Playa de Oro virus
Encyclopedia
Playa de Oro virus is a probable species of hantavirus
found in the rodents Oryzomys couesi and Sigmodon mascotensis in the Mexican state of Colima
. The former is thought to be the main host
. The sequences
of parts of the virus's RNA
-based genome
have been determined; they differ by 7–10% in amino acid
composition and 22–24% in nucleotide
composition from closely related viruses.
Playa de Oro virus was identified as a new species in 2008 and is most closely related to Bayou virus, Catacamas virus, Muleshoe virus, and Black Creek Canal virus, found in other species of Oryzomys
and Sigmodon. Catacamas virus is found in a different population of Oryzomys couesi, and the presence of different viruses in these two species has been used as an argument for classifying the two populations of the host as separate species.
, Colima
, western Mexico. The discovery was published in 2008 by Yong-Kyu Chu and colleagues. Among 600 small mammals, antibodies
against the hantavirus Sin Nombre virus
were found in 23 individuals (out of 358 studied) of Oryzomys couesi, a rice rat
that was the most common species found, six (out of 87) of the cotton rat
Sigmodon mascotensis, and one (out of 77) of the pygmy mouse
Baiomys musculus. In addition, twelve O. couesi and one S. mascotensis yielded hantavirus RNA
. Viruses were found in males more often than in females. Because the amino acid
sequences in sequenced parts of the virus's genome differed by as much as 7 to 10% from closely related hantaviruses, Chu and colleagues identified the virus found at Playa de Oro as a new species, called Playa de Oro virus or OROV. Although the authors could not prove that the virus fulfilled all the criteria for identifying a new virus species, they argued that it was likely that it did fulfill those criteria. It is currently treated as a probable species in the Hantavirus
genus.
that consists of three segments of single-stranded, negative-sense RNA (see RNA virus: Replication), called the large (L), medium (M), and small (S) segments. The entire S segment and a fragment of the M segment have been sequenced.
The S segment consists of 1953 bases, of which 1287 (starting at position 43) code for the nucleocapsid protein. In addition, a second 192-base open reading frame
occurs in the middle of this sequence (starting at position 122), as in several other hantaviruses. Among three specimens of O. couesi, the sequence in this segment differed by only 1%, and all changes were silent mutation
s. The amino acids of the S segment differ by 7 to 10% from those of the related hantaviruses Bayou virus (BAYV; from the marsh rice rat
, Oryzomys palustris), Catacamas virus (CATV; from a Honduras
population of Oryzomys couesi), and Black Creek Canal virus (BCCV; from the hispid cotton rat
, Sigmodon hispidus). The nucleotide sequence differs by 24% from those viruses.
Among 1537-base fragments of the sequence of the M segment, several variable sites were observed, including some non-silent mutations. The sequence differs by 8 to 10% from BAYV, CATV, and BCCV in terms of amino acids and by 22% in terms of nucleotides.
and various wild rodents are known to be reservoirs of hantavirus species. Thus, there is a potential risk of OROV infection in humans. Before the discovery of OROV, one hantavirus species had been identified in Mexico—El Moro Canyon virus from the small rodent Reithrodontomys megalotis.
formed by BAYV, CATV, BCCV, and Muleshoe virus (MUL; from the hispid cotton rat). In 2009, Piet Maes and colleagues proposed that the closely related BAYV, BCCV, and MUL be united into a single species. Chu and colleagues were surprised to find that the same species, Oryzomys couesi, harbored different viruses (OROV and CATV), though noted that the subspecies
infected by the two viruses were different. In 2010, Delton Hanson and colleagues suggested on the basis of various lines of evidence, including the presence of different hantaviruses, that western Mexican populations of Oryzomys couesi represent a different species, Oryzomys mexicanus.
Hantavirus
Hantaviruses are negative sense RNA viruses in the Bunyaviridae family. Humans may be infected with hantaviruses through rodent bites, urine, saliva or contact with rodent waste products...
found in the rodents Oryzomys couesi and Sigmodon mascotensis in the Mexican state of Colima
Colima
Colima is one of the 31 states which, with the Federal District, make up the 32 Federal Entities of Mexico. It shares its name with its capital and main city, Colima....
. The former is thought to be the main host
Host (biology)
In biology, a host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. In botany, a host plant is one that supplies food resources and substrate for certain insects or other fauna...
. The sequences
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
of parts of the virus's RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
-based genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
have been determined; they differ by 7–10% in amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
composition and 22–24% in nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
composition from closely related viruses.
Playa de Oro virus was identified as a new species in 2008 and is most closely related to Bayou virus, Catacamas virus, Muleshoe virus, and Black Creek Canal virus, found in other species of Oryzomys
Oryzomys
Oryzomys is a genus of semiaquatic rodents in the tribe Oryzomyini living in southern North America and far northern South America. It includes eight species, two of which—the marsh rice rat of the United States and O. couesi of Mexico and Central America—are widespread; the six others have...
and Sigmodon. Catacamas virus is found in a different population of Oryzomys couesi, and the presence of different viruses in these two species has been used as an argument for classifying the two populations of the host as separate species.
History and occurrence
Playa de Oro virus was first identified in rodents collected in 2004 as part of a survey of wild mammals at Playa de Oro in ManzanilloManzanillo, Colima
The name Manzanillo refers to the city as well as its surrounding municipality in the Mexican state of Colima. The city, located on the Pacific Ocean, contains Mexico's busiest port. Manzanillo was the third port created by the Spanish in the Pacific during the New Spain period...
, Colima
Colima
Colima is one of the 31 states which, with the Federal District, make up the 32 Federal Entities of Mexico. It shares its name with its capital and main city, Colima....
, western Mexico. The discovery was published in 2008 by Yong-Kyu Chu and colleagues. Among 600 small mammals, antibodies
Antibody
An antibody, also known as an immunoglobulin, is a large Y-shaped protein used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, termed an antigen...
against the hantavirus Sin Nombre virus
Sin Nombre virus
The Sin Nombre virus is the prototypical etiologic agent of hantavirus cardiopulmonary syndrome ....
were found in 23 individuals (out of 358 studied) of Oryzomys couesi, a rice rat
Oryzomyini
Oryzomyini is a tribe of rodents in the subfamily Sigmodontinae of family Cricetidae. It includes about 120 species in about thirty genera, distributed from the eastern United States to the southernmost parts of South America, including many offshore islands...
that was the most common species found, six (out of 87) of the cotton rat
Cotton rat
A cotton rat is any member of the rodent genus Sigmodon. They are called cotton rats because they build their nests out of cotton, and can damage cotton crops. Cotton rats have small ears and dark coats, and are found in North and South America....
Sigmodon mascotensis, and one (out of 77) of the pygmy mouse
Baiomys
Baiomys is the genus of New World pygmy mice. Together with Scotinomys, it forms the tribe Baiomyini. It currently contains two extant species:*Southern Pygmy Mouse, Baiomys musculus*Northern Pygmy Mouse, Baiomys taylori-References:...
Baiomys musculus. In addition, twelve O. couesi and one S. mascotensis yielded hantavirus RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
. Viruses were found in males more often than in females. Because the amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
sequences in sequenced parts of the virus's genome differed by as much as 7 to 10% from closely related hantaviruses, Chu and colleagues identified the virus found at Playa de Oro as a new species, called Playa de Oro virus or OROV. Although the authors could not prove that the virus fulfilled all the criteria for identifying a new virus species, they argued that it was likely that it did fulfill those criteria. It is currently treated as a probable species in the Hantavirus
Hantavirus
Hantaviruses are negative sense RNA viruses in the Bunyaviridae family. Humans may be infected with hantaviruses through rodent bites, urine, saliva or contact with rodent waste products...
genus.
Virology
Hantaviruses have a genomeGenome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
that consists of three segments of single-stranded, negative-sense RNA (see RNA virus: Replication), called the large (L), medium (M), and small (S) segments. The entire S segment and a fragment of the M segment have been sequenced.
The S segment consists of 1953 bases, of which 1287 (starting at position 43) code for the nucleocapsid protein. In addition, a second 192-base open reading frame
Open reading frame
In molecular genetics, an open reading frame is a DNA sequence that does not contain a stop codon in a given reading frame.Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop...
occurs in the middle of this sequence (starting at position 122), as in several other hantaviruses. Among three specimens of O. couesi, the sequence in this segment differed by only 1%, and all changes were silent mutation
Silent mutation
Silent mutations are DNA mutations that do not result in a change to the amino acid sequence of a protein. They may occur in a non-coding region , or they may occur within an exon in a manner that does not alter the final amino acid sequence...
s. The amino acids of the S segment differ by 7 to 10% from those of the related hantaviruses Bayou virus (BAYV; from the marsh rice rat
Marsh Rice Rat
The marsh rice rat is a semiaquatic North American rodent in the family Cricetidae. It is found mostly in the eastern and southern United States, from New Jersey and Kansas south to Florida and northeasternmost Tamaulipas, Mexico; its range previously extended further west and north, where it may...
, Oryzomys palustris), Catacamas virus (CATV; from a Honduras
Honduras
Honduras is a republic in Central America. It was previously known as Spanish Honduras to differentiate it from British Honduras, which became the modern-day state of Belize...
population of Oryzomys couesi), and Black Creek Canal virus (BCCV; from the hispid cotton rat
Hispid Cotton Rat
The Hispid Cotton Rat is a rodent species long thought to occur in parts of South America, Central America, and southern North America. However, recent taxonomic revisions, based on mitochondrial DNA sequence data, have split this widely distributed species into three separate species. Carroll et...
, Sigmodon hispidus). The nucleotide sequence differs by 24% from those viruses.
Among 1537-base fragments of the sequence of the M segment, several variable sites were observed, including some non-silent mutations. The sequence differs by 8 to 10% from BAYV, CATV, and BCCV in terms of amino acids and by 22% in terms of nucleotides.
Epidemiology and effects
Because OROV occurs frequently in Oryzomys couesi, Chu and colleagues suggested that it is the primary host of the virus and that infections in Sigmodon mascotensis are the result of spillover between these two rodent species, which occur closely together. Hantavirus pulmonary syndrome, the disease caused by hantaviruses such as Sin Nombre virus, has never been reported in Mexico, but antibodies against hantaviruses have been found in human blood samples in YucatánYucatán
Yucatán officially Estado Libre y Soberano de Yucatán is one of the 31 states which, with the Federal District, comprise the 32 Federal Entities of Mexico. It is divided in 106 municipalities and its capital city is Mérida....
and various wild rodents are known to be reservoirs of hantavirus species. Thus, there is a potential risk of OROV infection in humans. Before the discovery of OROV, one hantavirus species had been identified in Mexico—El Moro Canyon virus from the small rodent Reithrodontomys megalotis.
Relationships
According to phylogenetic analyses based on the sequences of both the S and M segments, OROV is most closely related to the cladeClade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
formed by BAYV, CATV, BCCV, and Muleshoe virus (MUL; from the hispid cotton rat). In 2009, Piet Maes and colleagues proposed that the closely related BAYV, BCCV, and MUL be united into a single species. Chu and colleagues were surprised to find that the same species, Oryzomys couesi, harbored different viruses (OROV and CATV), though noted that the subspecies
Subspecies
Subspecies in biological classification, is either a taxonomic rank subordinate to species, ora taxonomic unit in that rank . A subspecies cannot be recognized in isolation: a species will either be recognized as having no subspecies at all or two or more, never just one...
infected by the two viruses were different. In 2010, Delton Hanson and colleagues suggested on the basis of various lines of evidence, including the presence of different hantaviruses, that western Mexican populations of Oryzomys couesi represent a different species, Oryzomys mexicanus.