Japanese Journal of Infectious Diseases
Online ISSN : 1884-2836
Print ISSN : 1344-6304
ISSN-L : 1344-6304
75 巻, 1 号
選択された号の論文の19件中1~19を表示しています
Original Articles
  • Amjad Ahmadi, Atefeh Mousavi, Himen Salimizand, Manouchehr Ahmadi Heda ...
    2022 年 75 巻 1 号 p. 1-4
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/05/31
    ジャーナル フリー

    Neisseria gonorrhoeae is the causative agent of the sexually transmitted disease gonorrhoea. This bacterium infects the epithelial cells of the cervix of women and the urethra of men. However, its disease symptoms in the lower genitalia are found only in a small percentage of people. This study aimed to compare the frequency of N. gonorrhoeae genital infection among two groups of pregnant women, those with spontaneous abortions and those with normal pregnancies. This cross-sectional study was conducted in Western Iran. It included 417 women: 109 of whom had spontaneous abortions, 109 had normal deliveries, 100 were fertile, and 99 were infertile. Specific primers were used and DNA was extracted by endocervical swabs. A polymerase chain reaction test was then performed to detect N. gonorrhoeae. Data analysis was performed using the chi-squared test and t-tests. In all the above steps, a level of 5% was considered statistically significant, and the average ages in women with normal delivery, women with spontaneous abortion, fertile women, and infertile women were 27.8 ± 4.87, 29.6 ± 5.9, 32.1 ± 5.1, and 29.1 ± 6.3 years, respectively. The total frequency of N. gonorrhoeae infection was 0 (0%). The prevalence of N. gonorrhoeae infection was zero, and the disease was not associated with spontaneous abortion or infertility.

  • Xiaohua Wang, Lu Lu, Jin Miao, Jian Ma, Nana Wu, Yun Cao, Chuanqing Wa ...
    2022 年 75 巻 1 号 p. 5-9
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/05/31
    ジャーナル フリー

    This study aimed to determine the cause of the outbreak of nosocomial adenoviral conjunctivitis in the Neonatal Intensive Care Unit (NICU) and the impact of infection control measures. The objectives of the present study included investigating the association between hospital-borne infection and adenoviral conjunctivitis, analyzing the possible risk factors, and setting bundled infection control measures, which were adjusted according to the control effect. This study also aimed to observe the effects of different intervention measures on controlling adenoviral conjunctivitis. During the first and second intervention periods, 635 and 597 patients in the NICU were enrolled, respectively. Ophthalmoscopy was performed in 188 ( first intervention) and 184 (second intervention) patients (P > 0.05) 417 and 457 times, respectively (P < 0.001). During the first intervention and second interventions, 13 patients and no patient had adenoviral conjunctivitis, respectively (P < 0.001). All adenoviral conjunctivitis cases were reported 6–27 days (mean, 12 days) after ophthalmoscopy. Hydrogen peroxide disinfection bundled measures can effectively restrict the prevalence of adenoviral conjunctivitis associated with ophthalmoscopy in premature infants.

  • Cunye Yan, Yue Chen, Chenyu Sun, Mubashir Ayaz Ahmed, Chandur Bhan, Zh ...
    2022 年 75 巻 1 号 p. 10-15
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/05/31
    ジャーナル フリー

    The findings of previous research on the association between proton pump inhibitor (PPI) use and the treatment and prevention of coronavirus disease 2019 (COVID-19) are inconsistent. Therefore, this meta-analysis was conducted to clarify the outcomes of patients taking PPIs. This analysis included 14 articles with more than 268,683 subjects. PPI use was not associated with increased or decreased risk of COVID-19 infection (odds ratio [OR] 1.64, 95% confidence interval [CI] = 0.54–5.00, P = 0.39) or mortality (OR = 1.91, 95% CI = 0.86–4.24, P = 0.11). However, PPI use increased the risks of severe disease (OR 1.67, 95% CI = 1.37–2.02, P < 0.00001) and secondary infection (OR 4.62, 95% CI = 2.55–8.39, P < 0.00001). In summary, PPI use was not associated with an increased risk of infection and mortality in COVID-19 but appeared to be associated with an increased risk of progression to severe disease and secondary infection. However, more original studies are urgently needed to further clarify the relationship between PPI use and COVID-19.

  • Fatima Kanani, Saba Jamal, Saira Khowaja, Bushra Kaleem, Sabiha Anis, ...
    2022 年 75 巻 1 号 p. 16-23
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/05/31
    ジャーナル フリー

    Accurate and rapid diagnosis of coronavirus disease 2019 (COVID-19) is critical for proper care and identification of affected individuals. This led to early availability of many serological assays in the market, but with limited validation. In this study, we aimed to validate the serological assays based on different techniques. We evaluated 15 different assays based on four immunoassay techniques in 235 patients. The most sensitive kits employed were as follows: immunochromatography (Zybio severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] IgM/IgG Antibody Assay Kit – 83%), ELISA (Aeskulisa SARS-CoV-2 NP IgG –88.1%), chemiluminescence (Alinity SARS-CoV-2 IgG – 82.2%), and immunofluorescence (Lifotronic FA160 (Shenzhen SARS-CoV-2 Assay Kit [IgG]) – 88.9%). The kits by Uniper (Singuway Biotec COVID-19 IgM/IgG Presumptive Kit), Genrui 2019-nCoV IgM/IgG Test Kit, Wondfu SARS-CoV-2 Antibody Test, and Aeskulisa SARS-CoV-2 NP IgG exhibited 100% specificity, whereas IgG assay using Lifotronic FA160 (Shenzhen SARS-CoV-2 Assay Kit) exhibited the lowest specificity at 58%. Maximum agreement was observed between Aeskulisa SARS-CoV-2 NP IgG and Alinity SARS-CoV-2 IgG at 94%. Serological tests are practical alternatives, but their reliability depends on critical validation. The COVID-19 pandemic warranted investment in healthcare research at both the national and international levels.

  • Siriporn Kowaboot, Wilarat Puangmanee, Surachet Benjathummarak, Khwanc ...
    2022 年 75 巻 1 号 p. 24-30
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/05/31
    ジャーナル フリー

    Mouse antibodies specific to dengue NS1 have been widely investigated for their cross-reactivity with several human biomolecules. This is the first study demonstrating the cross-reactivity of human monoclonal antibodies (HuMAbs) specific to dengue NS1 isolated from patients infected with dengue virus serotype-2 (DENV-2). Nine anti-NS1 HuMAbs, which were mainly derived from patients in convalescent-phase after secondary infection of DENV-2, were characterized. Their cross-reactivity with plasminogen, thrombin, and endothelial cells was investigated, following which plasmin-formation assays were performed. All anti-NS1 HuMAbs exhibited cross-reactivity with human plasminogen (Plg), but not with thrombin or endothelial cells. Moreover, all HuMAbs exhibiting cross-reactivity with Plg converted Plg to plasmin in the plasmin-formation assay. These results suggest the implications and drawbacks of using anti-NS1 antibodies in immunotherapy.

  • Jun Li, Hui Shen, Ting Yu, Xiao-Yan Tao, Yong-Mei Hu, Hai-Chen Wang, M ...
    2022 年 75 巻 1 号 p. 31-35
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/05/31
    ジャーナル フリー

    This study aimed to investigate the clinical features, distribution, and antimicrobial susceptibility of Nocardia species isolated from pulmonary nocardiosis cases in a tertiary hospital in China. The species were collected from January 1, 2018, to May 31, 2019, and identified using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry or polymerase chain reaction. Antimicrobial susceptibility testing was performed using the broth microdilution method. Within the 44 Nocardia species, N. farcinica was the most frequently identified species (n = 36), followed by N. nova (n = 5), N. otitidiscaviarum (n = 1), N. cyriacigeorgica (n = 1), and N. transvalensis (n = 1). The top 3 predisposing factors of pulmonary nocardiosis were chronic obstructive pulmonary disease (45.5%), hypertension (34.1%), and tuberculosis (31.8%). All 44 Nocardia species were susceptible to amikacin, trimethoprim/sulfamethoxazole, and linezolid. The resistance rates of Nocardia to amoxicillin-clavulanic acid, ciprofloxacin, clarithromycin, ceftriaxone, tobramycin, and imipenem were 4.5%, 9.1%, 79.5%, 72.7%, 63.6%, and 38.6%, respectively. Two Nocardia strains had decreased sensitivity to trimethoprim/sulfamethoxazole. In conclusion, N. farcinica was the most frequently isolated Nocardia species in the First Hospital of Changsha. All the isolated clinical Nocardia species showed susceptibility to amikacin, trimethoprim/sulfamethoxazole, and linezolid, suggesting that these drugs can be primary therapeutic choices for treating Nocardia infections.

  • Yutaro Akiyama, Noriko Kinoshita, Kenji Sadamasu, Mami Nagashima, Isao ...
    2022 年 75 巻 1 号 p. 36-40
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/05/31
    ジャーナル フリー

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be detected in the stool samples of patients with coronavirus disease 2019 (COVID-19), and this virus can be transmitted via the oral-fecal route. However, there are only few reports on the viral load in the stool samples. In this pilot study, we aimed to evaluate the clinical characteristics and viral load of SARS-CoV-2 in the stool samples of 13 patients with confirmed COVID-19 using pepper mild mottle virus as a control, which has been proposed as a potential marker of human feces contamination in the environmental water bodies. SARS-CoV-2 RNA was detected in the stool samples of four patients (31%), and among them, three exhibited symptoms of diarrhea. One patient who suffered from long-term diarrhea (22 days) exhibited highest level of viral RNA in the stool sample (8.28 log10 copies/g). However, we could not harvest SARS-CoV-2 from the stool sample of any patient, even after culturing with VeroE6/TMPRESS2 cells for four weeks. Our results suggest that SARS-CoV-2 RNA can be detected in the stool samples of patients with COVID-19 suffering from diarrhea. However, further studies elucidating the relationship between SARS-CoV-2 viral load in the stool samples and symptoms of diarrhea in large cohorts and upon adjusting other causative factors and virus infectivity are still warranted.

  • Jayathilake Sarangi, Nao Matsuo, Rina Nonogaki, Michiko Hayashi, Kumik ...
    2022 年 75 巻 1 号 p. 41-48
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/06/30
    ジャーナル フリー

    The Enterobacter cloacae complex (ECC) is one of the most common causes of bacteremia and leads to poor clinical outcomes. The aim of this study was to clarify the antimicrobial susceptibility profiles and genetic backgrounds of non-carbapenemase-producing reduced-carbapenem-susceptible (RCS) ECC blood isolates in Japan using agar dilution antimicrobial susceptibility testing, whole-genome sequencing, and quantitative polymerase chain reaction for ampC, ompC, and ompF transcripts. Forty-two ECC blood isolates were categorized into RCS and carbapenem-susceptible groups based on the minimum inhibitory concentration of imipenem. The RCS ECC blood isolates belonged to distinct species and sequence types and produced varying class C β-lactamases. The E. roggenkampii, E. asburiae, and E. bugandensis isolates belonged only to the RCS group. Some E. hormaechei ssp. steigerwaltii isolates from the RCS group exhibited AmpC overexpression caused by amino acid substitutions in AmpD and AmpR along with ompF downregulation. These findings suggest that non-carbapenemase-producing RCS ECC blood isolates are genetically diverse.

  • Yaoyao Zhuge, Chenxi Ding, Xiufang Gong, Dan Hu, Jin Zhu, Changjun Wan ...
    2022 年 75 巻 1 号 p. 49-55
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/06/30
    ジャーナル フリー

    Severe fever with thrombocytopenia syndrome virus (SFTSV) is a newly emerging tick-borne virus with a fatality rate between 12% and 50%. Currently, effective vaccines or antiviral drugs are not available to treat SFTSV infection, and a diagnostic method for its detecting is urgently needed. Monoclonal (MAb) and polyclonal antibodies (PAbs) against SFTSV were prepared by immunizing animals with the SFTSV nucleocapsid protein (NP). We developed 2 double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISAs) to detect the SFTSV NP, which was captured using the MAbs and PAbs generated. Both methods were applicable for the diagnosis of SFTSV-infected patients, as confirmed by a quantitative polymerase chain reaction. Furthermore, the sensitivity and specificity of the 2 assays for diagnosing severe fever with thrombocytopenia syndrome were 100% and the antibodies did not react with recombinant Dabieshan NP or recombinant dengue virus NS1 subtype 1 and 2 proteins. In addition, 2 standard curves were established for quantitative detection of the NP: the monoclonal antibody-based ELISA (MAb-based ELISA) had a lower limit of detection than the polyclonal-based ELISA. Therefore, the MAb-based ELISA can be employed for convenient and effective detection of SFTSV.

  • Subhabrata Sarkar, Radha Kanta Ratho, Meenu Singh, Mini Pritam Singh, ...
    2022 年 75 巻 1 号 p. 56-62
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/06/30
    ジャーナル フリー

    Both human respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause immune-mediated under-five acute respiratory infections (ARIs), but differences in their disease pathogenesis, if any, are not well-known. This study was undertaken to analyze the epidemiological and immunological features of RSV and hMPV infections. Nasopharyngeal aspirates from children (aged 2 months to 5 years) with ARI, presenting to our tertiary care center between December 2013 and March 2016, were subjected to real-time polymerase chain reaction for the detection of RSV and hMPV. Positive samples were analyzed for co-infection and cytokine levels. Of the 349 nasopharyngeal aspirates, RSV was detected in 40.68% (142/349), hMPV in 6.59% (23/349), and both in 1.4% (5/349). Co-infections were common, with rhinovirus being the most common co-offender. The demographic and clinical parameters of RSV- and hMPV-infected children were comparable. The MMP-9/TIMP-1 ratio was significantly higher in RSV-mediated ARI and IFN-γ in hMPV-mediated ARI. Both RSV and hMPV are common among North Indian children with ARI, and coinfections are common. Their clinical features are non-discriminatory, and molecular diagnosis should be utilized to ascertain their individual epidemiology. The differences in their immune-pathogenesis (MMP-9/TIMP-1 ratio in RSV and IFN-γ in hMPV) could serve as useful tools for developing newer drugs.

  • Yasuto Fukushima, Yuzo Tsuyuki, Mieko Goto, Haruno Yoshida, Takashi Ta ...
    2022 年 75 巻 1 号 p. 63-69
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/06/30
    ジャーナル フリー

    This study assessed the biofilm production ability (BPA) and other microbiological features of Streptococcus canis strains. Forty strains of companion-animal origin, including the host information, from 2015 and 2017 were randomly selected, and three strains of blood-origin from two humans and one dog were included. We measured BPA using crystal violet staining, along with S. canis M-like protein (SCM) allele typing, sequence type (ST) determination, antimicrobial resistance (AMR) phenotyping/genotyping, and virulence-associated gene profiling (gbp, ap1, fp1, and brp). BPA measurements revealed 35 strains with BPA and 48 strains without BPA. There was an association between the producer and the isolation year (2017). Moreover, we observed an association between the non-producer and SCM allele 1 and ST9, and between the producer and SCM allele 10 and ST21. Furthermore, we observed a correlation between the producer and the presence of AMR genotypes. Specifically, there was an association between the producer and ap1 detection, and between non-producer and gbp detection. Our results suggest a correlation between biofilm producers and other microbiological features (i.e. isolation year, SCM allele type 10, ST21, presence of AMR genotypes, and ap1 detection).

  • Kübra Evren, Rukiye Berkem, Mihriban Yücel
    2022 年 75 巻 1 号 p. 70-75
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/06/30
    ジャーナル フリー

    We analyzed the performance parameters of the traditional and reverse algorithms to determine which is more convenient for serodiagnosis of syphilis. In total, 4,789 serum samples were obtained from a cross-sectional study. Venereal Disease Research Laboratory (VDRL), Treponema pallidum hemagglutination assay (TPHA), and chemiluminescent microparticle immunoassay (CMIA) tests were performed on each serum sample. In case of discordance between results, TPHA was applied as a second treponemal test. Overall, 207 patients were serodiagnosed with syphilis. Among the 4,789 samples tested, 125 (2.6%) and 206 (4.3%) were positive using the traditional and reverse algorithms, respectively. The missed diagnosis rate of the traditional algorithm was 42.5%. The reverse algorithm had a higher sensitivity than that of the traditional algorithm. The sensitivity levels of the traditional and reverse algorithms were 57.49% and 99.85% respectively. The false positivity rate of the reverse algorithm was 0.02%.

  • Xuefei Wang, Fen Yang, Lisong Huang, Ruifeng Chen, Yi Shan, Yiqing Jia ...
    2021 年 75 巻 1 号 p. 76-82
    発行日: 2021/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/06/30
    ジャーナル フリー

    This retrospective cross-sectional single-center study included patients with category III exposure to rabies virus between January and December 2019. Exposure characteristics and clinical data were compared and statistically analyzed between groups who were willing and unwilling to receive the rabies immunoglobin (RIG) injection, and the determinants of its administration were identified by stepwise multivariate logistic regression analyses. In total, 1,757 patients with category III exposure were enrolled: 845 men (48.1%) and 912 women (51.9%; median age: 28 [9–50] years). Among them, 1,297 (73.8%) received the RIG injection (median age: 28 [8–50] years) and 460 (26.2%) refused to receive the injection (median age: 25 [15–48] years). Patients aged 16–25 years (odds ratio [OR] = 3.006, 95% confidence interval [CI] = 1.957–4.619), 26–45 years (OR = 2.940, 95% CI = 2.011–4.298), 46–55 years (OR = 3.647, 95% CI = 2.233–5.959), and above 56 years (OR = 6.660, 95% CI = 4.009–11.062); those with injuries caused by cats (OR = 1.937, 95% CI = 1.476–2.542); and people with scratch (OR = 3.319, 95% CI = 2.510–4.390) and minor (OR = 35.281, 95% CI = 18.524–64.198), and moderate (OR = 12.711, 95% CI = 7.221–22.375) injuries were more likely to refuse injection. The RIG administration level in the settings studied herein was found to be insufficient. Educational and awareness programs on rabies prevention, especially those targeted at people not injured by dogs, people with minor injuries, and the elderly should be considered.

Short Communications
  • Elok Puspita Rini, Michihito Sasaki, Dwi Astuti, Vetnizah Juniantito, ...
    2022 年 75 巻 1 号 p. 83-85
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/04/30
    ジャーナル フリー

    Coxiella burnetii is a bacterial pathogen that causes Q fever, which is widespread worldwide. Livestock such as cattle, goats, and sheep are the main sources of C. burnetii infection. C. burnetii infection causes abortion in livestock, resulting in economic damage. Q fever is a zoonotic disease and a potential public health hazard. To date, little is known about C. burnetii infection in livestock in Indonesia. The objective of this study was to screen the genome of C. burnetii bacteria in beef cattle in West Java, Indonesia. Organ tissue samples were collected from cattle slaughtered in slaughterhouses in West Java. C. burnetii genome was detected in cattle samples obtained from three sampling areas using nested PCR, targeting the com1 gene of C. burnetii. Sequencing analysis of the 16S rRNA gene revealed that the amplicons showed 99.9% nucleotide identity to the C. burnetii strains: Heizberg, 1843, 2574, 701CbB1, and 14160-001. Our results indicate that C. burnetii infection occurs in Indonesian beef cattle and highlight the risk of exposure to C. burnetii infection in humans.

  • Kei Kubota, Ken-ichi Nagakura, Motohiro Ebisawa, Goro Kaneda, Noriyuki ...
    2022 年 75 巻 1 号 p. 86-88
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/05/31
    ジャーナル フリー

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become a major public health problem. Although real-time reverse-transcription polymerase chain reaction (RT-PCR) is the gold standard for diagnosing coronavirus disease 2019 (COVID-19) and there are many reports discussing it, reports about loop-mediated isothermal amplification (LAMP) tests for SARS-CoV-2, especially in children, are limited. In this study, we present the results of LAMP test in three children with COVID-19 in a family cluster, and assess these results. The LAMP test results of these children showed a sensitivity and specificity of 63.6% and 100%, respectively, and that was comparable to the RT-PCR results. The results of both LAMP test and RT-PCR test using nasopharyngeal swab (NPS) were almost consistently similar in two school children throughout hospitalization except at the very early stages of infection. The preliminary results suggest that saliva samples would be less sensitive than NPS for LAMP testing in the late stages of infection, and that LAMP test would not provide accurate results in neonates.

  • Taichiro Muto, Nami Nakamura, Yu Masuda, Shingo Numoto, Shunsuke Kodam ...
    2021 年 75 巻 1 号 p. 89-91
    発行日: 2021/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/06/30
    ジャーナル フリー

    To investigate the usefulness of quenching probe polymerase chain reaction (Q-probe PCR) for the detection of macrolide-resistant Mycoplasma pneumoniae (MP), we retrospectively analyzed the clinical course of 21 children with MP infection. The rate of macrolide-resistant MP was 66.7%. The duration of pyrexia after the initial antibiotic treatment was longer in patients with macrolide-resistant MP infection than in those with macrolide-sensitive MP infection. The duration of pyrexia after Q-probe PCR was not significantly different between patients with macrolide-resistant and -sensitive MP infection. Antibiotic use based on qPCR may reduce the duration of pyrexia. Q-probe PCR is useful in determining the appropriate antibiotics and improves the clinical course of MP infections.

  • Alexandra Sashova Alexandrova, Daniela Rosenova Pencheva, Ivan Gergov ...
    2022 年 75 巻 1 号 p. 92-95
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/06/30
    ジャーナル フリー

    Streptococcus pneumoniae is still a leading bacterial pathogen of acute otitis media (AOM), despite the availability of pneumococcal conjugate vaccines (PCVs). We conducted a study on the population structure, antibiotic nonsusceptibility, serotype distribution, and presence of pilus in middle ear fluids ‒ S. pneumoniae isolates recovered from PCV10-vaccinated children with suppurative АОМ in Bulgaria. Non-susceptibility was observed in 68.75% (n = 33) of the isolates, and multidrug resistance (MDR) was detected in 60.4% of the patients. The dual macrolide resistance mechanism was predominant. The most common serotypes were non-PCV10 serotypes 3 (27.1%, n = 13), 19A (25.0%, n = 12), and VT 19F (23.0%, n = 11). Overall, 64.6% were non-PCV10-serotypes. The presence of Pilus type I was observed mostly in the PCV10-serotypes. We found a strong association between clonal complexes (CCs), serotypes, and antimicrobial resistance. Multilocus sequence typing revealed the presence of four CCs: CC320 (39.6%), CC505 (12.5%), CC1377 8.3%), and CC230 (8.3%). The most abundant CC320 comprised MDR 19A and 19F isolates. CC230 clustered MDR isolates from serotypes 19A, 6C, and 14. CC505 and CC1377 were serotype 3 susceptible isolates. The vaccine-induced changes and trends in antimicrobial resistance and clonality must be the focus of systematic investigations.

  • Kazuya Shirato, Shutoku Matsuyama, Makoto Takeda
    2022 年 75 巻 1 号 p. 96-101
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/06/30
    ジャーナル フリー

    Various variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began emerging worldwide from the end of 2020 to the beginning of 2021. The variants GRY/VOC202012/01 (B1.1.7), GH/N501Y.V2 (B1.351), and GR/N501Y.V3 (P1) are characterized by N to Y amino acid substitution at position 501 in the S protein. The variant containing L to R substitution at position 452 in the S protein G/L452R.V3 (B1.617) was endemic to India. The heightened concern regarding these variants is related to their increased viral infectivity. Information about nucleotide mismatch(es) on the primer/probe sequence is important for maintaining good performance of real-time PCR assays. In this study, real-time RT-PCR assays developed by the National Institute of Infectious Diseases, Japan (NIID-N2 and NIID-S2 assays), were reviewed to analyze nucleotide mismatches of variants in primer/probe sequences. The frequency of mismatched sequences in three variants (GRY/VOC202012/01, GH/N501Y.V2, and GR/N501Y.V3) was lower than that in all SARS-CoV-2 sequences. The mismatch, that G to C substitution at nucleotide 8 in reverse primer of S2 set, elevated to about 16.3% in G/L452R.V3, however the substitution did not affect the analytical sensitivity of assay. Therefore, the study indicates that the NIID-N2 and NIID-S2 sets detect VOCs of SARS-CoV-2 with reliable efficiency.

  • Tomoyuki Sasaki, Osamu Inoue, Shinji Ogihara, Kayo Kubokawa, Saori Ois ...
    2022 年 75 巻 1 号 p. 102-104
    発行日: 2022/01/31
    公開日: 2022/01/24
    [早期公開] 公開日: 2021/07/30
    ジャーナル フリー

    Coronavirus disease 2019 is diagnosed based on the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasopharyngeal swabs or saliva samples using reverse-transcription quantitative polymerase chain reaction. Nasopharyngeal swabs should be collected by medical professionals who are covered with full personal protective equipment (PPE), while saliva samples can be collected by patients themselves without any PPE. However, collecting saliva is difficult for people who are unable to follow instructions, including infants or unconscious patients. Owing to the high viscosity of saliva, special attention is required to handle saliva samples in laboratories. To solve these problems, we compared lingual and buccal mucosal swabs (oral swabs) with nasopharyngeal swabs and saliva samples. Among 13 patients who had a positive result for SARS-CoV-2 RNA in their nasopharyngeal swabs, 8 and 10 patients had a positive result for SARS-CoV-2 RNA in their saliva (concordance rate, 61.5%) and oral swabs (76.9%), respectively. Among the eight patients with a positive result for SARS-CoV-2 RNA in saliva, seven (87.5%) had SARS-CoV-2 detected in their oral swabs. We could not obtain saliva samples from four patients, but we found perfect concordance of SARS-CoV-2 positivity between the nasopharyngeal and oral swabs. Therefore, oral swabs can be used for SARS-CoV-2 RNA detection.

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