Publications - Publications

Protein quality of edible insects in the view of current assessment methods

Malla, N., Nørgaard, J. V., Roos, N. — Tue, 01 Aug 2023 16:53:21 +0200

Dromedaries (Camelus dromedarius) are of Low Susceptibility to Inoculation with Foot-and-Mouth Disease Virus Serotype O

Alexandersen, S., Wernery, U., Nagy, P., Frederiksen, T., Normann, P. — Sat, 01 Nov 2008 16:53:21 +0100

Two sheep and five dromedaries were inoculated with a highdose of a cattle-passaged type O strain of foot-and-mouth disease virus (FMDV). The sheep developed typical FMD. The inoculated camels, which were placed in contact with five further dromedaries and four sheep, showed no visible signs of illness or vesicular lesions. However, one of them had a raised body temperature at 3 days post-inoculation (pi) and a viraemia from days 2 to 10; probang samples from this animal were negative for infectious virus, but a low level of FMDV RNA was detected in a sample taken on day 6 pi, five other samples taken from days 3 to 28 being negative. Examination of mouth swabs indicated a low level of FMDV RNA at days 1-5 pi in four of the five inoculated camels, but no infectious FMDV or FMDV RNA was detected in serum, probang or mouth swab samples from contact-exposed animals (camels and sheep). All the contact-exposed camels and sheep and two of the inoculated camels were serologically negative for FMD when tested up to day 28. In contrast, the camel with viraemia became serologically positive from day 14, and the other two inoculated camels (which had been exposed to FMDV in an earlier experiment) became serologically positive from day 10. The experiment suggested that dromedaries (1) are of low susceptibility to FMDV serotype O, (2) do not transmit infection, even by close contact, and (3) are unlikely to play a significant epidemiological role in FMD.

Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks

Vibin, J., Chamings, A., Klaassen, M., Alexandersen, S. — Tue, 01 Dec 2020 16:53:21 +0100

Birds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ducks, Chestnut teals and Grey teals collected at different time points from a single location. We characterised a likely new species of duck aviadenovirus and a novel duck gyrovirus. We also report what, to the best of our knowledge, is the first finding of an avian orthoreovirus from Pacific black ducks and a rotavirus F from Chestnut teals. Other viruses characterised from the samples from these wild ducks belong to the virus families Astroviridae, Caliciviridae and Coronaviridae. Some of the viruses may have potential cross-species transmissibility, while others indicated a wide genetic diversity of duck viruses within a genus. The study also showed evidence of potential transmission of viruses along the East Asian—Australasian Flyway; potentially facilitated by migrating shorebirds. The detection and characterisation of several avian viruses not previously described, and causing asymptomatic but potentially also symptomatic infections suggest the need for more virus surveillance studies for pathogenic and potential zoonotic viruses in wildlife reservoirs.

Sequence comparison of the non-structural genes of four different types of Aleutian mink disease parvovirus indicates an unusual degree of variability

Gottschalck, E., Alexandersen, S., Storgaard, T., Bloom, M. E., Aasted, B. — Thu, 01 Sep 1994 16:53:21 +0200

The present work shows that at least four different sequence types of Aleutian mink disease parvovirus (ADV) are present in ADV isolates from mink. We here report the nucleotide sequences of these four types of ADV from nucleotide 123 to 2208 (map unit 3 to 46). This part of the genome encodes three non-structural (NS) proteins of ADV. Comparison of the deduced amino acid sequences of these NS proteins showed that the ADV proteins are much less conserved than the NS proteins from other members of the autonomous group of parvoviruses. In general, we found that the middle region of the ADV NS-1 protein was relatively well conserved among the types, while both the amino-and carboxy-terminal ends of the protein had higher amino acid variability. Interestingly, the putative NS-3 protein from type 3 ADV is truncated in the carboxy-terminal end. The molecular evolutionary relationship among the four types of ADV was examined. This analysis, taken together with the unusually high degree of variability of the ADV types, indicates that the ADV infection in mink is likely to be an old infection compared to the other parvovirus infections or, alternatively, that ADV accumulates sequence changes much faster than other parvoviruses.

Effect of the initial dose of foot-and-mouth disease virus on the early viral dynamics within pigs

Tue, 06 Oct 2009 16:53:21 +0200

This paper investigates the early viral dynamics of foot-and-mouth disease (FMD) within infected pigs. Using an existing within-host model, we investigate whether individual variation can be explained by the effect of the initial dose of FMD virus. To do this, we consider the experimental data on the concentration of FMD virus genomes in the blood (viral load). In this experiment, 12 pigs were inoculated with one of three different doses of FMD virus: low; medium; or high. Measurements of the viral load were recorded over a time course of approximately 11 days for every 8 hours. The model is a set of deterministic differential equations with the following variables: viral load; virus in the interstitial space; and the proportion of epithelial cells available for infection, infected and uninfected. The model was fitted to the data for each animal individually and also simultaneously over all animals varying only the initial dose. We showthat the general trend in the data can be explained by varying only the initial dose. The higher the initial dose the earlier the development of a detectable viral load.

Pathogenesis of disease caused by Aleutian mink disease parvovirus

Alexandersen, S. — Mon, 01 Jan 1990 16:53:21 +0100

A review of the pathogenesis of Aleutian mink disease parvovirus (ADV) infection based on recent knowledge gained by the author and collaborators is given. The review focuses mainly on the following topics. 1) Development of an easy, sensitive and fast assay for detection of ADV antigens and antibodies directed against these antigens. A highly sensitive rocket line immunoelectrophoretic assay (RLIE) was developed. This assay turned out to be 32 times more sensitive than the counter current electrophoresis assay routinely used to detect anti-ADV antibodies in ADV eradication programs, and moreover, ADV associated antigens could simultaneously be quantitatively detected in the same electrophoretic run. Later the assay was improved to make it more economical and easy to use and finally the assay, now termed the counter current line absorption immunoelectrophoresis (CCLAIE) assay, was slightly modified to adapt the test to screening programs. 2) Examination of surface properties of the virus and the antigens expressed during in vivo infection. In this chapter studies on the surface charge properties of ADV are described. Using charge-shift crossed immunoelectrophoresis the occurrence of amphiphilic proteins associated with ADV is shown and the significance of these findings in regard to biological properties are discussed. The first demonstration of intact ADV structural and nonstructural proteins in mink tissues is described and it is shown that the structural proteins of the cell culture adapted strain of ADV (ADV-G) also in vivo is 2-3000 dalton smaller than those of other ADVs, i.e. 75,000 and 85,000 dalton in ADV-G as opposed to 78,000 and 88,000 dalton in the other ADVs. 3) Studies on the pathogenesis of interstitial pneumonia caused by ADV in newborn mink kits. The features of ADV-induced interstitial pneumonia are described. Using Southern blot and in situ hybridization techniques it is shown that ADV replicates to high levels in alveolar type II cells and it is suggested that the permissive replication of the virus in these cells causes direct cytopathology, followed by decreased surfactant production and development of the characteristic clinical and pathological features of respiratory distress and hyaline membrane disease. 4) Comparison of the pathogenesis of acute versus chronic disease caused by ADV infection. The data obtained by in situ hybridization analysis of ADV infected mink, mink kits, and mink kits treated with anti-ADV antibodies are compared. The accumulated data suggested that the development of severe acute ADV-induced disease is linked to low or absent antibody titers paired with high levels of viral replication. In contrast, chronic disease is associated with high antibody titers and low levels of viral replication. 5) The molecular biology of ADV with special reference to the pathogenesis of disease caused by this virus. The biological significance of the DNA nucleotide sequence, the open reading frames, and the palindromic termini of ADV are briefly summarized. The transcription program and putative protein translation scheme of ADV-G is mentioned in detail and the similarities with and differences from the transcription maps of other parvoviruses are discussed. Finally, the possible roles of the unique features found in ADV transcription are related to the special pathogenic features of this virus.

Relative resistance of pigs to infection by natural aerosols of FMD virus

Donaldson, A. I., Alexandersen, S. — Sat, 12 May 2001 16:53:21 +0200

Detection and characterisation of coronaviruses in migratory and non-migratory Australian wild birds

Sat, 01 Dec 2018 16:53:21 +0100

We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016-17. Coronaviruses were detected in 141 samples (15.3%) from species of ducks, shorebirds and herons and from multiple sampling locations. Sequencing of selected positive samples found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive samples. Sequencing of the relatively conserved Orf1 PCR amplicons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.

Picornaviruses

Alexandersen, S., Knowles, N. J., Belsham, G. J., et al. — Fri, 29 Mar 2019 16:53:21 +0100

Picornaviruses are small, roughly spherical viruses with a protein shell. The picornavirus genome includes two untranslated regions, one preceding and one following the single open reading frame (ORF). The ORF is translated into a polyprotein that is usually processed by one or two virus-encoded proteinases. The variety of diseases caused by picornaviruses ranges from acute and sometimes fatal paralysis to mild respiratory disease and to inapparent infections in many hosts. Foot-and-mouth disease is a severe, clinically acute vesicular disease of cloven-hoofed animals, including domesticated and wild swine and ruminants. Swine vesicular disease virus (SVDV) is classified as an enterovirus within the family Picornaviridae and belongs to the species Enterovirus B. Like other picornaviruses, SVDV is non-enveloped. Encephalomyocarditis virus (EMCV) were subsequently detected in a variety of animal species. The impact of EMCV on public health is believed to be minimal.

The phosphoprotein gene of a dolphin morbillivirus isolate exhibits genomic variation at the editing site

Bolt, G., Alexandersen, S., Blixenkrone-Moller, M. — Sun, 01 Jan 1995 16:53:21 +0100

The nucleotide sequence of the phosphoprotein (P) gene of a dolphin morbillivirus (DMV) isolate was determined. Like those of other morbilliviruses the DMV P gene encoded P and C proteins in overlapping open reading frames and V protein by editing the P gene transcript. Among P mRNA based clones the editing site variants GGGC, GGGG, GAGC and GGGGGGC predicting a P protein, and the variants GGGGC and GGGGG predicting a V protein, were found. Surprisingly, the three variants GGGC, GGGG and GAGC were also found among clones generated from genomic RNA of the DMV isolate. Thus, more than one viral genome type appeared to be present in cells infected with the DMV isolate. By a similar analysis of the virus genomes in the tissue from which the DMV isolate was obtained, only the GGGC type was found, indicating that the GGGG and GAGC types arose during adaptation of the virus to growth in cell cultures. No editing site variants likely to have arisen by editing the GAGC type were encountered, and it remains to be determined whether mRNA encoding V protein can be transcribed from genomes with this editing site. Using antisera raised against the common N terminus and unique C termini of the predicted P and V proteins, the in vivo expression of these proteins was demonstrated.

The pathogenesis and diagnosis of foot-and-mouth disease

Alexandersen, S., Zhang, Z., Donaldson, A. I., Garland, A. J.M. — Tue, 01 Jul 2003 16:53:21 +0200

The pathogenesis of foot-and-mouth disease (FMD) is reviewed, taking account of knowledge gained from field and experimental studies and embracing investigations at the level of the virus, the cell, the organ, the whole animal and the herd or flock. The review also addresses the immune response and the carrier state in FMD. Progress made in understanding the pathogenesis of the disease is highlighted in relation to developments in diagnosis and methods of control.

Production of organic beef from dairy bull calves in Denmark - Effect of different production strategies on productivity, carbon footprint and biodiversity estimated by modelling

Mogensen, L., Kristensen, T., Kramer, C., Munk, A., Spleth, P., Vestergaard, M. — Sun, 01 Oct 2023 16:53:21 +0200

In Denmark, organic male calves from the dairy system are typically raised as steers leading to a high carbon footprint per kg meat produced, compared to other types of rearing. Therefore, there is a need to find mitigation options and develop future production systems with a lower climate impact. The aim of this study was to develop strategies for the rearing of organic bull calves considering the following factors: season of birth, feeding strategy, age at slaughter, and breed-type, where all strategies focus on achieving the lowest possible carbon footprint per kg carcass. A total of 10 strategies were compared for each of three breed types: Holstein, Charolais x Holstein, and Angus x Holstein. The carbon footprint was estimated using Life Cycle Assessment including all emissions until the animals leave the farm for slaughter and expressed per kg carcass taking into account different dressing percentages due to breed and age at slaughter. The carbon footprint per kg carcass including contribution from soil carbon changes was 18–32% lower for raising organic young bulls compared with that of organic steers. The strategy with a high feeding intensity and a slaughter age of 13 months had the lowest carbon footprint per kg carcass due to the lowest feed consumption per kg live weight gain (4.9 kg DM compared to 7.4 kg DM for the steer) and use of a high proportion of concentrated feed in the ration. In the strategy with slaughter age of 17 months, but the same high feeding intensity, carbon footprint per kg carcass increased around 6%. This was due to an increase in feed consumption and reduction in feed conversion due to the increasing age at slaughter. The strategy with a low feeding intensity and a high slaughter age (17 months) gave the highest carbon footprint per kg carcass amongst the rearing strategies compared for organically produced bulls, as a greater proportion of roughage in the ration increases enteric methane production from the digestion of the feed. The crossbred bulls compared to purebred dairy bulls had a lower carbon footprint (4–7%) due to higher dressing percentage, higher carcass weight (both types of crosses), and higher growth rates (Charolais crosses).

Effects of journey duration and temperature during pre-slaughter transport on behaviour of cull sows in lairage

Wed, 01 Nov 2023 16:53:21 +0100

This observational field study investigated the effects of journey duration, temperature, and waiting duration before unloading on the behaviour of 562 cull sows during lairage from 23 commercial loads. Each load consisted of sows originating from more than one herd, thus experiencing variable pre-slaughter transport and management. In lairage, sows were mixed in groups of 25, involving animals from all journey durations (min-max: 0.8–8.4 h) and video monitored for 60 min. At first most sows were in upright position (approximately 80–90%), decreasing to 30–40% after 30 min. After 60 min, 42% of the sows had initiated aggression (min-max: 0–43 events/sow), 28% had been subjected to aggressive behaviour (min-max: 0–14 events/sow), and 36% s were observed drinking (min-max: 0–16 events/sow). Several significant interactions were found between journey duration, the average temperature in the vehicle and lairage pen (averages: 4.3–26.2 °C) and waiting duration before unloading (min-max: 3–25 min). For example, after short journeys, sows exposed to higher temperature carried out more aggressive behaviour, while a higher temperature after long journeys was associated with more lying and less drinking. This suggests that the sows prioritised lying behaviour over drinking and establishing a dominance hierarchy. We discuss how the results may be interpreted as behavioural signs of fatigue, but further studies, for example involving quantification of physiological and motivational indicators, are needed to clarify this. Irrespectively, the present findings suggest that a stay in a lairage pen, as part of the pre-slaughter logistic chain, involves challenges for the welfare of the cull sows.

Detection and characterisation of canine astrovirus, canine parvovirus and canine papillomavirus in puppies using next generation sequencing

Bhatta, T. R., Chamings, A., Vibin, J., Alexandersen, S. — Sun, 01 Dec 2019 16:53:21 +0100

Gastroenteritis in young animals is a clinical presentation with many infectious and non- infectious aetiologies. We used next generation sequencing (NGS) to investigate the possible infectious causes of gastroenteritis in puppies from a dog kennel in Victoria, Australia. The near complete genome of a canine astrovirus was obtained from pooled faecal samples, and was found to be 94.7% identical with a canine astrovirus detected in the United Kingdom in 2012. The phylogenetic analysis of the capsid gene found similarities to those of canine astroviruses identified in Italy in 2005 and in UK and Hungary in 2012, but distant from that of a canine astrovirus previously identified in Australia in 2012. Thus, different serotypes of canine astrovirus are likely circulating in Australia. The close relationship to European astroviruses also suggested that there had been recent movements of ancestor canine astroviruses between Australia and Europe. NGS also detected other infections in the puppies including several canine papillomaviruses and a canine parvovirus (vaccine strain) as well as a very low level of campylobacter. Canine astrovirus was the probable cause of diarrhoea in these puppies, with the possible involvement of campylobacter bacteria. NGS was effective as a non-targeted method to determine the likely infectious cause of gastroenteritis.

Passive transfer of antiviral antibodies restricts replication of Aleutian mink disease parvovirus in vivo.

Alexandersen, S., Larsen, S., Cohn, A., et al. — Sun, 01 Jan 1989 16:53:21 +0100

When mink kits were infected neonatally with a highly virulent strain of Aleutian disease virus (ADV), 100% of both Aleutian and non-Aleutian genotype mink died of interstitial pneumonia characterized by permissive ADV infection of alveolar type II cells. Treatment of infected kits with either mink anti-ADV gamma globulin or mouse monoclonal antibodies against ADV structural proteins reduced mortality by 50 to 75% and drastically reduced the severity of clinical signs. Interestingly, mink kits that survived the acute pulmonary disease all developed the chronic form of immune complex-mediated Aleutian disease. Thus, the antibodies directed against ADV structural proteins were capable of modulating the in vivo pathogenicity from an acute fulminant disease to a chronic immune complex-mediated disorder. The mechanism of this modulation was examined by strand-specific in situ hybridization. We found that the number of ADV-infected type II cells was the same in both untreated and antibody-treated kits. However, in the treated kits, viral replication and transcription were restricted at the cellular level. These data suggested that antibodies prevented acute viral pneumonia by restricting the intracellular level of viral replication and that the relevant antigenic determinants were contained within the viral structural proteins. The restricted levels of viral replication and transcription seen in antibody-treated mink kits resembled the levels observed in infected adult mink and suggested a role of antiviral antibodies in development of persistent infection and chronic immune complex disease.

RESTRICTED HETEROGENEITY OF THE EARLY ANTIBODY RESPONSE TO ALEUTIAN DISEASE VIRUS IN MINK KITS

Alexandersen, S., Aasted, B. — Sat, 01 Nov 1986 16:53:21 +0100

Mink kits born of Aleutian disease (AD) negative dams were infected neonatally with different isolates of Aleutian disease virus (ADV). They were then sacrified at different days after infection (10 — 45 days) and their sera were analysed by different techniques for concentrations of immunoglobulins and quality of the produced antibodies to ADV. The infected mink kits produced significantly higher concentrations of IgM and IgG immunoglobulins than non‐infected‐age matched control mink (p<0.001). Eight percent of the sera from the infected mink kits exhibited a restricted heterogeneous gammaglobulin profile as shown by serum electrophoresis. These findings were further investigated by other techniques such as SDS‐PAGE and crossed serum line immunoelectrophoresis. It is concluded that mink kits when infected neonatally with ADV start to develop hypergammaglobulinemia soon after infection, and that a small percentage of the mink react with a gammaglobulin response of restricted heterogeneity. 1986 Acta Pathologica, Microbiologica et Immunologica Scandinavica

Patterns, risk factors and characteristics of reported and perceived foot-and-mouth disease (FMD) in Uganda

Ayebazibwe, C., Tjørnehøj, K., Mwiine, F. N., et al. — Fri, 01 Jan 2010 16:53:21 +0100

Patterns of outbreaks of foot-and-mouth disease (FMD) in Uganda were elucidated from spatial and temporal retrospective data retrieved from monthly reports from District Veterinary Officers (DVOs) to the central administration for the years spanning 2001-2008. An assessment of perceived FMD occurrence, risk factors and the associated characteristics was made based on semistructured questionnaires administered to the DVOs. During this period, a total of 311 FMD outbreaks were reported in 56 (70%) out of Uganda's 80 districts. The number of reported FMD outbreaks changed over time and by geographical regions. Occurrence of FMD was significantly associated with the dry season months (p = 0.0346), the time when animals movements are more frequent. The average number of FMD outbreaks was higher for some sub-counties adjacent to national parks than for other subcounties, whilst proximity to international border only seemed to play a role at the southern border. DVOs believed that the major risk factor for FMD outbreaks was animal movements (odds ratio OR 50.8, confidence interval CI 17.8-144.6) and that most outbreaks were caused by introduction of sick animals.

Evolutionary and network analysis of virus sequences from infants infected with an Australian recombinant strain of human parechovirus type 3

Alexandersen, S., Nelson, T. M., Hodge, J., Druce, J. — Fri, 01 Dec 2017 16:53:21 +0100

We present the near complete virus genome sequences with phylogenetic and network analyses of potential transmission networks of a total of 18 Australian cases of human parechovirus type 3 (HPeV3) infection in infants in the period from 2012-2015. Overall the results support our previous finding that the Australian outbreak strain/lineage is a result of a major recombination event that took place between March 2012 and November 2013 followed by further virus evolution and possibly recombination. While the nonstructural coding region of unknown provenance appears to evolve significantly both at the nucleotide and amino acid level, the capsid encoding region derived from the Yamagata 2011 lineage of HPeV3 appears to be very stable, particularly at the amino acid level. The phylogenetic and network analyses performed support a temporal evolution from the first Australian recombinant virus sequence from November 2013 to March/April 2014, onto the 2015 outbreak. The 2015 outbreak samples fall into two separate clusters with a possible common ancestor between March/April 2014 and September 2015, with each cluster further evolving in the period from September to November/December 2015.

Sites of replication of bovine respiratory syncytial virus in naturally infected calves as determined by in situ hybridization

Viuff, B., Uttenthal, Å., Tegtmeier, C., Alexandersen, S. — Mon, 01 Jul 1996 16:53:21 +0200

Replication of bovine respiratory syncytial virus (BRSV) was studied in three naturally infected calves by in situ hybridization using strand-specific RNA probes. One of the calves was a 5-month-old Friesian, the other two calves were a 3-month-old and a 3-week-old Jersey. Two Jersey calves, 3 months and 3 weeks of age, served as controls. Replication of BRSV took place in the luminal lining of the respiratory tract. In one of the BRSV infected animals (calf No. 1), replication was especially seen in the bronchi, whereas in the two other animals (calf Nos. 2 and 3) replication of BRSV was demonstrated in the bronchiolar epithelial cells and in alveolar cells. Syncytia were often observed in the bronchiolar walls and in alveoli and such syncytia were always replicating BRSV. By immunohistochemistry it was possible to demonstrate BRSV antigen at the same location as replication of BRSV was detected. In tissue outside the respiratory tract neither BRSV antigen nor replication of BRSV could be demonstrated.

The protective capacity of high payload FMDV A22 IRQ vaccine in sheep against direct-contact challenge with a heterologous, contemporary FMDV A strain from South East Asia

Horsington, J., Nfon, C., Bittner, H., et al. — Fri, 01 Jun 2018 16:53:21 +0200

Foot-and-mouth disease (FMD) is an acute, highly contagious viral disease of domestic and wild cloven-hoofed animals, caused by FMD virus (FMDV). An FMD outbreak can cause major production losses and have significant implications for trade. Vaccination can assist in controlling the disease, and emergency vaccination using high antigen payload vaccines (>6 PD₅₀/dose) is considered an important control approach in the event of an outbreak. In recent years there has been a divergence of serotype A viruses in South East Asia (SEA) into several distinct genetic and antigenic clusters. Numerous variants were found to poorly match serotype A vaccines commonly included in international antigen banks. This study examined the ability of single vaccination with high-potency monovalent A22 IRQ vaccine to protect sheep following challenge with the A/VIT/15/2012 strain, just four days following vaccination. The vaccine proved effective at limiting clinical disease but did not prevent infection.

Antibodies against foot-and-mouth disease (FMD) virus in African Buffalos syncerus caffer in selected national parks in Uganda (2001-2003)

Ayebazibwe, C., Mwiine, F. N., Balinda, S. N., et al. — Sun, 01 Aug 2010 16:53:21 +0200

In East Africa, the foot-and-mouth disease (FMD) virus (FMDV) isolates have over time included serotypes O, A, C, Southern African Territories (SAT) 1 and SAT 2, mainly from livestock. SAT 3 has only been isolated in a few cases and only in African buffalos (Syncerus caffer). To investigate the presence of antibodies against FMDV serotypes in wildlife in Uganda, serological studies were performed on buffalo serum samples collected between 2001 and 2003. Thirty-eight samples from African buffalos collected from Lake Mburo, Kidepo Valley, Murchison Falls and Queen Elizabeth National Parks were screened using Ceditest ^® FMDV NS to detect antibodies against FMDV non-structural proteins (NSP). The seroprevalence of antibodies against non-structural proteins was 74%. To characterize FMDV antibodies, samples were selected and titrated using serotype-specific solid phase blocking enzyme linked immunosorbent assay (ELISAs). High titres of antibodies (≥1 : 160) against FMDV serotypes SAT 1, SAT 2 and SAT 3 were identified. This study suggests that African buffalos in the different national parks in Uganda may play an important role in the epidemiology of SAT serotypes of FMDV.

Epidemiological and Evolutionary Inference of the Transmission Network of the 2014 Highly Pathogenic Avian Influenza H5N2 Outbreak in British Columbia, Canada

Xu, W., Berhane, Y., Dubé, C., et al. — Thu, 04 Aug 2016 16:53:21 +0200

The first North American outbreak of highly pathogenic avian influenza (HPAI) involving a virus of Eurasian A/goose/Guangdong/1/1996 (H5N1) lineage began in the Fraser Valley of British Columbia, Canada in late November 2014. A total of 11 commercial and 1 non-commercial (backyard) operations were infected before the outbreak was terminated. Control measures included movement restrictions that were placed on a total of 404 individual premises, 150 of which were located within a 3 km radius of an infected premise(s) (IP). A complete epidemiological investigation revealed that the source of this HPAI H5N2 virus for 4 of the commercial IPs and the single non-commercial IP likely involved indirect contact with wild birds. Three IPs were associated with the movement of birds or service providers and localized/environmental spread was suspected as the source of infection for the remaining 4 IPs. Viral phylogenies, as determined by Bayesian Inference and Maximum Likelihood methods, were used to validate the epidemiologically inferred transmission network. The phylogenetic clustering of concatenated viral genomes and the median-joining phylogenetic network of the viruses supported, for the most part, the transmission network that was inferred by the epidemiologic analysis.

Further studies to quantify the dose of natural aerosols of foot-and-mouth disease virus for pigs

Alexandersen, S., Donaldson, A. I. — Tue, 01 Jan 2002 16:53:21 +0100

Foot-and-mouth disease virus (FMDV) can be spread by a variety of mechanisms, including wind. Simulation models, developed to predict the risk of airborne spread, have played an important part in decision making in some outbreaks. The amount of airborne virus excreted as well as the minimal infectious dose (MID) of FMDV for different species are important determinants of airborne spread. The objective of this study was to obtain data for the O₁ Lausanne, O SKR 2000 and O UKG 2001 strains of FMDV to enhance the capability of such models. Pigs were exposed to naturally generated aerosols of the three strains using an experimental design which delivered high doses of the two strains O₁ Lausanne and O SKR 2000 over a short period, or of the O UKG 2001 strain over an extended period. The average excretion of the O₁ Lausanne strain was 10^6.4 TCID₅₀ per pig per hour. The excretion of the O SKR 2000 strain averaged 10^5.8 and the O UKG 2001 strain 10^6.1 TCID per pig per 24 h. The results show that the previous estimate of 'above' 800 TCID₅₀ as the MID50 for the O₁ Lausanne strain is a considerable under-estimate and that the real dose may be as high as 6000 TCID₅₀. A dose of around 650 TCID₅₀ of the O SKR 2000 strain failed to infect any pigs. Thus, the aerosol MID₅₀ for pigs for this isolate is at least 1000 TCID₅₀ and likely to be as high or higher than the O₁ Lausanne strain. The exposure of pairs of recipient pigs kept physically separated from donor pigs in a series of rooms to aerosol exposure doses of the O UKG 2001 strain of around 50 TCID₅₀ per min for 24-48 h failed to infect any of eight pigs. Thus, the present experiment confirms our previous findings [1, 2] that pigs, compared to cattle and sheep, are relatively resistant to infection with airborne FMDV.

Prevalence estimates of antibodies towards foot-and-mouth disease virus in small ruminants in uganda

Balinda, S. N., Tjørnehøj, K., Muwanika, V. B., et al. — Tue, 01 Dec 2009 16:53:21 +0100

Foot-and-mouth disease (FMD) is endemic in Uganda with control strategies focusing on vaccination of cattle, while small ruminants are largely ignored. In order for Uganda to establish effective control strategies, it is crucial that the epidemiology of the disease is fully understood. This study summarizes results of serological investigations of sheep and goats for antibodies to FMDV from four districts in 2006 following an FMD outbreak in the region and from an attempted comprehensive random sampling in two districts in 2007. Antibodies were quantified and serotyped using competitive ELISA for antibodies towards non-structural proteins (NSP) and structural proteins towards serotype O, and blocking ELISA for antibodies towards the seven serotypes of FMD virus (FMDV). In 2006, sheep and goats in Bushenyi and Isingiro districts were free from antibodies towards FMDV, while herds in Kasese and Mbarara districts excluding Kahendero village were all positive for antibodies towards NSP and SP-O. In 2007, mean prevalence estimates of antibodies towards FMDV NSP was 14% in goats and 22% in sheep in Kasese district, while Bushenyi was still free. The difference between these two districts probably reflects different levels of FMDV challenge attributed to the variation in exposure rates which again in part may be as a result of the differing husbandry practices. Contrary to 2006, with clear antibodies towards serotype O, the serotype-specificity of the antibodies was less clear in 2007, as antibodies towards both serotype O and SAT serotypes were identified. Our results show that goats and sheep are infected during FMD outbreaks, and that they may be useful for determining the serotype of FMD outbreaks in Uganda, if they are sampled shortly after an outbreak.

Advantages and Disadvantages of Using Live Vaccines Risks and Control Measures

Alexandersen, S. — Mon, 01 Jan 1996 16:53:21 +0100

Acute interstitial pneumonia in mink kits

Alexandersen, S. — Wed, 01 Jan 1986 16:53:21 +0100

Organ homogenates from kits that died of interstitial pneumonia were inoculated into adult Aleutian disease virus (ADV)-negative mink and shown to contain infectious ADV. Acute interstitial pneumonia was experimentally reproduced with the organ homogenate but only by inoculation of newborn kits born from ADV-negative dams. Older kits and kits from ADV-positive dams did not develop interstitial pneumonia, but later developed the classic form of Aleutian disease. Electron microscopic examination was done on purified suspensions of defined ADV isolates and on purified organ homogenates from kits with spontaneous or experimental interstitial pneumonia. In kits from both groups a virus, morphologically resembling the defined ADV isolates, was demonstrated. Findings of intranuclear inclusion bodies and intranuclear ADV antigen in alveolar type-II cells in affected lungs and the lack of immunologically mediated lesions suggest that lung lesions result from primary viral injury to alveolar type-II cells. Experiments also showed that infection of dams with ADV before pregnancy decreased the number of kits per mated dam and infection with ADV in mid-pregnancy caused fetal death, fetal resorption, or abortion.

Purification and characterization of the major nonstructural protein (NS- 1) of Aleutian mink disease parvovirus

Christensen, J., Pedersen, M., Aasted, B., Alexandersen, S. — Sun, 01 Jan 1995 16:53:21 +0100

We have previously described the expression of the major nonstructural protein (NS-1) of Aleutian mink disease parvovirus (ADV) in insect cells by using a baculovirus vector (J. Christensen, T. Storgaard, B. Bloch, S. Alexandersen, and B. Aasted, J. Virol. 67:229-238, 1993). To study its biochemical properties, ADV NS-1 was expressed in Sf9 insect cells and purified to apparent homogeneity with a combination of nuclear extraction, Zn²⁺ ion chromatography, and immunoaffinity chromatography on monoclonal antibodies. The purified protein showed ATP binding and ATPase- and ATP- or dATP-dependent helicase activity requiring either Mg²⁺ or Mn²⁺ as a cofactor. The ATPase activity of NS-1 was efficiently stimulated by single- stranded DNA and, to a lesser extent, double-stranded DNA. We also describe the expression, purification, and characterization of a mutant NS-1 protein, in which a lysine in the putative nucleotide binding consensus sequence of the molecule was replaced with serine. The mutated NS-1 was expressed at 10- fold higher levels than wild-type NS-1, but it exhibited no ATP binding, ATPase, or helicase activity. The availability of large amounts of purified functional NS-1 protein will facilitate studies of the biochemistry of ADV replication and gene regulation leading to disease in mink.

The early pathogenesis of foot-and-mouth disease in pigs infected by contact

Alexandersen, S., Oleksiewicz, M. B., Donaldson, A. I. — Mon, 01 Jan 2001 16:53:21 +0100

Foot-and-mouth disease (FMD) is a highly contagious, economically important virus disease of cloven-hoofed animals. The objective of the present study was to examine the early pathogenesis of FMD in pigs by a quantitative time-course study. Under experimental conditions, recipient pigs were infected by contact with donor pigs affected by FMD. Every 24 h from day 1 to day 4 after exposure, two recipient pigs were selected randomly, killed and necropsied. A range of tissues were analysed by a quantitative TaqMan RT-PCR method and by titration of FMD virus on primary bovine thyroid cells. The titres of virus determined by assay in cell culture and calculated from the quantitative TaqMan data correlated strongly (r > 0.9), thereby establishing the validity of the TaqMan calculations. The data indicated that the replication of virus in the lungs contributes only in small part to airborne virus excretion. Sites in the pharynx, trachea and nasal mucosa are probably more important in that regard. The sites of earliest virus infection and possibly replication in recipient pigs appeared to be in the pharynx (soft palate, tonsil and floor of pharynx). The data indicated that FMD virus replication in pigs is rapid and that the majority of virus amplification occurs in the skin. A model for the progression of infection is proposed, indicating initial spread from the pharyngeal region, through regional lymph nodes and via the blood to epithelial cells, resulting in several cycles of virus amplification and spread.

Evaluation of automated RT-PCR to accelerate the laboratory diagnosis of foot-and-mouth disease virus

Reid, S. M., Grierson, S. S., Ferris, N. P., Hutchings, G. H., Alexandersen, S. — Sat, 01 Feb 2003 16:53:21 +0100

Automated fluorogenic (5′ nuclease probe-based) reverse transcription polymerase chain reaction (RT-PCR) procedures were evaluated for the diagnosis of foot-and-mouth disease (FMD) using suspensions of vesicular epithelium, heparinised or clotted blood, milk and oesophageal-pharyngeal fluid ('probang') samples from the United Kingdom (UK) 2001 epidemic and on sera from animals experimentally infected with the outbreak serotype O FMD virus strain. A MagNA Pure LC was initially programmed to automate the nucleic acid extraction and RT procedures with the PCR amplification carried out manually by fluorogenic assay in a GeneAmp® 5700 Sequence Detection System. This allowed 32 samples to be tested by one person in a typical working day or 64 samples by two people within 10-12 h. The PCR amplification was later automated and a protocol developed for one person to complete a single test incorporating 96 RT-PCR results within 2 working days or for two people to do the same thing in around 12 h. The RT-PCR results were directly compared with those obtained by the routine diagnostic tests of ELISA and virus isolation in cell culture. The results on blood, probang and milk samples were in broad agreement between the three procedures but specific RT-PCR protocols for such material have to be fully optimised as perhaps have the positive-negative acceptance criteria. However, the automated RT-PCR achieved definitive diagnostic results (positive or negative) on supernatant fluids from first passage inoculated cell cultures and its sensitivity was greater than ELISA on suspensions of vesicular epithelium (ES) and at least equivalent to that of virus isolation in cell culture. The combined tests of ELISA, virus isolation in cell culture and RT-PCR might, therefore, only be required for confirmation of a first outbreak of FMD in a previously FMD-free country. Should a prolonged outbreak subsequently occur, then either ELISA plus RT-PCR or else RT-PCR alone could be used as the laboratory diagnostic tool(s). Either approach would eliminate the requirement for sample passage in cell culture and considerably advance the issue of laboratory diagnostic test results.

Localization of growth factor mRNA in the bovine oviduct

Viuff, D., Hyttel, P., Greve, T., Alexandersen, S. — Fri, 01 Oct 1993 16:53:21 +0100

Predicting the spread of foot and mouth disease by airborne virus

Donaldson, A. I., Alexandersen, S. — Sun, 01 Dec 2002 16:53:21 +0100

Foot and mouth disease (FMD) can spread by a variety of mechanisms which, under certain climatic and epidemiological conditions, includes the windborne spread of disease. Recent advances in knowledge of the aerobiological features of FMD are described. The strain of virus and species of infected animal are major determinants of airborne virus emission. Pigs emit most virus, cattle and sheep lesser but similar amounts to each other. Peak excretion of airborne virus by sheep occurs before the clinical phase of disease, whereas with cattle and pigs, it coincides with the development of early clinical disease. The probability of aerogenous infection differs greatly between livestock species. Cattle are the most susceptible, followed by sheep, whereas pigs are very resistant. Computer-based simulation models have been developed to analyse and predict the risk of airborne spread of FMD and have been used successfully during outbreaks to support decision-making. Further research is required to refine and extend the models for operational use.

Nucleotide sequence analysis of aleutian mink disease parvovirus shows that multiple virus types are present in infected mink

Tue, 01 Jan 1991 16:53:21 +0100

Different isolates of Aleutian mink disease parvovirus (ADV) were cloned and nucleotide sequenced. Analysis of individual clones from two in vivo-derived isolates of high virulence indicated that more than one type of ADV DNA were present in each of these isolates. Analysis of several clones from two preparations of a cell culture-adapted isolate of low virulence showed the presence of only one type of ADV DNA. We also describe the nucleotide sequence from map units 44 to 88 of a new type of ADV DNA. The new type of ADV DNA is compared with the previously published ADV sequences, to which it shows 95% homology. These findings indicate that ADV, a single-stranded DNA virus, has a considerable degree of variability and that several virus types can be present simultaneously in an infected animal.

Severe Human Case of Zoonotic Infection with Swine-Origin Influenza A Virus, Denmark, 2021

Andersen, K. M., Vestergaard, L. S., Nissen, J. N., et al. — Thu, 01 Dec 2022 16:53:21 +0100

During routine surveillance at the National Influenza Center, Denmark, we detected a zoonotic swine influenza A virus in a patient who became severely ill. We describe the clinical picture and the genetic characterization of this variant virus, which is distinct from another variant found previously in Denmark.

Novel Human Parechovirus 3 Diversity, Recombination, and Clinical Impact Across 7 Years

Bialasiewicz, S., May, M., Tozer, S., et al. — Sun, 15 Jan 2023 16:53:21 +0100

Background: A novel human parechovirus 3 Australian recombinant (HPeV3-AR) strain emerged in 2013 and coincided with biennial outbreaks of sepsis-like illnesses in infants. We evaluated the molecular evolution of the HPeV3-AR strain and its association with severe HPeV infections. Methods: HPeV3-positive samples collected from hospitalized infants aged 5-252 days in 2 Australian states (2013-2020) and from a community-based birth cohort (2010-2014) were sequenced. Coding regions were used to conduct phylogenetic and evolutionary analyses. A recombinant-specific polymerase chain reaction was designed and utilized to screen all clinical and community HPeV3-positive samples. Results: Complete coding regions of 54 cases were obtained, which showed the HPeV3-AR strain progressively evolving, particularly in the 3′ end of the nonstructural genes. The HPeV3-AR strain was not detected in the community birth cohort until the initial outbreak in late 2013. High-throughput screening showed that most (>75%) hospitalized HPeV3 cases involved the AR strain in the first 3 clinical outbreaks, with declining prevalence in the 2019-2020 season. The AR strain was not statistically associated with increased clinical severity among hospitalized infants. Conclusions: HPeV3-AR was the dominant strain during the study period. Increased hospital admissions may have been from a temporary fitness advantage and/or increased virulence.

Neonatal parechovirus infection

Wed, 01 Jun 2022 16:53:21 +0200

Diverse Bacterial Resistance Genes Detected in Fecal Samples From Clinically Healthy Women and Infants in Australia—A Descriptive Pilot Study

Guernier-Cambert, V., Chamings, A., Collier, F., Alexandersen, S. — Fri, 17 Sep 2021 16:53:21 +0200

The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs), the so-called “resistome.” In Australia, where antibiotic use is high and resistance rates in some common pathogens are increasing, very little is known about the human resistome. To assess the presence and diversity of ARGs in the gut of Australians from south-eastern Victoria, we investigated fecal samples from clinically healthy infants and pregnant women using non-targeted (shotgun metagenomics sequencing or SMS) and targeted sequencing (two Ion Ampliseq^TM panels). All methods detected ARGs in all samples, with the detection overall of 64 unique genes conferring resistance to 12 classes of antibiotics. Predominant ARGs belonged to three classes of antibiotics that are the most frequently prescribed in Australia: tetracycline, β-lactams and MLS_B (macrolide, lincosamide, streptogramin B). The three bacterial Orders commonly identified as carrying ARGs were Clostridiales, Bacteroidales, and Enterobacteriales. Our preliminary results indicate that ARGs are ubiquitously present and diverse among the gut microbiota of clinically healthy humans from south-eastern Victoria, Australia. The observed resistance pattern partly overlaps with antimicrobial usage in human medicine in Australia, but ARGs to tetracycline are more common than could be expected. Our current sample is small and limited to south-eastern Victoria, and more data on healthy individuals will be needed to better depict resistance patterns at the population level, which could guide population and/or environmental monitoring and surveillance of antibiotic resistance on various spatio-temporal scales in Australia. For future studies, we recommend using the Ion Ampliseq^TM Antimicrobial Resistance Research panel, which is sensitive and user-friendly, or combining several methods to increase the detected diversity.

Ability to detect antibodies to beak and feather disease virus in blood on filter paper decreases with duration of storage

Wed, 01 Dec 2021 16:53:21 +0100

Background: Beak and feather disease virus (BFDV) is a circovirus that infects captive and wild psittacine birds, and is of conservation concern. The haemagglutination inhibition (HI) assay is used to determine antibody titres against BFDV, and the use of dried blood spots (DBS) on filter paper stored at room temperature has been suggested to be an equally valid technique to the use of frozen serum. However, research on other pathogens has found variable results when investigating the longevity of antibodies stored on DBS at room temperature. Consequently, we aimed to test the temporal stability of antibodies to BFDV in DBS samples stored long-term at room temperature. A further goal was to add to the current knowledge of antibody response to naturally acquired BFDV infection in crimson rosellas (Platycercus elegans). Methods: Blood was collected from wild P. elegans in Victoria, Australia, that had been live-trapped (n = 9) or necropsied (n = 11). BFDV virus load data were obtained from blood stored in ethanol by real-time quantitative PCR (qPCR); antibody titres were obtained by HI assay from either DBS or serum samples, which had been collected concurrently. All HI assays were performed commercially by the Veterinary Diagnostic Laboratory (VDL) in Charles Sturt University, Australia, who were blind to BFDV blood status. Results: HI titres from DBS stored at room temperature declined significantly over time (∼80 weeks). By contrast, frozen serum samples assayed after 80 weeks in storage all had high HI titres, only varying up to one dilution step from the initial HI titres obtained from DBS at 3-6 weeks after sampling. Weak HI titres from DBS samples all came back negative when the test was repeated only nine weeks later. Novel high HI titres were reported in P. elegans, and while most birds with high antibody titres had corresponding negative qPCR results, a single subadult presented with high HI titres and virus load simultaneously. Conclusion: Detection of antibodies on filter paper stored at room temperature decreases over time, increasing the chances of false negatives in these samples, and in repeated testing of samples with weak HI titres. Consequently, serum should be the preferred sample type to use for seroepidemiological studies on BFDV in parrots and other bird species. When not possible, it may help to store DBS on filter paper at -20 °C or lower. However, prompt testing of DBS samples (e.g., <6 weeks in storage) is recommended pending further research on antibody temporal stability. We also show that P. elegans, especially adults, can produce high antibody titres against BFDV, which may help them resist infection.

Exploring the cause of diarrhoea and poor growth in 8–11-week-old pigs from an australian pig herd using metagenomic sequencing

Bhatta, T. R., Chamings, A., Alexandersen, S. — Sun, 01 Aug 2021 16:53:21 +0200

Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.

Comparative subgenomic mRNA profiles of SARS-CoV-2 Alpha, Delta and Omicron BA.1, BA.2 and BA.5 sub-lineages using Danish COVID-19 genomic surveillance data

Tang, M. H. E., Ng, K. L., Edslev, S. M., et al. — Sat, 01 Jul 2023 16:53:21 +0200

Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly spread worldwide in the population since it was first detected in late 2019. The transcription and replication of coronaviruses, although not fully understood, is characterised by the production of genomic length RNA and shorter subgenomic RNAs to make viral proteins and ultimately progeny virions. Observed levels of subgenomic RNAs differ between sub-lineages and open reading frames but their biological significance is presently unclear. Methods: Using a large and diverse panel of virus sequencing data produced as part of the Danish COVID-19 routine surveillance together with information in electronic health registries, we assessed the association of subgenomic RNA levels with demographic and clinical variables of the infected individuals. Findings: Our findings suggest no significant statistical relationship between levels of subgenomic RNAs and host-related factors. Interpretation: Differences between lineages and subgenomic ORFs may be related to differences in target cell tropism, early virus replication/transcription kinetics or sequence features. Funding: The author(s) received no specific funding for this work.

Replacing silage with large amounts of concentrate and straw affects milk production, economics and climate differently in Holstein and Jersey Cows

Børsting, C. F., Olijhoek, D. W., Hellwing, A. L.F., et al. — Fri, 01 Sep 2023 16:53:21 +0200

With droughts becoming more frequent due to climate changes alternative feeding strategies are required. The aim of this study was to examine the effects of replacing all or part of the silage component with barley straw and concentrates for Holstein and Jersey cows. Forty-nine Holstein and 43 Jersey cows were fed either the C49 diet (Roughage-to-concentrate ratio [% of DM; dry matter] of 51:49), a diet where concentrate constituted 70% of DM (i.e., diet C70; 30:70), or the extreme diet (i.e., C91; 9:91), where 91% of DM was concentrate and 9% of DM was barley straw. Cows were allowed up to 2.65 kg DM per day from concentrate in the automatic milking system (AMS). Cows were fed their diets for 5 weeks. All diets were formulated to provide the same daily net energy intake. Daily feed intake and milk production responses were recorded. Volatile fatty acid profiles in rumen fluid were measured for Holstein cows. Impact on economy and carbon footprint were calculated. Data were analyzed using a general linear mixed model. For both breeds, total dry matter intake (i.e., AMS concentrate + partially mixed ration) decreased with increasing concentrate proportion. In neither Holstein nor Jersey, experimental diet affected milk yield. A decrease in fat percentage and ECM was observed for both breeds, when the level of concentrate was increased. However, there was an interaction between diet and breed for fat percentage and for energy-corrected milk yield (ECM), and there was an interaction for feed efficiency expressed as kg of ECM/kg of DM intake. For Holstein cows, acetate molar proportion in rumen liquid decreased and propionate molar proportion increased when silage was reduced. Regardless of breed, increasing concentrate in the ration did not affect carbon footprint per kg ECM, but caused a decrease per cow per day, and per kg DM intake. However, if the contribution from direct land use changes and soil C were taken into account, increasing concentrate in the ration reduced carbon footprint per kg ECM due to decreased proportion of soybean meal in C75 and C91 diets. Production of milk from predominantly concentrate based diets containing no grass silage reduced income over feed cost for both breeds but more for Holsteins. In conclusion, results showed that it is possible to keep dairy herds and produce milk even during extreme drought, when availability of silage is minimal, whereas such ration decreased income over feed cost.

Bioacoustics as a tool to assess health and welfare of farm animals: opportunities and limitations

Coutant, M. P., Briefer, E. F., Villain, A. S. . — Tue, 01 Aug 2023 16:53:21 +0200

Relationship among indicators of pain and stress in response to piglet surgical castration: an exploratory analysis

Coutant, M. P., Malmkvist, J., Foldager, L., Herskin, M. S. — Sun, 01 Jan 2023 16:53:21 +0100

Multi-dimensional approaches are suggested as advantageous for evaluation of pain and/or stress at piglet castration, but the interpretation of data from such approaches is limited by a lack of understanding of relationships among different types of indicators and associated parameters. This paper used an exploratory approach to evaluate the interrelationships between different physiological, vocal, and behavioral indicators obtained during and after surgical castration of 580 piglets aged 3-4 days. The data, obtained from two experimental studies, were examined by analyses of correlations and by principal component analyses (PCA). Principal components were analyzed in mixed effects models. Each type of indicator (vocalization, resistance movement, saliva cortisol concentration, behavioral response in a social motivation test, behavior in the home pen, reaction to human) mainly contributed to separate principal components in the PCA and showed relatively low correlation coefficients between each other, indicating a variation in the response explained by the indicator types. Even within a type of indicator, specific parameters were, in several cases, found to explain different aspects of the piglet response. Overall, the results point to the importance of careful consideration of the differences existing among indicator types and highlight the need for further methodological development in that domain.

Invited review

Welk, A., Otten, N. D., Jensen, M. B. — Fri, 01 Sep 2023 16:53:21 +0200

The aim of this systematic review was to summarize the literature assessing the effects of milk feeding practices on behavior, health, and performance on dairy calves. Peer-reviewed, published articles, written in English, directly comparing the effects of milk allowance, milk feeding methods, or milk feeding frequency on dairy calves were eligible for inclusion. Outcome measures could include sucking behavior, sucking on a teat (nutritive sucking, non-nutritive sucking on a teat), abnormal sucking behavior (non-nutritive sucking on pen fixtures, other oral behaviors, or cross-sucking), signs of hunger (vocalizations or unrewarded visits at the milk feeder), activity (lying time or locomotor play), feeding behavior (milk intake, starter intake, milk meal duration, or starter meal duration), growth (body weight or average daily gain), and health (occurrence of diarrhea, respiratory disease, or mortality). We conducted 2 targeted searches using Web of Science and PubMed to identify key literature. The resulting articles underwent a 2-step screening process. This process resulted in a final sample of 94 studies. The majority of studies investigated milk allowance (n = 69). Feeding higher milk allowances had a positive or desirable effect on growth, reduced signs of hunger, and increased locomotor play behavior during the preweaning period, whereas starter intake was reduced. Studies addressing health pointed to no effect of milk allowance, with no consistent evidence indicating that higher milk allowances result in diarrhea. Studies addressing milk feeding methods (n = 14) found that feeding milk by teat reduced cross-sucking and other abnormal oral behaviors. However, results on the effect of access to a dry teat were few and mixed. Milk feeding frequency (n = 14 studies) appeared to have little effect on feed intakes and growth; however, there is some evidence that calves with lower feeding frequency experience hunger. Overall, findings strongly suggest feeding higher volumes of milk using a teat; however, further work is needed to determine the optimal feeding frequency for dairy calves.

Invited review

Ritter, C., Koralesky, K. E., Saraceni, J., Roche, S., Vaarst, M., Kelton, D. — Fri, 01 Sep 2023 16:53:21 +0200

The use of qualitative research in dairy science has increased considerably in recent years, providing the opportunity to inform research and practice. This review aims to enhance the accessibility of qualitative research among a range of audiences and specifically: (1) provide an overview of what qualitative research is and the value it can bring to scientific inquiries in the dairy context, (2) illustrate the emergence of qualitative dairy science research in the past 15 to 20 years, (3) outline the role of the researcher and key philosophical assumptions underlying qualitative research, (4) describe qualitative research approaches and methods used in dairy science research, and (5) highlight key aspects of qualitative inquiry used to ensure research trustworthiness. Qualitative approaches in dairy science enable researchers to understand myriad topics including stakeholder relationships, decision-making, and behaviors regarding dairy cattle management, animal welfare, and disease prevention and control measures. Approaches that were used often for qualitative data collection were individual interviews and focus groups, and variations of thematic analysis were common analytical frameworks. To assess public values, attitudes, and perceptions, mixed methods questionnaires that combined quantitative data with qualitative data from open-ended questions were used regularly. Although still used infrequently, action research and participatory approaches have the potential to bridge the research-implementation gap by facilitating group-based learning and on-farm changes. Some publications described the philosophical assumptions inherent to qualitative research, and many authors included reflexivity and positionality statements. Although a comprehensive description of strategies to meet trustworthiness criteria for qualitative research was uncommon, many publications mentioned certain aspects of trustworthiness, such as member checking, researcher triangulation, and the recording of reflexive notes. Qualitative research has been used to deepen our understanding of phenomena relevant to the dairy sector and has opened the door for a broad array of new opportunities. In addition to having merit on its own, qualitative research can guide, inform, and expand on quantitative research, and an understanding of the core pillars of qualitative research can foster interdisciplinary collaborations.

Towards a socially sustainable dairy sector with cow-calf contact systems

Neave, H., Bertelsen, M., Jensen, E. H., Jensen, M. B. — Fri, 01 Sep 2023 16:53:21 +0200

High risk of dairy cow mortality in early lactation

Thomsen, P. T. — Fri, 01 Sep 2023 16:53:21 +0200

Nutrient digestibility in broiler chickens fed diets containing high levels of soybean oil is affected by the source of fiber

Faryadi, S., Lashkari, S., Ndou, S. P., Woyengo, T. A. — Thu, 01 Jun 2023 16:53:21 +0200

This study evaluated the effects of including soluble and insoluble dietary fiber sources in soybean oil-containing diet for broiler chickens on coefficient of apparent ileal digestibility (AID) of amino acids, coefficient of apparent retention (AR) of nutrients, and nitrogen-corrected apparent metabolizable energy (AMEn). A total of 180 broilers were divided into 30 groups and fed 3 diets from day 14 to 21 of age. The diets were corn-soybean meal containing 6.8% soybean oil without or with soybean hulls (SBH) or sugar beet pulp (SBP) at 8.0% as sources of insoluble and soluble fiber, respectively. The SBH and SBP contained 6.0% and 14.7% of soluble dietary fiber and 60.5% and 37.0% of insoluble dietary fiber, respectively. The AID of indispensable amino acids was decreased (P < 0.05) due to dietary inclusion of SBH, but not of SBP. Dietary SBH and SBP reduced the AR of gross energy (by 14% and 8%, respectively) and AMEn (by 20% and 14%, respectively). Overall, inclusion of SBH or SBP at 8.0% in a corn-soybean meal-based diet for broilers that contains high level of soybean oil might not improve nutrient digestibility. However, SBP has less detrimental effects on nutrient digestibility than SBH.

Enteric methane emission of dairy cows supplemented with iodoform in a dose–response study

Thorsteinsson, M., Lund, P., Weisbjerg, M. R., et al. — Tue, 01 Aug 2023 16:53:21 +0200

Enteric methane (CH₄) emission is one of the major greenhouse gasses originating from cattle. Iodoform has in studies been found to be a potent mitigator of rumen CH₄ formation in vitro. This study aimed to quantify potential of iodoform as an anti-methanogenic feed additive for dairy cows and investigate effects on feed intake, milk production, feed digestibility, rumen microbiome, and animal health indicators. The experiment was conducted as a 4 × 4 Latin square design using four lactating rumen, duodenal, and ileal cannulated Danish Holstein dairy cows. The treatments consisted of four different doses of iodoform (1) 0 mg/day, (2) 320 mg/day, (3) 640 mg/day, and (4) 800 mg/day. Iodoform was supplemented intra-ruminally twice daily. Each period consisted of 7-days of adaptation, 3-days of digesta and blood sampling, and 4-days of gas exchange measurements using respiration chambers. Milk yield and dry matter intake (DMI) were recorded daily. Rumen samples were collected for microbial analyses and investigated for fermentation parameters. Blood was sampled and analyzed for metabolic and health status indicators. Dry matter intake and milk production decreased linearly by maximum of 48% and 33%, respectively, with increasing dose. Methane yield (g CH₄/kg DMI) decreased by maximum of 66%, while up to 125-fold increases were observed in hydrogen yield (g H₂/kg DMI) with increasing dose of iodoform. Total tract digestibility of DM, OM, CP, C, NDF, and starch were unaffected by treatments, but large shifts, except for NDF, were observed for ruminal to small intestinal digestion of the nutrients. Some indicators of disturbed rumen microbial activity and fermentation dynamics were observed with increasing dose, but total number of ruminal bacteria was unaffected by treatment. Serum and plasma biomarkers did not indicate negative effects of iodoform on cow health. In conclusion, iodoform was a potent mitigator of CH₄ emission. However, DMI and milk production were negatively affected and associated with indications of depressed ruminal fermentation. Future studies might reveal if depression of milk yield and feed intake can be avoided if iodoform is continuously administered by mixing it into a total mixed ration.

Gene coexpression network analysis reveals perirenal adipose tissue as an important target of prenatal malnutrition in sheep

Ahmad, S., Drag, M. H., Mohamad Salleh, S., Cai, Z., Nielsen, M. O. — Fri, 01 Sep 2023 16:53:21 +0200

We have previously demonstrated that pre- and early postnatal malnutrition in sheep induced depot- and sex-specific changes in adipose morphological features, metabolic outcomes, and transcriptome in adulthood, with perirenal (PER) as the major target followed by subcutaneous (SUB) adipose tissue. We aimed to identify coexpressed and hub genes in SUB and PER to identify the underlying molecular mechanisms contributing to the early nutritional programming of adipose-related phenotypic outcomes. Transcriptomes of SUB and PER of male and female adult sheep with different pre- and early postnatal nutrition histories were used to construct networks of coexpressed genes likely to be functionally associated with pre- and early postnatal nutrition histories and phenotypic traits using weighted gene coexpression network analysis. The modules from PER showed enrichment of cell cycle regulation, gene expression, transmembrane transport, and metabolic processes associated with both sexes' prenatal nutrition. In SUB (only males), a module of enriched adenosine diphosphate metabolism and development correlated with prenatal nutrition. Sex-specific module enrichments were found in PER, such as chromatin modification in the male network but histone modification and mitochondria- and oxidative phosphorylation-related functions in the female network. These sex-specific modules correlated with prenatal nutrition and adipocyte size distribution patterns. Our results point to PER as a primary target of prenatal malnutrition compared to SUB, which played only a minor role. The prenatal programming of gene expression and cell cycle, potentially through epigenetic modifications, might be underlying mechanisms responsible for observed changes in PER expandability and adipocyte-size distribution patterns in adulthood in both sexes.

An attempt to aggregate pig welfare indicators from sensors: achievements and barriers

Amorim Franchi, G., Pedersen, L. J., Jensen, M. B., et al. — Sun, 01 Jan 2023 16:53:21 +0100