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DISPATCHESTable 1. Small mammals captured in Namibia during 2010–2012 and tested for arenaviruses*Mammal species Common name Localities of capture† No. positive/no. testedAethomys chrysophilus Red veld rat Be, CCF, Ok, Pa, Ta 0/64Micaelamys namaquensis Namaqua rock mouse CCF, Ma, Ok, Pa, Ru 4/266Crocidura fuscomurina Bicolored musk shrew CCF, Pa, Ru 0/4Crocidura hirta Lesser red musk shrew Ma 0/5Dendromus melanotis Gray climbing mouse Ta 0/1Elephantulus intufi Bushveld sengi CCF, Ma, Ok 0/14Gerbilliscus spp. Gerbil Wi 0/6Gerbilliscus leucogaster Bushveld gerbil Be, CCF, Ma, Ok, Pa, Ru, Ta 0/228Gerbillurus paeba Hairy-footed gerbil Be 0/3Gerbillurus setzeri Namib brush-tailed gerbil Be 0/1Lemniscomys rosalia Single-striped grass mouse Be 0/2Mastomys spp. Multimammate mouse Be, CCF, Ma, Ok, Pa, Ru, Ta 0/114Mus indutus Desert pygmy mouse Ma, Pa 0/5Petromyscus collinus Pygmy rock mouse Pa 0/3Rhabdomys pumilio Four-striped grass mouse CCF, Ma, Pa, Ok, Wi 0/73Saccostomus campestris Pouched mouse Be, CCF, Ok, Pa, Ru 0/17Thallomys paedulcus Acacia rat Pa 0/4u.u. Soricidae Shrew Wi 0/2Total 4/812*Morphologic species identification of the arenavirus positive rodent samples was confirmed by sequencing of partial mitochondrial cytochrome b gene(GenBank accession nos.: N27, KP752173; N73, KP752175; N80, KP752176; N85, KP752174).†Abbreviations and sampling dates for trapping localities: Be, Ben Hur (11/2011); CCF, Cheetah Conservation Fund (02/2011); Ok, Okahandja (06/2012),Pa, Palmwag (09/2010), Ta, Talismanis (12/2011), Ma, Mariental (06/2012), Ru, Rundu (01/2011),Wi, Windhoek (09/2010 and 01/2012).arenavirus PCR, frozen lung tissue aliquots were homogenizedand added to confluent Vero-E6 cells (ATCC CRL-1586; American Type Culture Collection, Manassas, VA,USA) for virus isolation.For genome sequencing, pellets from ultracentrifugedsupernatant of infected cell cultures were lysed, and totalRNA was purified. RNA was then subjected to randomprimedRT-PCR as described (11). Next-generation sequencingwas performed by using a 454 Genome SequencerJunior (Roche, Indianapolis, IN, USA), and resultswere aligned against the virus database by using blastn andblastx algorithms (http://blast.ncbi.nlm.nih.gov/Blast.cgi).Sequencing results matching arenavirus sequences weremapped to the LASV strain Josiah (GenBank accession no.AY628203). Because of low coverage for N27, an additionalMiSeq (Illumina, San Diego, CA, USA) run was performed.De novo assembly of the data was performed withGeneious software (Biomatters, Auckland, New Zealand)(12). Sequence gaps or regions with low coverage wereverified by Sanger sequencing (Applied Biosystems, FosterCity, CA, USA). Genome segment outermost noncodingtermini were sequenced after linkage by T4-RNA-Ligase(New England Biolabs, Ipswich, MA, USA) and RT-PCRamplification.Of the 812 rodents and shrews tested (Table 1), arenavirusRNA was found in lung tissue samples of 4 Namaquarock mice (Micaelamys [Aethomys] namaquensis), 3 fromOkahandja (N73, N80, N85) and 1 from Mariental (N27).Sanger sequencing of PCR products from a 338-nt fragmentof the viral polymerase gene confirmed arenaviruslikeorigin. Initial phylogenetic analysis showed that theOkahandja specimens were related to MWV, but the samplefrom Mariental was a highly divergent member of the genusArenavirus (Figure 2, panel A). Cell culture isolationwas performed with samples N27 and N73 and resulted in2 novel arenavirus isolates: Mariental virus (MRTV) andOkahandja virus (OKAV), respectively.The genomes of the 2 arenaviruses were investigatedby using next-generation sequencing and RT-PCR Sangersequencing. The genome data obtained for MRTV andOKAV showed a typical arenavirus nucleotide compositionwith the L segment (MRTV: 6,840 nt; OKAV: 7,170nt) coding for RNA polymerase and matrix protein and theS segment (MRTV: 3,360 nt; OKAV: 3,379 nt) coding forglycoprotein and nucleocapsid protein. Table 2 shows thenucleotide and amino acid sequence identities of nucleocapsidand glycoprotein open reading frame with other OldWorld (i.e., Eastern Hemisphere locations such as Europe,Asia, Africa) representatives of genus Arenavirus. Onthe basis of the nucleocapsid amino acid identity, OKAVis most related to MWV (75.7% identity). Furthermore,MRTV has the highest amino acid identity with IPPYV(71.4% identity) and with Gbagroube, Lassa, Luna, andMobala viruses (≈70% identity).In the nucleocapsid-based phylogenetic tree, OKAVclusters with 100% bootstrap support with MWV detectedin Myotomys unisulcatus rodents in South Africa (Figure2, panel B), and MRTV forms a clade with IPPYV isolatedfrom Praomys spp. in the Central African Republic. Thebootstrap support of this monophyletic group of the tree liesat 56%. The analysis of the glycoprotein open reading frame(Figure 2, panel C) leads to a similar result; OKAV sharesthe most recent common ancestor with MWV, and MRTVclusters with IPPYV but with a weaker bootstrap support.1214 Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 21, No. 7, July 2015
Novel Arenaviruses, Southern AfricaFigure 2. Phylogenetic analysis of Okahandja and Mariental viruses performed with maximum-likelihood method. A) Phylogeneticanalysis of partial L segment sequence (338 nt) of Okahandja and Mariental viruses obtained from reverse transcription PCRscreening and performed with MEGA 6.0 (13) with maximum-likelihood method (general time reversible plus gamma model with7 discrete Gamma categories; 1,000 bootstrap replications). Values at the branches are bootstrap values of the correspondingneighbor-joining tree (maximum composite likelihood method); values
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July 2015SynopsisOn the CoverMarian
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1240 Gastroenteritis OutbreaksCause
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SYNOPSISDisseminated Infections wit
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Disseminated Infections with Talaro
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Disseminated Infections with Talaro
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Macacine Herpesvirus 1 inLong-Taile
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Macacine Herpesvirus 1 in Macaques,
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Malaria among Young Infants, Africa
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RESEARCHFigure 3. Dynamics of 19-kD
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Transdermal Diagnosis of MalariaUsi
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RESEARCHFigure 2. A) Acoustic trace
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RESEARCHof malaria-infected mosquit
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Lack of Transmission amongClose Con
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RESEARCH(IFA) and microneutralizati
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RESEARCHoropharyngeal, and serum sa
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RESEARCH6. Assiri A, McGeer A, Perl
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RESEARCHadvanced genomic sequencing
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RESEARCHTable 2. Next-generation se
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RESEARCHTable 3. Mutation analysis
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RESEARCHReferences1. Baize S, Panne
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Parechovirus Genotype 3 Outbreakamo
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RESEARCHFigure 1. Venn diagramshowi
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RESEARCHTable 2. HPeV testing of sp
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RESEARCHFigure 5. Distribution of h
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RESEARCHReferences1. Selvarangan R,
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RESEARCHthe left lobe was sampled b
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RESEARCHTable 2. Middle East respir
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RESEARCHseroprevalence in domestic
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RESEARCHmeasure their current surve
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RESEARCHTable 2. States with labora
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Page 78 and 79: RESEARCHpresence of Legionella spp.
Page 80 and 81: Seroprevalence for Hepatitis Eand O
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Page 90 and 91: POLICY REVIEWDutch Consensus Guidel
Page 92 and 93: POLICY REVIEWTable 3. Comparison of
Page 94 and 95: POLICY REVIEW6. Botelho-Nevers E, F
Page 96 and 97: DISPATCHESFigure 1. Phylogenetic tr
Page 98 and 99: DISPATCHESSevere Pediatric Adenovir
Page 100 and 101: DISPATCHESTable 1. Demographics and
Page 102 and 103: DISPATCHES13. Kim YJ, Hong JY, Lee
Page 104 and 105: DISPATCHESTable. Alignment of resid
Page 106 and 107: DISPATCHESFigure 2. Interaction of
Page 108 and 109: DISPATCHESSchmallenberg Virus Recur
Page 110 and 111: DISPATCHESFigure 2. Detection of Sc
Page 112 and 113: DISPATCHESFigure 1. Histopathologic
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Page 117 and 118: Influenza Virus Strains in the Amer
Page 119: Novel Arenavirus Isolates from Nama
Page 123 and 124: Readability of Ebola Informationon
Page 125 and 126: Readability of Ebola Information on
Page 127 and 128: Patients under investigation for ME
Page 129 and 130: Patients under investigation for ME
Page 131 and 132: Wildlife Reservoir for Hepatitis E
Page 133 and 134: Asymptomatic Malaria and Other Infe
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Page 137 and 138: Bufavirus in Wild Shrews and Nonhum
Page 139 and 140: Bufavirus in Wild Shrews and Nonhum
Page 141 and 142: Range Expansion for Rat Lungworm in
Page 143 and 144: Slow Clearance of Plasmodium falcip
Page 145 and 146: Slow Clearance of Plasmodium falcip
Page 147 and 148: Gastroenteritis Caused by Norovirus
Page 149 and 150: Ebola Virus Stability on Surfaces a
Page 151 and 152: Ebola Virus Stability on Surfaces a
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Page 155 and 156: Outbreak of S. sonnei, South KoreaT
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Page 161 and 162: Cluster of Ebola Virus Disease, Lib
Page 163 and 164: ANOTHER DIMENSIONThe Past Is Never
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Page 167 and 168: LETTERSInfluenza A(H5N6)Virus Reass
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LETTERS3. Van Hong N, Amambua-Ngwa
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LETTERSTable. Prevalence of Bartone
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LETTERSavian influenza A(H5N1) viru
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LETTERSprovinces and a total of 200
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LETTERS7. Manian FA. Bloodstream in
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LETTERSforward projections. N Engl
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LETTERS3. Guindon S, Gascuel OA. Si
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BOOKS AND MEDIAin the port cities o
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ABOUT THE COVERNorth was not intere
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Earning CME CreditTo obtain credit,
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Emerging Infectious Diseases is a p
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