild-type) and the seed stock of culture-adapted AU-1 genomes were sequenced using the Illumina's MiSeq platform to determine the authentic AU-1 sequence and to identify what mutational changes were selected during cell-culture adaptation. The wild-type and culture-adapted AU-1 genomes were identical except for one VP4-P475L substitution. Their VP7 gene was 99.9% identical to the previously reported AU-1 VP7 under accession number AB792641 but only 92.5% to that under accession number D86271. Thus, the wild-type sequences determined in this study (accession numbers OR727616-OR727626) should be used as the reference. The VP4-P475L mutation was more likely incidental than inevitable during cell-culture adaptation. This was the first study in which the whole genomes of both wild-type and cultured RVA strains were simultaneously determined by deep sequencing.

Chromosomally located blaCMH in Enterobacter cloacae complex across human-bird-environment interfaces: A one-health perspective

To improve the understanding of antimicrobial resistance (AMR) in migratory birds derived-Enterobacter cloacae (E. cloacae) complex and its spread at the human-bird-environment interface, we isolated 11 strains of third-generation cephalosporin-resistant E. cloacae from 1003 specimens from 29 migratory bird species over two years in Chongming, Shanghai, China. The comprehensive analysis incorporated second- and third-generation sequencing techniques and extensive bioinformatic analysis. Four human-associated E. cloacae sequence types (STs), including ST432, ST412, ST1, and ST639, were found in migratory birds. We confirmed that the blaCMH-4 and blaCMH-6 genes were the major genotypes of the β-lactamase resistance genes in E. cloacae found in migratory birds. In addition, a thorough genomic analysis was performed on a global collection of 398 E. cloacae isolates carrying the blaCMH gene from 46 different countries. China had the highest proportion with 19.10 % (76/398), followed by Singapore with 18.34 % (73/398), Nigeria with 15.83 % (63/398), and the USA with 14.07 % (56/398). The first transmission of E. cloacae carrying blaCMH-4 and blaCMH-6 was defined around 1894 and 1549, respectively. Time-based phylogenetic analysis revealed that host jumps among humans, birds, and the environment led to the emergence of modern strains with ESBL- and carbapenem-resistant genes from about 2004 to 2016. The detection rate of insertion sequences (IS) of E. cloacae carrying blaCMH from human sources is higher than that from migratory bird sources, which is related to the different genetic environments caused by antibiotic selective pressure. It is crucial to have a comprehensive understanding of the characteristics exhibited by blaCMH producing E. cloacae in different ecological environments. Our results contribute to the effective monitoring and implementation of proactive strategies to reduce the spread of multidrug-resistant E. cloacae.

Longitudinal survey of hepatitis E virus in extensively raised pigs in Spain

Hepatitis E virus (HEV) is an emerging zoonotic virus of public health concern, of which pigs, wild boar and red deer are the main reservoirs. The European Food Safety Authority (EFSA) has recently prioritized the development of monitoring programs of HEV at different stages of the pig food chain, including outdoor pig farming. Pigs managed under these extensive production systems frequently share habitat and natural resources with wild boar and red deer during fattening stages and cross-species transmission of HEV among these species has previously been suggested. In this context, we aimed to (I) to evaluate the risk of HEV circulation within the production phases of extensively raised pigs and at the domestic-wildlife interface, and (II) to identify the genotypes circulating within these hosts. A total of 1452 pigs from seven different pig farms were longitudinally sampled during the breeding, rearing, and fattening production phases. In addition, 138 and 252 sympatric wild boar and red deer, respectively, were analysed. Anti-HEV antibodies were found in 1245 (85.7 %) out of the 1452 Iberian pigs sampled. The seroprevalence was 30.4 % in the breeding phase, 95.4 % in the rearing phase and 97.0 % in the fattening phase. Statistically significant differences (P < 0.05) were found among the three production phases. The seroprevalence was significantly higher (P < 0.001) in fattening pigs compared to those found in sympatric wild boar (31.9 %) and red deer (2.0 %). Three (1.0 %) out of the 293 serum pools analysed were positive for viral RNA. One of them was identified in pigs at the rearing phase (genotype 3 f) and two in wild boar (genotypes 3 f and 3 m). The high seroprevalence detected in extensively raised pigs, together with the detection of the zoonotic HEV-3 f and HEV-3 m subtypes in sympatric domestic and wild swine, highlights the risk of zoonotic transmission and the need to establish surveillance programs and control measures, particularly in breeding and rearing phase, in these epidemiological scenarios.

Whole genome characteristics of hedgehog coronaviruses from Poland and analysis of the evolution of the Spike protein for its interspecies transmission potential

BackgroundThe hedgehogs have been recently identified as possible reservoir of Middle East respiratory syndrome coronavirus like (MERS-CoV-like). These viruses were classified as a distinct Betacoronavirus erinacei (BCoV-Eri) species within the MerBCoV-Eriirus subgenus. As coronaviruses are known for their ability to jump between different hosts, including humans, this can pose a particular threat to people in direct contact with hedgehogs, such as those working at animal asylums. Our previous studies have shown the presence of BCoV-Eri strains in animals collected in the wildlife rehabilitation centre. This study aimed to investigate the presence of CoV in subsequent hedgehogs collected from the urban area of Poland and their molecular characteristics.ResultsMonitoring for the presence of coronavirus infection in hedgehogs revealed five positive individuals. The presence of BCoV-Eri was found in a total of 20% of animals tested. Our analyses revealed no correlation between CoVs positivity and animal health conditions but a higher probability of such infection in juveniles and females. The whole genome of two Polish Hedgehog coronavirus 1 strains were sequenced and compared with available counterparts from European and Asian countries. Phylogenetic analysis showed that both CoV strains formed common cluster with other similar MerBCoV-Eriirus, but they were also found to be genetically variable and most changes in the S protein were identified. Our analysis revealed that some S protein sites of the Hedgehog coronavirus 1 strains evolved under positive selection pressure and of five such sites, three are in the S1 region while the other two in the S2 region of the Spike.ConclusionsBCoV-Eri is to some extent prevalent in wildlife asylums in Poland. Given that the S protein of BCoVs-Eri is highly variable and that some sites of this protein evolve under positive selection pressure, these strains could potentially acquire a favourable feature for cross-species transmission. Consequently, the threat to humans working in such asylums is particularly high. Adequate biosecurity safeguards, but also human awareness of such risks, are therefore essential.