Time scale evolution of avipoxviruses

AbstractAvipoxviruses are divided into three clades: canarypox-like viruses, fowlpox-like viruses, and psittacinepox-like viruses. Several molecular clock and demographic models available in the BEAST package were compared on three avipoxvirus genes (P4b, cnpv186 and DNA polymerase genes), which enabled to determine that avipoxviruses evolved at a rate of 2–8×10−5substitution/site/year, in the range of poxviruses previously reported evolution rates. In addition, the date of mean time of divergence of avipoxviruses from a common ancestor was extrapolated to be about 10,000–30,000years ago, at the same period as modern poxvirus species. Our findings will facilitate epidemiological investigations on avipoxviruses’ spread, origin and circulation

Replacement of Sublineages of Avian Influenza (H5N1) by Reassortments, Sub-Saharan Africa

The 3 sublineages initially introduced into Nigeria in 2006 were gradually replaced by different reassortants

Filogenetska i molekularna analiza gena hemaglutinina virusa ptičje gripe h9n2 izoliranih u jatima peradi u Maroku između 2016. i 2018. godine

Avian influenza viruses of the H9N2 subtype continue to spread in wild birds and poultry worldwide. Infection with H9N2 avian influenza virus was detected for the first time in Morocco in January 2016. In this study, a total of 105 organ and tracheal swab samples from 21 broiler farms in Morocco were collected from July 2016 to October 2018 for H9N2 screening. The suspicion of disease was based on severe respiratory signs such as sneezing, coughing, rales and gasping, while H9N2 virus infection was confirmed by real-time RT-PCR. Hemagglutinin (HA) genes of four isolates were amplified by conventional RT-PCR, sequenced, and aligned for phylogenetic analyses. Among the 21 flocks, 48% (10/21) were qRT-PCR positive for H9, with the cycle threshold values ranging from18.6 to 34.8. The maximum similarity in nucleotide and protein sequences (96-98%) was observed between the Moroccan viruses and an H9 virus isolated from broiler chickens in 2017 in Burkina Faso (A/chicken/BurkinaFaso/17RS93-19/2017) and from a layer chicken in the United Arab Emirates in 2015 (A/chicken/Dubai/D2506/2015). The HA genes revealed the close relationship between the four Moroccan viruses, with 97.9%-99.9% nucleotide identity. Phylogenetic analysis showed that the Moroccan viruses belonged to the G1 lineage, and likely originated from the Middle East, as previously reported in 2016.Virusi ptičje gripe H9N2 nastavljaju se širiti u peradi i divljih ptica širom svijeta. Infekcija niskopatogenim virusom influence H9N2 prvi je put otkrivena u Maroku u siječnju 2016. godine. U ovom je istraživanju za probir na H9N2 prikupljeno ukupno 105 organa i obrisaka iz dušnika s 21 farme brojlera od srpnja 2016. do listopada 2018. iz različitih regija Maroka. Sumnja na bolest temeljila se na teškim respiracijskim znakovima kao što su kihanje, kašljanje, hropanje i hripanje, a infekcija virusom H9N2 potvrđena je PCR-om obrnute transkripcije u stvarnom vremenu. Sekvencije gena za hemaglutinin (HA) od četiri izolata amplificirane su pomoću RT-PCR qRT-PCR poravnane za filogenetsku i analizu sličnosti aminokiselina. Od 21 uzorka jata 48 % (10/21) bilo je pozitivno na H9 s pragom broja ciklusa u rasponu od 18,6 do 34,8. Maksimalna sličnost u nukleotidnim i proteinskim sekvencijama (96 -98 %) uočena je između marokanskih virusa i virusa H9 izoliranih iz brojlerskih pilića u 2017. u Burkini Faso (A/piletina/BurkinaFaso/17RS93-19) i od kokošjeg pileta u Ujedinjenim Arapskim Emiratima u 2015. (A/piletina/ Dubai/D2506/2015). HA geni otkrili su blisku vezu između četiriju virusa, s 97,9 % -99,9 % nukleotidnog identiteta. Filogenetska analiza pokazala je da marokanski virusi pripadaju lozi G1 i vjerojatno potječu s Bliskog istoka, kao što je objavljeno 2016. godine

Detection of Influenza D-Specific Antibodies in Bulk Tank Milk from Swedish Dairy Farms

Influenza D virus (IDV) has been detected in bovine respiratory disease (BRD) outbreaks, and experimental studies demonstrated this virus's capacity to cause lesions in the respiratory tract. In addition, IDV-specific antibodies were detected in human sera, which indicated that this virus plays a potential zoonotic role. The present study aimed to extend our knowledge about the epidemiologic situation of IDV in Swedish dairy farms, using bulk tank milk (BTM) samples for the detection of IDV antibodies. A total of 461 and 338 BTM samples collected during 2019 and 2020, respectively, were analyzed with an in-house indirect ELISA. In total, 147 (32%) and 135 (40%) samples were IDV-antibody-positive in 2019 and 2020, respectively. Overall, 2/125 (2%), 11/157 (7%) and 269/517 (52%) of the samples were IDV-antibody-positive in the northern, middle and southern regions of Sweden. The highest proportion of positive samples was repeatedly detected in the south, in the county of Halland, which is one of the counties with the highest cattle density in the country. In order to understand the epidemiology of IDV, further research in different cattle populations and in humans is required

Isolation of a Novel Swine Influenza Virus from Oklahoma in 2011 Which Is Distantly Related to Human Influenza C Viruses

Of the Orthomyxoviridae family of viruses, only influenza A viruses are thought to exist as multiple subtypes and has nonhuman maintenance hosts. In April 2011, nasal swabs were collected for virus isolation from pigs exhibiting influenza-like illness. Subsequent electron microscopic, biochemical, and genetic studies identified an orthomyxovirus with seven RNA segments exhibiting approximately 50% overall amino acid identity to human influenza C virus. Based on its genetic organizational similarities to influenza C viruses this virus has been provisionally designated C/Oklahoma/1334/2011 (C/OK). Phylogenetic analysis of the predicted viral proteins found that the divergence between C/OK and human influenza C viruses was similar to that observed between influenza A and B viruses. No cross reactivity was observed between C/OK and human influenza C viruses using hemagglutination inhibition (HI) assays. Additionally, screening of pig and human serum samples found that 9.5% and 1.3%, respectively, of individuals had measurable HI antibody titers to C/OK virus. C/OK virus was able to infect both ferrets and pigs and transmit to naive animals by direct contact. Cell culture studies showed that C/ OK virus displayed a broader cellular tropism than a human influenza C virus. The observed difference in cellular tropism was further supported by structural analysis showing that hemagglutinin esterase (HE) proteins between two viruses have conserved enzymatic but divergent receptor-binding sites. These results suggest that C/OK virus represents a new subtype of influenza C viruses that currently circulates in pigs that has not been recognized previously. The presence of multiple subtypes of co-circulating influenza C viruses raises the possibility of reassortment and antigenic shift as mechanisms of influenza C virus evolution

Prévalence de la maladie de la bronchite infectieuse aviaire au Maroc entre Juin 2018 et Avril 2019

Avian infectious bronchitis (IB) is mainly an upper respiratory tract infection caused by infectious bronchitisvirus (IBV) belonging to the Coronaviridae family. This work aims to assess the prevalence of IBV in different regions of Morocco using real-time RT-PCR, in order to better understand the epidemiological situation of the disease in these regions. Epidemiological analyses have shown that the IBV circulates with a high prevalence of 61% between 2018 and 2019, thus, the results obtained were valued and evaluated by a statistical study using the SPSS version 13 (Statistical Package for the Social Sciences). IB circulated with distinct prevalence’s in the different regions of Morocco, but this difference was not statistically significant. A peak of positivity was found in the BeniMellal-Khenifra, Draa-Tafilalet, and Souss-Massa regions. On the other hand, a very high vaccination rate against IB (90% of farms) in Morocco has been observed. Keywords: Avian infectious bronchitis, real-time RT-PCR, Prevalence, MoroccoLa bronchite infectieuse aviaire (BI) est principalement une infection des voies respiratoires supérieures causée par le virus de la bronchite infectieuse aviaire (IBV) appartenant à la famille des Coronaviridae. Le présent travail a pour objectif d’évaluer la prévalence de l’IBVdans sept différentes régions du Maroc en utilisant la RT-PCR en temps réel, afin de mieux connaitre la situation épidémiologique de la maladie dans ces régions. L’analyse épidémiologique a montré que l’IBV a circulé avec une forte prévalence de 61% entre 2018 et 2019, ainsi, les résultats obtenues ont été valorisées et évaluées par une étude statistique via la version 13 du logiciel SPSS (Statistical Package for the Social Sciences). L’infection à l’IBV a circulé avec des prévalences distinctes dans les différentes régions du Maroc, mais cette différence n’était pas statistiquement significative. Un pic de positivité a été mis en évidence dans les régions BeniMellal-Khenifra, Draa-Tafilalet, et Souss-Massa. D’autre part, un taux de vaccination très élevé contre la BI (90% des élevages) au Maroc a été constaté. Mots clés: Bronchite infectieuse aviaire, RT-PCR en temps réel, Prévalence, Maro

Genotypic characterisation of Avian paramyxovirus type-1 viruses isolated from aquatic birds in Uganda

Avian paramyxovirus type-1 (APMV-1) viruses of the lentogenic pathotypes are often isolated from wild aquatic birds and may mutate to high pathogenicity when they cross into poultry and cause debilitating Newcastle disease. This study characterised AMPV-1 isolated from fresh faecal droppings from wild aquatic birds roosting sites in Uganda. Fresh faecal samples from wild aquatic birds at several waterbodies in Uganda were collected and inoculated into 9–10-day-old embryonated chicken eggs. After isolation, the viruses were confirmed as APMV-1 by APMV-1-specific polymerase chain reaction (PCR). The cleavage site of the fusion protein gene for 24 representative isolates was sequenced and phylogenetically analysed and compared with representative isolates of the different APMV-1 genotypes in the GenBank database. In total, 711 samples were collected from different regions in the country from which 72 isolates were recovered, giving a prevalence of 10.1%. Sequence analysis of 24 isolates revealed that the isolates were all lentogenic, with the typical 111GGRQGR’L117 avirulent motif. Twenty-two isolates had similar amino acid sequences at the cleavage site, which were different from the LaSota vaccine strain by a silent nucleotide substitution T357C. Two isolates, NDV/waterfowl/Uganda/MU150/2011 and NDV/waterfowl/Uganda/MU186/2011, were different from the rest of the isolates in a single amino acid, with aspartate and alanine at positions 124 and 129, respectively. The results of this study revealed that Ugandan aquatic birds indeed harbour APMV-1 that clustered with class II genotype II strains and had limited genetic diversity

Enhanced Pathogenesis Caused by Influenza D Virus and Mycoplasma bovis Coinfection in Calves: a Disease Severity Linked with Overexpression of IFN-gamma as a Key Player of the Enhanced Innate Immune Response in Lungs

Bovine respiratory disease (BRD) is a major disease of young cattle whose etiology lies in complex interactions between pathogens and environmental and host factors. Despite a high frequency of codetection of respiratory pathogens in BRD, data on the molecular mechanisms and pathogenesis associated with viral and bacterial interactions are still limited. In this study, we investigated the effects of a coinfection with influenza D virus (IDV) and Mycoplasma bovis in cattle. Naive calves were infected by aerosol with a French IDV strain and an M. bovis strain. The combined infection shortened the incubation period, worsened the disease, and led to more severe macroscopic and microscopic lesions compared to these parameters in calves infected with only one pathogen. In addition, IDV promoted colonization of the lower respiratory tract (LRT) by M. bovis and increased white cell recruitment to the airway lumen. The transcriptomic analysis highlighted an upregulation of immune genes in the lungs of coinfected calves. The gamma interferon (IFN-gamma) gene was shown to be the gene most statistically overexpressed after coinfection at 2 days postinfection (dpi) and at least until 7 dpi, which correlated with the high level of lymphocytes in the LRT. Downregulation of the PACE4 and TMPRSS2 endoprotease genes was also highlighted, being a possible reason for the faster clearance of IDV in the lungs of coinfected animals. Taken together, our coinfection model with two respiratory pathogens that when present alone induce moderate clinical signs of disease was shown to increase the severity of the disease in young cattle and a strong transcriptomic innate immune response in the LRT, especially for IFN-gamma.IMPORTANCE Bovine respiratory disease (BRD) is among the most prevalent diseases in young cattle. BRD is due to complex interactions between viruses and/or bacteria, most of which have a moderate individual pathogenicity. In this study, we showed that coinfection with influenza D virus (IDV) and Mycoplasma bovis increased the severity of the respiratory disease in calves in comparison with IDV or M. bovis infection. IDV promoted M. bovis colonization of the lower respiratory tract and increased white cell recruitment to the airway lumen. The transcriptomic analysis highlighted an upregulation of immune genes in the lungs of coinfected calves. The IFN-gamma gene in particular was highly overexpressed after coinfection, correlated with the disease severity, immune response, and white cell recruitment in the lungs. In conclusion, we showed that IDV facilitates coinfections within the BRD complex by modulating the local innate immune response, providing new insights into the mechanisms involved in severe respiratory diseases