First report of a Plasmodium malariae SSU rRNA gene variant in Africa associated with reduced amplification by nested PCR
Abstract Background Nested polymerase chain reaction (PCR) targeting the small subunit ribosomal ribonucleic acid (SSU rRNA, 18S rRNA) region is widely used to differentiate Plasmodium species. We identified a variant of the Plasmodium malariae SSU rRNA gene that suggests nested PCR may fail to dete...
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BMC
2025-08-01
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| Series: | Tropical Medicine and Health |
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| Online Access: | https://doi.org/10.1186/s41182-025-00787-5 |
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| author | Maki Goto Kei Yamamoto Kanako Komaki-Yasuda Shigeyuki Kano Norio Ohmagari |
| author_facet | Maki Goto Kei Yamamoto Kanako Komaki-Yasuda Shigeyuki Kano Norio Ohmagari |
| author_sort | Maki Goto |
| collection | DOAJ |
| description | Abstract Background Nested polymerase chain reaction (PCR) targeting the small subunit ribosomal ribonucleic acid (SSU rRNA, 18S rRNA) region is widely used to differentiate Plasmodium species. We identified a variant of the Plasmodium malariae SSU rRNA gene that suggests nested PCR may fail to detect P. malariae strains with unknown mutations. Case presentation A 56-year-old Japanese man developed a fever 2 months after returning from a 2-month stay in Sierra Leone. Quartan malaria was suspected based on blood smear findings, and nested PCR confirmed P. malariae infection. However, the secondary PCR band obtained using P. malariae-specific primers was fainter than the primary PCR band amplified with universal primers—a reversal of the typical pattern. Sequence analysis revealed a four-base deletion in the SSU rRNA gene within the primer-binding site of the species-specific reverse primer used in the secondary PCR, suggesting that mutations in this region may partially impair amplification and hinder species identification. Cytochrome b gene sequencing confirmed 100% identity with P. malariae. Conclusions These findings underscore the need for continued molecular surveillance and sequence-based validation to ensure accurate diagnosis of Plasmodium infections, particularly in regions where genetic variants and zoonotic strains are emerging. |
| format | Article |
| id | doaj-art-66d2ebf86e5d48bea890201b4ce2219b |
| institution | Kabale University |
| issn | 1349-4147 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
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| series | Tropical Medicine and Health |
| spelling | doaj-art-66d2ebf86e5d48bea890201b4ce2219b2025-08-20T04:02:44ZengBMCTropical Medicine and Health1349-41472025-08-015311510.1186/s41182-025-00787-5First report of a Plasmodium malariae SSU rRNA gene variant in Africa associated with reduced amplification by nested PCRMaki Goto0Kei Yamamoto1Kanako Komaki-Yasuda2Shigeyuki Kano3Norio Ohmagari4Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan Institute for Health Security (JIHS)Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan Institute for Health Security (JIHS)Department of Tropical Medicine and Malaria, Research Institute of Global Health and Medicine, JIHSDepartment of Tropical Medicine and Malaria, Research Institute of Global Health and Medicine, JIHSDisease Control and Prevention Center, National Center for Global Health and Medicine, Japan Institute for Health Security (JIHS)Abstract Background Nested polymerase chain reaction (PCR) targeting the small subunit ribosomal ribonucleic acid (SSU rRNA, 18S rRNA) region is widely used to differentiate Plasmodium species. We identified a variant of the Plasmodium malariae SSU rRNA gene that suggests nested PCR may fail to detect P. malariae strains with unknown mutations. Case presentation A 56-year-old Japanese man developed a fever 2 months after returning from a 2-month stay in Sierra Leone. Quartan malaria was suspected based on blood smear findings, and nested PCR confirmed P. malariae infection. However, the secondary PCR band obtained using P. malariae-specific primers was fainter than the primary PCR band amplified with universal primers—a reversal of the typical pattern. Sequence analysis revealed a four-base deletion in the SSU rRNA gene within the primer-binding site of the species-specific reverse primer used in the secondary PCR, suggesting that mutations in this region may partially impair amplification and hinder species identification. Cytochrome b gene sequencing confirmed 100% identity with P. malariae. Conclusions These findings underscore the need for continued molecular surveillance and sequence-based validation to ensure accurate diagnosis of Plasmodium infections, particularly in regions where genetic variants and zoonotic strains are emerging.https://doi.org/10.1186/s41182-025-00787-5Plasmodium malariaeNested PCRSSUrRNA18S rRNASpecies-specific primerSequence analysis |
| spellingShingle | Maki Goto Kei Yamamoto Kanako Komaki-Yasuda Shigeyuki Kano Norio Ohmagari First report of a Plasmodium malariae SSU rRNA gene variant in Africa associated with reduced amplification by nested PCR Tropical Medicine and Health Plasmodium malariae Nested PCR SSUrRNA 18S rRNA Species-specific primer Sequence analysis |
| title | First report of a Plasmodium malariae SSU rRNA gene variant in Africa associated with reduced amplification by nested PCR |
| title_full | First report of a Plasmodium malariae SSU rRNA gene variant in Africa associated with reduced amplification by nested PCR |
| title_fullStr | First report of a Plasmodium malariae SSU rRNA gene variant in Africa associated with reduced amplification by nested PCR |
| title_full_unstemmed | First report of a Plasmodium malariae SSU rRNA gene variant in Africa associated with reduced amplification by nested PCR |
| title_short | First report of a Plasmodium malariae SSU rRNA gene variant in Africa associated with reduced amplification by nested PCR |
| title_sort | first report of a plasmodium malariae ssu rrna gene variant in africa associated with reduced amplification by nested pcr |
| topic | Plasmodium malariae Nested PCR SSUrRNA 18S rRNA Species-specific primer Sequence analysis |
| url | https://doi.org/10.1186/s41182-025-00787-5 |
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