Biology subjects

Botner, A.

Publications and source records attributed to Botner, A..

5 recordsLinked to original sources

bioRxiv2024

Emergence and spread of SARS-CoV-2 variants from farmed mink to humans and back during the epidemic in Denmark, June-November 2020.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) not only caused the COVID-19 pandemic but also had a major impact on farmed mink production in several European countries. In Denmark, the entire population of farmed mink (over 15 million animals) was culled in late 2020. During the period of June to November 2020, mink on 290 farms (out of about 1100 in the country) were shown to be infected with SARS-CoV-2. Genome sequencing identified changes in the virus within the mink and it is estimated that about 4000 people in Denmark became infected with these mink virus variants. However, the routes of transmission of the virus to, and from, the mink have been unclear. Phylogenetic analysis revealed the generation of multiple clusters of the virus within the mink. Detailed analysis of changes in the virus during replication in mink and, in parallel, in the human population in Denmark, during the same time period, has been performed here. The majority of cases in mink involved variants with the Y435F substitution and the H69/V70 deletion within the Spike (S) protein; these changes emerged early in the outbreak. However, further introductions of the virus, by variants lacking these changes, from the human population into mink also occurred. Based on phylogenetic analysis of viral genome data, we estimate, using a conservative approach, that about 17 separate examples of mink to human transmission occurred in Denmark but up to 59 such events (90% credible interval: (39-77)) were identified using parsimony to count cross-species jumps on transmission trees inferred using Bayesian methods. Using the latter approach, 136 jumps (90% credible interval: (117-164)) from humans to mink were found, which may underlie the farm-to-farm spread. Thus, transmission of SARS-CoV-2 from humans to mink, mink to mink, from mink to humans and between humans were all observed. (298 words) Author summaryIn addition to causing a pandemic in the human population, SARS-CoV-2 also infected farmed mink. In Denmark, after the first identification of infection in mink during June 2020, a decision was made in November 2020 to cull all the farmed mink. Within this outbreak, mink on 290 farms (out of about 1100 in the country) were found to have been infected. We showed, by analysis of the viruses from the mink, that the viruses on the farms were mainly of three different, but closely related, types (termed Clusters 2, 3 and 4) that shared certain distinctive features. Thus, we found that many outbreaks in mink resulted from transmission of the virus between mink farms. However, we identified that new introductions of other virus variants, presumably from infected humans, also occurred. Furthermore, we showed that spread of the virus from infected mink to humans also happened on multiple occasions. Thus, transmission of these viruses from humans to mink, mink to mink, from mink to humans and between humans were all observed. (172 words)

microbiology↗

bioRxiv2023

Inefficient transmission of African swine fever virus to sentinel pigs from environmental contamination under experimental conditions

Knowledge about African swine fever virus (ASFV) transmission and its survival in the environment is mandatory to develop rational control strategies and combat this serious disease in pigs. In this study, the risk that environmental contamination poses for infection of naive pigs was investigated. Naive pigs were introduced as sentinels into contaminated pens either on the same day or up to three days after ASFV-infected pigs were removed. Three experiments were carried out in which four to six pigs per pen were inoculated with virulent ASFV isolates OURT88/1 (genotype I), Georgia 2007/1 or POL/2015/Podlaskie (genotype II), respectively. The majority of the inoculated pigs developed acute disease but with no evident haemorrhagic lesions or haemorrhagic diarrhoea and were culled at the predefined humane endpoint. The levels of ASFV DNA detected in the blood of the infected animals reached 107-9 genome copies/ml before euthanasia. Environmental swabs were taken from different surfaces in the animal rooms, as well as from faeces and urine, close to the time of introduction of the naive animals. Relatively low quantities of virus DNA were detected in the environmental samples, in the order of 103-7 genome copies. Neither clinical signs nor virus genomes were detected in the blood of any of the sentinel pigs over a period of two to three weeks after exposure, indicating that transmission from the ASFV-contaminated environment did not occur. Interestingly, viral DNA was detected in nasal and oral swabs from some of the sentinel animals at early days of exposure (ranging between 103.7-5.8 genome copies), though none of them developed ASF. The results indicate a relatively low risk of ASFV transmission from a contaminated environment in the absence of blood from infected animals.

microbiology↗

bioRxiv2023

Release of fragmented host, cell-free, genomic DNA into the circulation of pigs during infection by virulent African swine fever virus

African swine fever virus (ASFV) causes a severe hemorrhagic disease in domestic pigs resulting in high case fatality rates. The virus replicates in circulating cells of the monocyte-macrophage lineage and within lymphoid tissues, e.g. tonsils, spleen and lymph nodes. The infection results in high fever and a variety of clinical signs from about 3 days post infection. In this study, it was observed that one of many changes resulting from ASFV- infection within pigs was a large (>1000-fold) increase in the level of circulating cell-free DNA (cfDNA), including the beta-actin gene, derived from the nuclei of host cells, in the serum. This change occurred in parallel with the increase in circulating ASFV DNA. In addition, elevated levels (about 30-fold higher) of host mitochondrial DNA (mtDNA) were detected in serum from ASFV-infected pigs, but with a much higher baseline level of mtDNA in sera from uninfected pigs. The host derived cfDNA is derived from dead cells which may, or may not, have been infected. For comparison, the release of the cellular enzyme, lactate dehydrogenase (LDH), a commonly used marker of cellular damage, was also found to be elevated during the infection. The cfDNA is readily detected in serum and is a more sensitive host marker of ASFV infection than the release of mtDNA or LDH. In addition, sera from pigs infected by classical swine fever virus (CSFV), which causes a clinically similar disease as ASFV, were also tested but this infection did not result in the release of cfDNA, mtDNA or LDH. Author summaryAfrican swine fever virus causes a severe hemorrhagic disease in domestic pigs and wild boar, which often leads to death within a week. The infection results in a spectrum of different clinical signs and other changes within infected animals. In this study, we have shown, for the first time, that one consequence of infection by a highly virulent strain of this virus is the release into the blood of host genomic DNA, in a highly fragmented form. We found an increase of >1000-fold in the level of this cell-free DNA within the serum of infected animals. Furthermore, we also showed that the level of the small circular DNA from the cell mitochondria is also elevated in serum from infected animals as is the cellular enzyme lactate dehydrogenase but these changes were less marked and occurred later. The increase in the level of the cell-free host DNA is coincident with the increase in level of the viral DNA within blood and may act as a marker for infection by a highly virulent form of the virus. Remarkably, pigs infected by classical swine fever virus, which produces similar clinical signs, did not have elevated levels of these markers in their serum.

microbiology↗

bioRxiv2021

Infection, recovery and re-infection of farmed mink with SARS-CoV-2

Mink, on a farm with about 15,000 animals, became infected with SARS-CoV-2. Over 75% of tested animals were positive for SARS-CoV-2 RNA in throat swabs and 100% of tested animals were seropositive. The virus responsible had a deletion of nucleotides encoding residues H69 and V70 within the spike protein gene. The infected mink recovered and after free-testing of the mink, the animals remained seropositive. During follow-up studies, after a period of more than 2 months without virus detection, over 75% of tested animals scored positive again for SARS-CoV-2 RNA. Whole genome sequencing showed that the virus circulating during this re-infection was most closely related to the virus identified in the first outbreak on this farm but additional sequence changes had occurred. Animals had much higher levels of anti-SARS-CoV-2 antibodies after re-infection than at free-testing. Thus, following recovery from an initial infection, seropositive mink rapidly became susceptible to re-infection by SARS-CoV-2. Article Summary LineFollowing widespread infection with SARS-CoV-2 of mink on a farm, all tested animals had seroconverted and the farm was then tested free of infection; however, less than 3 months later, a further round of infection affected more than 75% of tested animals.

microbiology↗

bioRxiv2019

Evolutionary stasis of an RNA virus indicates arbovirus re-emergence triggered by accidental release

The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. Bluetongue virus serotype 8 (BTV-8), an insect-borne virus of ruminants, emerged in livestock in Northern Europe in 2006, spreading to most European countries by 2009 and causing losses of billions of Euros. Though the outbreak was successfully controlled through vaccination by early 2010, puzzlingly a closely-related BTV-8 strain re-emerged in France in 2015, triggering a second outbreak that is still ongoing. The origin of this virus and the mechanisms underlying its re-emergence are unknown. Here, we performed phylogenetic analyses of 164 whole BTV-8 genomes sampled throughout the two outbreaks. We demonstrate consistent clock-like virus evolution during both epizootics but found negligible evolutionary change between them. We estimate that the ancestor of the second outbreak dates from the height of the first outbreak in 2008. This implies that the virus had not been replicating for multiple years prior to its re-emergence in 2015. Given the absence of any known natural mechanism that could explain BTV-8 persistence over this period without replication, we conclude that the second outbreak was most likely initiated by accidental exposure of livestock to frozen material contaminated with virus from approximately 2008. Our work highlights new targets for pathogen surveillance programmes in livestock and illustrates the power of genomic epidemiology to identify pathways of infectious disease emergence.

evolutionary biology↗