You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
an investigation was initiated to characterize the virus and identify the patient s infection source .
phylogenetic inference was based on 9 genes located within the central , conserved region of the genome ( supplementary methods ) .
methods used to identify the patient s infection source included interviews with the patient , contact tracing and analysis of serum samples for the presence of anti - orthopoxvirus immunoglobulin ( ig ) g and igm , and a visit to the patient s residence to conduct environmental sampling and peridomestic small - mammal trapping . given the uncertainty about an incubation period for this novel poxvirus ,
a conservative threshold of 4 weeks was assumed based on the incubation period of human monkeypox .
the patient was asked to identify persons with whom she had regular or close contact during the 4 weeks before and after symptom onset . the patient and each contact
were interviewed to ascertain whether they had ever received a smallpox vaccination , had traveled recently , or had experienced any unusual health events during the presumptive incubation period .
serum samples were obtained from these persons and tested with enzyme - linked immunosorbent assays to determine the presence of anti - orthopoxvirus igm and igg antibodies . on 8 september ,
environmental samples were collected in and around the patient s home during a site visit .
household surfaces that the patient indicated had been contacted by wild small mammals that periodically entered the home and possible fomites associated with international travel by the patient s partner were swabbed by using hydraflock dacron swab samples ( puritan medical ) .
approximately 6 weeks later , small mammals were trapped around the perimeter of the patient s home and at a site approximately 1 km away where she and her partner were building a new home ( supplementary methods ) . environmental and nonblood small - mammal samples ( oral swab , liver tissue , and feces )
were tested using real - time pcr assays that target specific orthopoxvirus generic sequences [ 35 ] ; small - mammal blood samples were tested using enzyme - linked immunosorbent assays for anti - orthopoxvirus igg .
phylogenetic analyses of the concatenated sequence alignment ( 28037 base pairs in length ) indicate that the virus isolate represents a distinct genetic lineage of orthopoxvirus that is highly divergent from congeners included in our analysis .
a well - supported topology was recovered in which the grouping of taterapox virus and variola virus as sister taxa ( bayesian posterior probability , 0.5983 ) was the only node with a bayesian posterior probability < 0.999 ( figure 2 , supplementary figure 1 , and supplementary_table_1 ) . ak2015_poxvirus was grouped within the genus orthopoxvirus and recovered as sister to a monophyletic clade containing all old world orthopoxviruses with high support ; it was estimated to be 6.1%7.3% divergent from different species of old world orthopoxviruses , and 12.3%12.6% divergent from isolates within the north american clade .
the genetic distances estimated between examined isolates of recognized old world orthopoxvirus species varied from 0.6% ( taterapox virus to camelpox virus ) to 3.2% ( ectromelia virus to variola virus ) . results of bayesian phylogenetic inference , indicating the position of ak2015_poxvirus within the genus orthopoxvirus .
analysis was based on 9 genes located within the central , conserved region of the genome ( vaccinia virus copenhagen strain homologues a7l , a10l , a24r , d1r , d5r , e6r , e9l , h4l , and j6r ) .
electron microscopic observation of cells infected with ak2015_poxvirus demonstrated the presence of different morphological forms , including crescents ( figure 1c ) and immature virus particles ( figure 1d ) .
in addition , infected cells had inclusion bodies formed by accumulation of a - type inclusion proteins .
the inclusion bodies were embedded with mature virus particles and surrounded by ribosomes ( figure 1e ) . during interviews ,
the patient reiterated a lack of sick contacts during the 4 weeks before symptom onset . during the 4 weeks after symptom onset , she reported contact with 4 persons .
of 3 household contacts ( adult male partner and 2 teenaged children ) , all had regular , direct physical contact with her and with common household items , but none reported any unusual health events .
one social contact ( adult female friend ) reported a rash on her chest within 1 week of being in physical contact with the patient in the days after the patient s symptom onset .
a history of smallpox vaccination was reported by both adult contacts ( vaccination before 2003 ) but neither adolescent contact .
serological tests performed on specimens collected from these persons did not identify evidence of recent exposure among the contacts ; anti - orthopoxvirus igm was only detected in serum from the patient ( table 1 ) .
consistent with their self - reported smallpox vaccination histories , anti - orthopoxvirus igg was detected in the serum from both adult contacts but neither adolescent contact .
anti - orthopoxvirus igg and igm results for serum samples from the patient and 4 contacts abbreviation : ig , immunoglobulin . 

serum optical density ( od ) cutoff values ( od value  3 standard deviations of negative control ) at 1:50 and 1:100 dilutions were considered positive for igm and igg , respectively . 

the patient did not recall being vaccinated and did not have a vaccination scar . 

the sample from the patient s older child was positive for anti - orthopoxvirus igm , but because this value was low and the corresponding anti - orthopoxvirus igg result was negative , the result was interpreted as equivocal .
the patient reiterated that no out - of - state travel occurred during the 4 weeks before symptom onset .
she reported working intermittently in the petroleum industry in the north slope region of alaska , during february 
her cohabitating partner was also employed in the petroleum industry and had worked intermittently ( 5 weeks on and 5 weeks off ) on oil - drilling platforms in azerbaijan , from october 2013 to march 2015 .
he had no other out - of - state travel during this period and while overseas he remained almost exclusively on oil platforms with limited in - country travel .
he returned to alaska from his last trip to azerbaijan in march 2015 ( approximately 4 months before the patient s symptom onset ) and did not report any unusual health events during or within 4 weeks after the trip .
when he returned from a trip to azerbaijan in october 2014 ( approximately 9 months before the patient s symptom onset ) , he brought back souvenirs for the patient ( a wooden jewelry box containing a cloth jewelry pouch ) and a collared work jacket that he wore regularly during the trip and that the patient wore periodically after his return to alaska .
swab samples of the surfaces of these items were tested to determine whether any might have served as fomites .
no evidence of orthopoxvirus dna was detected . the home that the patient shared with her partner and 2 children
was located in a forested , low - density area , within 50 miles of fairbanks .
she reported that wild small mammals ( eg , shrews , voles , squirrels ) were abundant in this boreal forest environment , were regularly observed around the home s perimeter , and entered the home on occasion .
she also reported that her children periodically handled the carcasses of squirrels that they shot near the home using a pellet rifle . when asked about construction of her new home ,
the patient reported that she and her partner had used scrap wood from an abandoned shed located near her home that had been occupied by wild small mammals .
all 23 environmental samples collected during the site visit , including swab samples of scrap wood from the abandoned shed at the new home construction site , tested negative for orthopoxviruses by pcr ( supplementary_table_2 ) . at the time of the site visit to the patient s residence ( approximately 45 days after symptom onset ) , her symptoms included an active lesion that had decreased in size since initial presentation but remained raised , tender , and warm ( approximated in figure 1b ) .
thirty - one small - mammal samples , collected from 12 individual animals belonging to 2 species ( sorex cinereus , n = 3 ; myodes rutilus , n = 9 ) , tested negative for orthopoxviruses by pcr ( supplementary_table_3 ) .
no evidence of transmission from the index patient , or fatalities associated with infection , was reported .
epidemiologic information gathered during the investigation provides inconclusive evidence for 2 general hypotheses concerning the patient s route of exposure .
the first involves importation of an old world orthopoxvirus into alaska , either as an active infection in a person with whom the patient came into contact or by way of one or more fomites .
the limited number of contacts identified by the patient , and the apparent absence of additional cases , indicates that the probability of unidentified secondary spread is remote .
work - related travel to azerbaijan by the patient s partner represents a possible fomite - associated importation scenario , although sampling and testing of travel - related fomites returned negative results .
although the recent discovery of a novel , zoonotic orthopoxvirus in the nearby republic of georgia   indicates that unidentified orthopoxviruses might be circulating in this region , the delay between the arrival of these fomites in alaska and the timing of onset of the patient s symptoms indicates that infection by this route is unlikely .
the duration of viability of ak2015_poxvirus on fomites is uncertain ; however , a laboratory study of vaccinia virus demonstrated retention of viability on environmental surfaces for up to 56 days .
the presence of a - type inclusion bodies occluded with mature virus in the ak2015_poxvirus isolate observed by electron microscopy might be indicative of enhanced environmental resilience and prolonged viability .
alternatively , ak2015_poxvirus might be endemic to alaska , perhaps circulating within one or more wildlife reservoir population , and infection might have occurred through an animal exposure .
different species of wild small mammals occur in the boreal forest environment surrounding the patient s residence , and infection by indirect animal contact ( eg , contact with household surfaces , squirrels shot by the patient s children , or handling of potentially contaminated wood from the shed occupied by wild small mammals during construction of the new home ) might be implicated .
rodents and other small mammals are known or suspected reservoirs for multiple orthopoxviruses , and evidence of infection has been produced by serosurveys in eurasia [ 1114 ] , africa [ 5 , 15 ] , south america [ 16 , 17 ] , and the continental united states . among the limited number of wildlife serosurveys of terrestrial mammals conducted in alaska , the majority have focused on large mammals [ 1921 ] , and those that sampled small mammals did not test for evidence of a poxvirus infection or exposure [ 2224 ] .
small - mammal serosurveys in regions of northern europe that are ecologically similar to alaska have identified seropositive animals [ 2527 ] . although results of our small - mammal trapping and testing were negative , the sample was limited and taxonomically restricted .
phylogenetic analyses indicate that ak2015_poxvirus is more closely related to the old world orthopoxviruses than to north american congeners .
however , that the virus is known only from north america creates a discordance that precludes its assignment to one or the other of these geographically defined groups with confidence .
the global distribution of other genera and unassigned isolates within chordopoxvirinae , and incomplete sampling of potential reservoir taxa as part of our investigation , create additional uncertainty regarding this assignment .
nevertheless , given the inconsistent timelines of contact travel and patient symptom onset , negative results of travel - associated fomite testing , and the potential for regular and close contact with wild small mammals in and around the patient s home , the most parsimonious explanation of infection is exposure to ak2015_poxvirus near fairbanks .
evidence of virus circulation in alaska or elsewhere in north america ( ie , infections in persons or reservoir species ) would indicate either a new world origin of orthopoxviruses or an old world origin with multiple introductions to the new world .
both scenarios run counter to the present characterization of north american and old world orthopoxviruses as representing reciprocally monophyletic lineages , and challenge the currently accepted hypothesis of an old world origin of the genus orthopoxvirus with a solitary introduction of the new world orthopoxviruses to north america .
this discovery of a novel orthopoxvirus is the latest in a growing number of reports of human poxvirus infection published in recent years .
these include the emergence of novel poxviruses [ 7 , 2931 ] and the increased incidence of human monkeypox , an orthopoxvirus illness historically associated with relatively low incidence . because smallpox vaccination has been demonstrated to provide cross - protection against other orthopoxviruses [ 33 , 34 ] , these observations have been attributed to the cessation of routine smallpox vaccination after eradication of variola virus in 1980 and the subsequent waning of population - level vaccine - derived immunity [ 7 , 32 , 35 ] . continued emergence and reemergence of orthopoxviruses
is expected . to effectively treat persons infected by orthopoxviruses , clinicians should remain vigilant for signs of poxvirus infections and immediately alert public health officials when infection is suspected so that prompt diagnostic testing and appropriate control measures can be implemented . within alaska , populations that might represent foci for surveillance include persons , such as the patient s partner , who travel to geographic regions associated with the emergence or reemergence of orthopoxviruses , and persons with regular direct or indirect contact with wildlife ( eg , residents of rural settings , scientists , environmental consultants , hunters , and adventure guides )
. the latter population in alaska might be relatively large , given the high proportion of state residents and visitors who live , work , or recreate in wilderness areas .
consisting of data provided by the authors to benefit the reader , the posted materials are not copyedited and are the sole responsibility of the authors , so questions or comments should be addressed to the corresponding author .
summarya resident of interior alaska , was diagnosed with an orthopoxvirus infection . 
 phylogenetic analysis revealed it is a novel , previously undescribed orthopoxvirus species . 
 phylogenetically , the virus is sister to recognized old world orthopoxviruses , rather than north american orthopoxvirus species .