Journal of clinical virology plus最新文献

{"title":"Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification","authors":"Manon Balvers ,&nbsp;Isabelle F. Gordijn ,&nbsp;Ingrid A.I. Voskamp-Visser ,&nbsp;Merel F.A. Schelling ,&nbsp;Rob Schuurman ,&nbsp;Esther Heikens ,&nbsp;Rene Braakman ,&nbsp;Christoph Stingl ,&nbsp;Hans C. van Leeuwen ,&nbsp;Theo M. Luider ,&nbsp;Lennard J. Dekker ,&nbsp;Evgeni Levin ,&nbsp;Armand Paauw","doi":"10.1016/j.jcvp.2023.100147","DOIUrl":"10.1016/j.jcvp.2023.100147","url":null,"abstract":"<div><h3>Objectives</h3><p>Shotgun proteomics is a generic method enabling detection of multiple viral species in one assay. The reliable and accurate identification of these viral species by analyzing peptides from MS-spectra is a challenging task. The aim of this study was to develop an easy accessible proteome analysis approach for the identification of viruses that cause respiratory and gastrointestinal infections.</p></div><div><h3>Methods</h3><p>For this purpose, a shotgun proteomics based method and a web application, ‘proteome2virus’, were developed. Identified peptides were searched in a database comprising proteomic data of 46 viruses known to be infectious to humans.</p></div><div><h3>Results</h3><p>The method was successfully tested for cultured viruses and eight fecal samples consisting of ten different viral species from seven different virus families, including SARS-CoV-2. The samples were prepared with two different sample preparation methods and were measured with two different mass spectrometers.</p></div><div><h3>Conclusions</h3><p>The results demonstrate that the developed web application is applicable to different MS data sets, generated from two different instruments, and that with this approach a high variety of clinically relevant viral species can be identified. This emphasizes the potential and feasibility for the diagnosis of a wide range of viruses in clinical samples with a single shotgun proteomics analysis.</p></div>","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100147"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46633515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"COVID-19-induced headache in Boston and the vicinity","authors":"Bart K. Chwalisz,&nbsp;Vi K. Le,&nbsp;Jennifer R. Cheng,&nbsp;Aayushee Jain,&nbsp;M. Brandon Westover,&nbsp;Hsinlin T. Cheng","doi":"10.1016/j.jcvp.2023.100148","DOIUrl":"10.1016/j.jcvp.2023.100148","url":null,"abstract":"<div><p>Headache is a common neurological symptom of Coronavirus disease 2019 (COVID-19) patients. However, the prevalence, comorbidities, and ethnic susceptibilities of COVID-19-induced headaches are not well-defined.</p><p>We performed a retrospective chart review of patients who tested positive for SARS-CoV2 by reverse transcriptase-polymerase chain reaction (RT-PCR) in March and April 2020 at Massachusetts General Hospital, Boston, Massachusetts, USA.</p><p>In the study, we identified 450 patients, 202 (44.9%) male, and 248 (55.1%) female, who tested positive for COVID-19. Headache is a significant painful symptom affecting 26% of patients. Female predominance is determined in sore throat, nasal congestion, hypogeusia, headache, and ear pain. In contrast, pneumonia and inpatient hospitalization were more prevalent in males. Younger patients (&lt; 50) were more likely to develop sore throat, fatigue, anosmia, hypogeusia, ear pain, myalgia /arthralgia, and headache. In contrast, older (&gt; 50) patients were prone to develop pneumonia and required hospitalization.</p><p>Ethnic subgroup analysis suggests Hispanic patients were prone to headaches, nausea/vomiting, nasal congestion, fever, fatigue, anosmia, and myalgia/arthralgia compared to non-Hispanics. Headache risk factors include nausea/vomiting, sore throat, nasal congestion, fever, cough, fatigue, anosmia, hypogeusia, dizziness, ear pain, eye pain, and myalgia/arthralgia.</p><p>Our study demonstrates regional gender, age, and ethnic variabilities in COVID symptomatology in Boston and the vicinity. It identifies mild viral, painful, and neurological symptoms are positive predictors of headache development in COVID-19.</p></div>","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100148"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10079317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10022298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Measles surveillance: Lessons from the COVID-19 pandemic","authors":"Noosha Samieefar ,&nbsp;SeyedehFatemeh Mousavi ,&nbsp;Hediyeh Baghsheikhi ,&nbsp;Fahimeh Abdollahimajd","doi":"10.1016/j.jcvp.2023.100141","DOIUrl":"10.1016/j.jcvp.2023.100141","url":null,"abstract":"","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100141"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9859640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10020671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mpox infection investigation using multiplexed syndromic diagnostics: Evaluation of an AusDiagnostics multiplexed tandem PCR (MT-PCR) syndromic panel","authors":"M.J. Pond ,&nbsp;J. Al-Mufti ,&nbsp;P. Madona ,&nbsp;M.A. Crone ,&nbsp;K.G. Laing ,&nbsp;R.S. Hale ,&nbsp;D. Muir ,&nbsp;P. Randell","doi":"10.1016/j.jcvp.2023.100142","DOIUrl":"10.1016/j.jcvp.2023.100142","url":null,"abstract":"<div><h3>Background</h3><p>Detection of mpox virus during investigation of viral vesicular rash illness is required to identify mpox infection.</p></div><div><h3>Objectives</h3><p>This study evaluated the performance of a research-use-only (RUO) AusDiagnostics MT-PCR syndromic assay containing an mpox virus target.</p></div><div><h3>Methods</h3><p>The analytical specificity and limit of detection (LoD) of the AusDiagnostics MT-PCR mpox assay was verified using control material. Clinical performance was evaluated using anonymised residual nucleic acids extracted from swab specimens previously tested for mpox virus using a laboratory developed test (LDT). Residual nucleic acids were derived from consecutive sample panels collected during two periods in the 2022 mpox outbreak.</p></div><div><h3>Results</h3><p>The AusDiagnostics MT-PCR assay demonstrated an LoD of 35 input copies of mpox virus and correctly detected all relevant members of a specificity panel (<em>n</em> = 34). 175 residual nucleic acids were included in the study with a prevalence of mpox of 40.0% (95%CI 32.7–47.6). The AusDiagnostics MT-PCR mpox assay demonstrated an accuracy of 98.9% (95%CI 93.8–99.9), sensitivity of 94.2% (95%CI 85.2 – 98.1) and specificity of 100% (95%CI 95.6 -100), when compared to the LDT qPCR assay. The AusDiagnostics MT-PCR mpox assay detected additional vesicular rash pathogens in 26.8% samples. Co-detection with other vesicular rash pathogens was described in 12.8% of mpox virus detected samples</p></div><div><h3>Conclusions</h3><p>Performance of the RUO AusDiagnostics MT-PCR mpox assay was comparable to an LDT qPCR for the detection of mpox virus in nucleic acids extracted from swab specimens. The RUO AusDiagnostics MT-PCR mpox assay facilitated the simultaneous detection of additional infective etiologies of vesicular rash syndromes.</p></div>","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100142"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46722826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"COVID or no COVID: Interpreting inconclusive SARS-CoV-2 qPCR results in different populations and platforms","authors":"Christien Rondaan,&nbsp;Lilli Gard,&nbsp;Hubert G.M. Niesters,&nbsp;Coretta van Leer-Buter,&nbsp;Xuewei Zhou","doi":"10.1016/j.jcvp.2023.100145","DOIUrl":"10.1016/j.jcvp.2023.100145","url":null,"abstract":"<div><h3>Introduction</h3><p>High cycle threshold values (Ct) value) results for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be true infections or false-positive results. Misinterpretation of results has negative consequences. Goal of this study was to evaluate quantitative real-time polymerase chain reaction (qPCR) results with high Ct-values, to reach a point where a correct interpretation can be given.</p></div><div><h3>Methods</h3><p>High Ct-value results of SARS-CoV-2 in respiratory samples taken between April 2020 and January 2021 were analysed. Three different SARS-CoV-2 qPCR assays (in-house<em>,</em> Alinity M and Xpert Xpress<em>)</em> were used for screening patients and healthcare workers (HCW). High Ct-value results were defined as “inconclusive”. The Ct-value cut-off for the interpretation of the test as “positive” and “inconclusive” were based on quality assurance panel results and manufacturers’ instructions.</p></div><div><h3>Results</h3><p>Out of totally 50.295 samples tested for SARS-CoV-2, the in-house and Alinity M qPCR together yielded 379 inconclusive results. A second sample existed for 217 samples, allowing dynamics of the PCR in time. Of these, 187 were negative (86%), 11 again inconclusive (5%) and 19 positive (9%). Sixteen out of 19 persons with a positive result were HCW, 14 (74%) had a link to a SARS-CoV-2 infected person. The majority of inconclusive results detected with the Xpert Xpress (n=45 of 3603), were related to individuals with a known history of SARS-CoV-2 infection (n=28, 62%).</p></div><div><h3>Conclusion</h3><p>This study shows the importance of re-testing inconclusive SARS-CoV-2 qPCR results. Only then, the correct (true or false) interpretation can be given, leading to the right measures.</p></div>","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100145"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9646134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SARS-CoV-2 evolution during persistent infection in a CAR-T recipient shows an escape to both sotrovimab and T-cell responses","authors":"Paola Mazzetti ,&nbsp;Pietro Giorgio Spezia ,&nbsp;Anna-Lisa Capria ,&nbsp;Giulia Freer ,&nbsp;Maria Sidoti ,&nbsp;Silvia Costarelli ,&nbsp;Alice Cara ,&nbsp;Alfredo Rosellini ,&nbsp;Susi Frateschi ,&nbsp;Giovanna Moscato ,&nbsp;Iacopo Franconi ,&nbsp;Michele Curcio ,&nbsp;Maria Linda Vatteroni ,&nbsp;Michele Lai ,&nbsp;Paola Quaranta ,&nbsp;Daniele Focosi ,&nbsp;Spartaco Sani ,&nbsp;Mauro Pistello","doi":"10.1016/j.jcvp.2023.100149","DOIUrl":"10.1016/j.jcvp.2023.100149","url":null,"abstract":"","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100149"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10121064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9649663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical study to compare the efficacy and safety of casirivimab & imdevimab, remdesivir, and favipravir in hospitalized COVID-19 patients","authors":"Sahar K. Hegazy ,&nbsp;Samar Tharwat ,&nbsp;Ahmed H. Hassan","doi":"10.1016/j.jcvp.2023.100151","DOIUrl":"10.1016/j.jcvp.2023.100151","url":null,"abstract":"<div><h3>Background</h3><p>Corona Virus disease - 2019 (COVID-19) disease induces scientific research to find a control to this pandemic from 2020 year up to now. Recently, various advances in pharmacotherapy against COVID-19 have emerged.</p></div><div><h3>Objectives</h3><p>To compare the efficacy and safety of antibodies cocktail (casirivimab and imdevimab), Remdesivir, and Favipravir in the COVID-19 patients</p></div><div><h3>Study design</h3><p>This study is a single-blind non-Randomized Controlled Trial (non-RCT). The drugs of the study are prescribed by lectures on chest diseases, faculty of medicine-Mansoura University. The duration of the study is about six months after ethical approval.</p><p>265 hospitalized COVID-19 patients were used to represent the COVID-19 population and were assigned into three groups in a ratio of (1:2:2) respectively, Group (A) received REGN3048–3051(Antibodies cocktail (casirivimab and imdevimab)), group (B) received remdesivir, and group (C) received favipravir.</p></div><div><h3>Results</h3><p>Casirivimab and imdevimab achieve less 28-day mortality rate, and less mortality at hospital discharge than Remdesivir, and Favipravir.</p></div><div><h3>Conclusion</h3><p>From all of these results, it is concluded that Group A (Casirivimab &amp; imdevimab) achieves more favorable outcomes than B (Remdesivir) &amp; C (Favipravir) intervention groups.</p></div><div><h3>Clinical trial registration</h3><p>NCT05502081, 16/08/2022, Clinicaltrials.gov</p></div>","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100151"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10169321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9652475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay as a rapid molecular diagnostic tool for COVID-19 in healthcare workers","authors":"Victor dos Santos Barboza ,&nbsp;William Borges Domingues ,&nbsp;Thobias Toniolo de Souza ,&nbsp;Tiago Veiras Collares ,&nbsp;Fabiana Kommling Seixas ,&nbsp;Bruna Silveira Pacheco ,&nbsp;Fernanda Severo Sabedra Sousa ,&nbsp;Thaís Larré Oliveira ,&nbsp;Marcelo de Lima ,&nbsp;Claúdio Martin Pereira de Pereira ,&nbsp;Fernando Rosado Spilki ,&nbsp;Janice Luehring Giongo ,&nbsp;Rodrigo de Almeida Vaucher","doi":"10.1016/j.jcvp.2023.100134","DOIUrl":"10.1016/j.jcvp.2023.100134","url":null,"abstract":"<div><p>In December 2019, the Chinese Center for Disease Control (CDC of China) reported an outbreak of pneumonia in the city of Wuhan (Hubei province, China) that haunted the world, resulting in a global pandemic. This outbreak was caused by a betacoronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several of these cases have been observed in healthcare professionals working in hospitals and providing care on the pandemic's frontline. In the present study, nasopharyngeal swab samples of healthcare workers were used to assess the performance of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay and subsequently compared with the real‐time reverse-transcription quantitative PCR (RT-qPCR) method. Thus, in this study, we validated a method for detecting SARS-CoV-2 based on RT-LAMP that can be used to diagnose these workers. The methodology used was based on analyzing the sensitivity, specificity, evaluation of the detection limit, and cross-reaction with other respiratory viruses. The agreement was estimated using a dispersion diagram designed using the Bland-Altman method. A total of 100 clinical specimens of nasopharyngeal swabs were collected from symptomatic and asymptomatic healthcare workers in Pelotas, Brazil, during the SARS-CoV-2 outbreak. RT-LAMP assay, it was possible to detect SARS-CoV-2 in 96.7% of the healthcare professionals tested using the E gene and N gene primers approximately and 100% for the gene of human β-actin. The observed agreement was considered excellent for the primer set of the E and N genes (<em>k</em> = 0.957 and <em>k</em> = 0.896), respectively. The sensitivity of the RT-LAMP assay was positive for the primer set of the E gene, detected to approximately 2 copies per reaction. For the primer set of the N gene, the assay was possible to verify an LoD of approximately 253 copies per reaction. After executing the RT-LAMP assay, no positive reactions were observed for any of the virus respiratory tested. Therefore, we conclude that RT-LAMP is effective for rapid molecular diagnosis during the COVID-19 outbreak period in healthcare professionals.</p></div>","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100134"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9891106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9639175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of Real-time RT-PCR cycle threshold (Ct) values with clinical features and severity of COVID-19 disease among hospitalized patients in the first and second waves of COVID-19 pandemic in Chennai, India","authors":"Sudhakar Natarajan ,&nbsp;Mohan Ranganathan ,&nbsp;P L Natarajan ,&nbsp;Manohar Nesakumar ,&nbsp;S Anbalagan ,&nbsp;K Lucia Precilla ,&nbsp;H Hemalatha ,&nbsp;M Kannan ,&nbsp;G Narendran ,&nbsp;S Mahalakshmi ,&nbsp;Gomathi Karmegam ,&nbsp;Lakshmi Prakash ,&nbsp;K Narayanasamy ,&nbsp;Luke Elizabeth Hanna","doi":"10.1016/j.jcvp.2023.100146","DOIUrl":"10.1016/j.jcvp.2023.100146","url":null,"abstract":"<div><h3>Introduction</h3><p>Real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) of nasopharyngeal/ oropharyngeal swab has been the gold standard test for detection of SARS-CoV-2 infection The relationship between cycle threshold (Ct) values of rRT-PCR and severity of disease remain disputable and not clearly defined in COVID-19.</p></div><div><h3>Methodology</h3><p>This is a single-centered retrospective observational study conducted at Government Corona Hospital (GCH), Guindy, Chennai. In the present study, we compared the Ct value of rRT-PCR from nasopharyngeal swab specimens with a diverse range of symptoms and disease severity among 240 individuals who were hospitalized with COVID-19, viz., mild cases (MC; <em>n</em> = 160), moderately severe cases (MSC; <em>n</em> = 46) and severe cases (SC; <em>n</em> = 34) in the first and second waves of COVID-19 pandemic.</p></div><div><h3>Results</h3><p>The study included 240 hospitalized COVID-19 patients with a median age of 52 years (range 21 to 90 years). MC, MSC, and SC all had median Ct values of 25.0 (interquartile range – IQR 20.0 to 30.5), 29.5 (IQR 23.0 to 34.0), and 29.0 (IQR 24 to 37.5) for the <em>ORF1ab</em> gene. The Ct value differed significantly between mild vs moderate, and mild vs severe cases. The Ct value of SC group with co-morbidity of type 2 diabetes have a significant difference compared to non-diabetes group (p value &lt;0.05). There was a significant difference in the median Ct value of <em>ORF1ab</em> gene among the MSC group and MC but not in the SC group in the first and second waves of the pandemic (<em>p</em>&lt;0.05).</p></div><div><h3>Conclusion</h3><p>We conclude that SARS-CoV-2 Ct values of rRT-PCR alone does not have a role in aiding severity stratification among patients with COVID-19 since the viral dynamics and Ct value may vary due to the emerging variants that occur in different waves of the pandemic.</p></div>","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100146"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10043973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9649386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of HIV-1 subtype CRF18_cpx in a patient with multidrug resistance in KwaZulu-Natal, South Africa: An epidemiological worry?","authors":"Aabida Khan ,&nbsp;Melendhran Pillay ,&nbsp;Benjamin Chimukangara ,&nbsp;Lilishia Gounder ,&nbsp;Sontaga Manyana ,&nbsp;Kerri-Lee Francois ,&nbsp;Knowledge Chipango","doi":"10.1016/j.jcvp.2023.100143","DOIUrl":"10.1016/j.jcvp.2023.100143","url":null,"abstract":"<div><p>The most common HIV-1 subtype in South Africa is subtype C, and detection of other subtypes is rare. We report the first known case of HIV-1 subtype CRF18_cpx identified in KwaZulu-Natal, South Africa, the epicenter of the HIV epidemic, through HIV drug resistance genotyping.</p><p>The 31-year-old female patient was initiated on fixed dose combination (tenofovir, emtricitabine, efavirenz) in 2017, with failure to achieve virologic suppression. Change to second-line antiretroviral therapy (tenofovir, emtricitabine and ritonavir-boosted lopinavir) was made in 2018. Adherence was impacted by lopinavir-induced diarrhoea. In 2020, she was switched to zidovudine, lamivudine and ritonavir-boosted atazanavir. Virologic failure persisted, and HIV drug resistance genotyping in April 2021 showed multidrug resistance. Third-line regimen (tenofovir, lamivudine, dolutegravir and ritonavir-boosted darunavir) was commenced in May 2021 and virologic suppression was achieved.</p><p>Co-incidentally we discovered from the HIV drug resistance sequence report that the patient was infected with HIV-1 subtype CRF18_cpx. Analysis of the HIV sequence using REGA HIV-1 Subtyping Tool confirmed sequence subtype assignment as HIV-1 CRF 18_cpx (bootstrap confidence = 90%). Subtyping was also confirmed with the COMET HIV-1 tool, HIV BLAST tool and phylogenetic analysis.</p><p>Based on our incidental finding, CRF18_cpx may be circulating locally as the patient had no travel history. Introduction of non-subtype C and recombinant viruses are expected to have increased in South Africa due to increased travel. This highlights the need to characterize subtype diversity in South Africa, particularly in KwaZulu-Natal, as HIV subtype can influence pathogenesis, treatment response, drug resistance and efforts towards vaccine development.</p></div>","PeriodicalId":73673,"journal":{"name":"Journal of clinical virology plus","volume":"3 2","pages":"Article 100143"},"PeriodicalIF":1.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43884124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}