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1.
J Infect Public Health ; 15(9): 966-969, 2022 Jul 28.
Article in English | MEDLINE | ID: covidwho-1966858

ABSTRACT

We report a cluster of 12 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection in a long-term care facility in South Korea. There were two outbreaks of SARS-CoV-2 infection in the facility at the beginning and end of October 2021, respectively. All residents in the facility were screened for SARS-CoV-2 infection using RT-PCR as part of the investigation of the second outbreak. Twelve residents, who had infection confirmed during the first outbreak, were found to be re-positive for RT-PCR test at the second outbreak. 8 Of 12 RT-PCR re-positive cases were confirmed as reinfections based on investigation through the whole genome sequencing, viral culture, and serological analysis, despite of the short interval between the first and second outbreaks (29-33 days) and a history of full vaccination for 7 of the 12 re-positive cases. This study suggests that decreased immunity and underlying health condition in older adults makes them susceptible to reinfection, highlighting the importance of prevention and control measures regardless of vaccination status in long-term care settings.

2.
Asian Journal of Pharmaceutical and Clinical Research ; 15(7):110-113, 2022.
Article in English | EMBASE | ID: covidwho-1957633

ABSTRACT

Objective: To comprehend the evolution and spread of the severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) virus and also to prevent the future spread of the same, sequencing and analyzing the genomic data of SARS CoV-2 are essential. The objective of the present study is to describe the scope of improvement identified by the state of Madhya Pradesh in the data flow chain and the methodology designed to address the identified shortcomings. Methods: The number of sources of sample data collection was altered as well as a series of Google Sheets were formulated as an open-source tool, to implement an efficient sample data-sharing platform. The application of the proposed tool (Google Sheets as a source of data collection and information sharing) was within the state of Madhya Pradesh, India. Result: After utilizing this mechanism, the state was able to trace more than 80% VOCs and 3341 primary contacts and was also able to communicate this result to all stakeholders without much delay. Conclusion: Based on successful implementation and results, the authors suggest widening the domain of the proposed tool to other states.

3.
Virulence ; 13(1): 1242-1251, 2022 12.
Article in English | MEDLINE | ID: covidwho-1956537

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern have been emerging. However, knowledge of temporal and spatial dynamics of SARS-CoV-2 is limited. This study characterized SARS-CoV-2 evolution in immunosuppressed patients with long-term SARS-CoV-2 shedding for 73-250 days, without specific treatment. We conducted whole-genome sequencing of 27 serial samples, including 26 serial samples collected from various anatomic sites of two patients and the first positive sample from patient 2's mother. We analysed the intrahost temporal dynamics and genomic diversity of the viral population within different sample types. Intrahost variants emerging during infection showed diversity between individual hosts. Remarkably, N501Y, P681R, and E484K, key substitutions within spike protein, emerged in vivo during infection and became the dominant population. P681R, which had not yet been detected in the publicly available genome in Korea, appeared within patient 1 during infection. Mutually exclusive substitutions at residues R346 (R346S and R346I) and E484 (E484K and E484A) of spike protein and continuous turnover of these substitutions occurred. Unique genetic changes were observed in urine samples. A household transmission from patient 2 to his mother, at least 38 days after the diagnosis, was characterized. Viruses may differently mutate and adjust to the host selective pressure, which could enable the virus to replicate efficiently for fitness in each host. Intrahost variants could be candidate variants likely to spread to the population eventually. Our findings may provide new insights into the dynamics of SARS-CoV-2 in response to interactions between the virus and host.


Subject(s)
COVID-19 , Immunocompromised Host , SARS-CoV-2 , Virus Shedding , COVID-19/transmission , Humans , Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Whole Genome Sequencing
4.
Microbiol Res ; 263: 127133, 2022 Jul 22.
Article in English | MEDLINE | ID: covidwho-1956271

ABSTRACT

OBJECTIVES: Despite the quick implementation of infection prevention and control procedures and the use of personal protective equipment within healthcare facilities, many cases of nosocomial COVID-19 transmission have been reported. We aimed to estimate the frequency and impact of healthcare-associated COVID-19 (HA-COVID-19) and evaluate the contribution of whole-genome sequencing (WGS) in cluster investigation. METHODS: We estimated the frequency and mortality of HA-COVID-19 infections from September 1 to November 30, 2020, with a focus on the evolution of hospitalized community-associated COVID-19 (CA-COVID-19) cases and cases detected among healthcare workers (HCWs) within the Sorbonne University Hospital Group (Paris, France). We thoroughly examined 12 clusters through epidemiological investigations and WGS. RESULTS: Overall, 209 cases of HA-COVID-19 were reported. Evolution of HA-COVID-19 incidence closely correlated with the incidence of CA-COVID-19 and COVID-19 among HCWs. During the study period, 13.9 % of hospitalized patients with COVID-19 were infected in the hospital and the 30-day mortality rate of HA-COVID-19 was 31.5 %. Nosocomial transmission of SARS-CoV-2 led to clusters involving both patients and HCWs. WGS allowed the exclusion of one-third of cases initially assigned to a cluster. CONCLUSIONS: WGS analysis combined with comprehensive epidemiological investigations is essential to understand transmission routes and adapt the IPC response to protect both patients and HCWs.

5.
Medical Immunology ; 24(4):729-740, 2022.
Article in Russian | Academic Search Complete | ID: covidwho-1955151

ABSTRACT

Background: The global pandemic of coronavirus disease is a societal, economic, and publichealth crisis that is still underway. The spike glycoprotein of SARS-CoV-2 is one of the primary ingredients for virulence, tissue tropism, and host areas. Aim: This study aimed to determine mutations in the S protein of the Iraqi COVID-19 isolates. Full genome sequences of Iraqi strains were obtained from GISAID. Using statistical saturation mutagenesis and other informatics methods, we investigated 20 sequences of SARS-CoV-2 S protein missense mutation isolates in Iraq selected from NCBI. The following mutations were detected for all the strains under study compared to the wild type: L452R, A522V, E583D and D614G. The number of mutations in the strains was different depending on the location of the state from which the sample was collected The D614G mutation was found in 19 strains. One strain had three mutations, while the other was a wild form strain. The structure of the mutant protein changes dramatically, as does the energy of the atoms concerning the docking position, affecting the protein’s stability. The mutation sites would improve the S protein’s stability. Molecular docking of RBD-ACE2 is affected differently by residues L452R and A522V. (English) [ FROM AUTHOR] Глобальная пандемия коронавирусной инфекции стала длительной кризисной ситуацией для общества, экономики и здравоохранения, которая продолжается и сейчас. Спайк-гликопротеин вируса SARS-CoV-2 является одним из первичных компонентов вирулентности, тканевого тропизма и объектов носительства. Целью работы было определение мутаций S-белка в изолятах от больных COVID-19 в Ираке. Методы: полногеномные последовательности линий вируса в Ираке получали из базы GISAID. Используя статистики сатурационного мутагенеза и другие методики биинформатики, мы изучили 20 последовательностей изолятов SARS-CoV-2 с миссенс-мутацией данного белка, выявленных в Ираке и выбранных из базы данных NCBI. Результаты: во всех линиях вируса, при сравнении с диким типом, были выявлены следующие мутации: L452R, A522V, E583D and D614G. Число мутаций этих линий было различным, в зависимости от места сбора образцов. Мутация D614G была обнаружена в 19 линиях. Одна из линий имела 3 мутации, тогда как другая относились к дикому типу вируса. Структура мутантного белка существенно изменяется из-за энергетических взаимодействий атомов в зоне стыковки, что влияет на стабильность белка. Выводы: стабильность S-белка может изменяться в зависимости от места мутации. Стыковка молекулы RBD-ACE2 нарушается по-разному при заменах аминокислот L452R and A522V (Russian) [ FROM AUTHOR] Copyright of Medical Immunology (1563-0625) is the property of National Electronic-Information Consortium and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

6.
PeerJ ; 10: e13522, 2022.
Article in English | MEDLINE | ID: covidwho-1954767

ABSTRACT

Introduction: A global surge in SARS-CoV-2 cases is occurring due to the emergence of new disease variants, and requires continuous adjustment of public health measures. This study aims to continuously monitor and mitigate the impact of SARS-CoV-2 through genomic surveillance, to determine the emergence of variants and their impact on public health. Methods: Data were collected from 50 full-genome sequences of SARS-CoV-2 isolates from Makassar, South Sulawesi, Indonesia. Mutation and phylogenetic analysis was performed of SARS-CoV-2 from Makassar, South Sulawesi, Indonesia. Results: Phylogenetic analysis showed that two samples (4%) were of the B.1.319 lineage, while the others (96%) were of the B.1.466.2 lineage. Mutation analysis of the spike (S) protein region showed that the most common mutation was D614G (found in 100% of the sequenced isolates), followed by N439K (98%) and P681R (76%). Several mutations were also identified in other genomes with a high frequency, including P323L (nsp12), Q57H (ns3-orf3a), and T205I (nucleoprotein). Conclusion: Our findings highlight the importance of continuous genomic surveillance to identify new viral mutations and variants with possible impacts on public health.

7.
Front Med (Lausanne) ; 9: 877391, 2022.
Article in English | MEDLINE | ID: covidwho-1952387

ABSTRACT

Since the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African, European, American and Asian countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa.

8.
Front Genet ; 13: 839205, 2022.
Article in English | MEDLINE | ID: covidwho-1952304

ABSTRACT

The infection with SARS-CoV-2 virus in cats and dogs raised issue of human-to-animal transmission of SARS-CoV-2 in domestic pets in close contacts with their owners. Our study was designed to research this in the framework of Bosnia and Herzegovina. Using ELISA, AFIAS fluorescent immunoassay, RT-qPCR and WGS on Nanopore MinION platform with ARTIC Network Amplicon sequencing protocol for SARS-CoV-2, we showed that three out of thirteen dogs and one out of five cats from the households with confirmed human cases of COVID-19 in Bosnia-Herzegovina were infected with SARS-CoV-2. The high viral RNA load was detected in samples collected from a 4-year-old male Havanese (Ct = 12.52), a 6-year-old German Shepherd (Ct = 21.36) and a 9-year-old female American Staffordshire terrier (Ct = 25.74). The antibody response in dogs and one cat was observed. The viral genetic sequences from dogs were identical to the sequences detected in the owners suggesting the human-to-animal transmission of the virus. These findings, especially the low initial Ct values detected, from the public health perspective additionally stress the need for precautionary measures to protect both humans and animals.

9.
Syst Rev ; 11(1): 118, 2022 06 09.
Article in English | MEDLINE | ID: covidwho-1951339

ABSTRACT

BACKGROUND: Adolescent idiopathic scoliosis (AIS) is a structural lateral spinal curvature of ≥ 10° with rotation. Approximately 2-3% of children in most populations are affected with AIS, and this condition is responsible for approximately $1.1 billion in surgical costs to the US healthcare system. Although a genetic factor for AIS has been demonstrated for decades, with multiple potentially contributory loci identified across populations, treatment options have remained limited to bracing and surgery. METHODS: The databases MEDLINE (via PubMed), Embase, Google Scholar, and Ovid MEDLINE will be searched and limited to articles in English. We will conduct title and abstract, full-text, and data extraction screening through Covidence, followed by data transfer to a custom REDCap database. Quality assessment will be confirmed by multiple reviewers. Studies containing variant-level data (i.e., GWAS, exome sequencing) for AIS subjects and controls will be considered. Outcomes of interest will include presence/absence of AIS, scoliosis curve severity, scoliosis curve progression, and presence/absence of nucleotide-level variants. Analyses will include odds ratios and relative risk assessments, and subgroup analysis (i.e., males vs. females, age groups) may be applied. Quality assessment tools will include GRADE and Q-Genie for genetic studies. DISCUSSION: In this systematic review, we seek to evaluate the quality of genetic evidence for AIS to better inform research efforts, to ultimately improve the quality of patient care and diagnosis. SYSTEMATIC REVIEW REGISTRATION: PROSPERO registration #CRD42021243253.


Subject(s)
Scoliosis , Adolescent , Braces , Child , Female , Humans , Male , Mass Screening , Risk Assessment , Scoliosis/diagnosis , Scoliosis/genetics , Scoliosis/surgery , Systematic Reviews as Topic
10.
BMC Genomics ; 23(1): 406, 2022 May 30.
Article in English | MEDLINE | ID: covidwho-1951057

ABSTRACT

BACKGROUND: Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions. METHODS: The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing. RESULTS: The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection. CONCLUSIONS: The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , RNA Viruses , Genome, Viral , Humans , SARS-CoV-2/genetics , Whole Genome Sequencing
11.
Infect Genet Evol ; 102: 105300, 2022 08.
Article in English | MEDLINE | ID: covidwho-1946053

ABSTRACT

Since the beginning of the Coronavirus disease-2019 pandemic, there has been a growing interest in exploring SARS-CoV-2 genetic variation to understand the origin and spread of the pandemic, improve diagnostic methods and develop the appropriate vaccines. The objective of this study was to identify the SARS-CoV-2s lineages circulating in Tunisia and to explore their amino acid signature in order to follow their genome dynamics. Whole genome sequencing and genetic analyses of fifty-eight SARS-CoV-2 samples collected during one-year between March 2020 and March 2021 from the National Influenza Center were performed using three sampling strategies.. Multiple lineage introductions were noted during the initial phase of the pandemic, including B.4, B.1.1, B.1.428.2, B.1.540 and B.1.1.189. Subsequently, lineages B1.160 (24.2%) and B1.177 (22.4%) were dominant throughout the year. The Alpha variant (B.1.1.7 lineage) was identified in February 2021 and firstly observed in the center of our country. In addition, A clear diversity of lineages was observed in the North of the country. A total of 335 mutations including 10 deletions were found. The SARS-CoV-2 proteins ORF1ab, Spike, ORF3a, and Nucleocapsid were observed as mutation hotspots with a mutation frequency exceeding 20%. The 2 most frequent mutations, D614G in S protein and P314L in Nsp12 appeared simultaneously and are often associated with increased viral infectivity. Interestingly, deletions in coding regions causing consequent deletions of amino acids and frame shifts were identified in NSP3, NSP6, S, E, ORF7a, ORF8 and N proteins. These findings contribute to define the COVID-19 outbreak in Tunisia. Despite the country's limited resources, surveillance of SARS-CoV-2 genomic variation should be continued to control the occurrence of new variants.


Subject(s)
COVID-19 , SARS-CoV-2 , Amino Acids/genetics , COVID-19/epidemiology , Genome, Viral , Humans , Mutation , Phylogeny , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Tunisia/epidemiology
12.
Comp Clin Path ; 31(3): 355-363, 2022.
Article in English | MEDLINE | ID: covidwho-1941752

ABSTRACT

The coronavirus infectious disease (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses. The pandemic has emerged as a global public health crisis, and the threat of fast-spreading of the latest variants of the coronavirus (such as omicron, delta) is rampant. Therefore, a fast and reliable diagnostic assay is needed to make the clinical decision for further treatment. The study aims to develop a Centers for Disease and Prevention (CDC)-modified qualitative real-time reverse transcriptase PCR (RT-qPCR) assay and parallel assessment of commercially available RT-qPCR assay (Altona, Seegene, BD, and GBC) to detect SARS-CoV-2. Two hundred nine samples were chosen randomly out of around two hundred thousand samples. The panel consisted of SARS-CoV-2-positive (n = 156) and SARS-CoV-2-negative (n = 52) nasopharyngeal swab specimens for a primary clinical evaluation. Furthermore, 29 positive samples were sequenced using Oxford Nanopore Minion technology. Two hundred nine patient sample data of the cycle threshold (Ct) readings for target genes of five assays are 100% sensitive for Ct values. Mean Ct values for N1, N2, RdRp, S, and E of the positive controls in CDC assay, RealStar®, Allplex, GBC, and SD Biosensor were 17.5 ± 0.49, 16.9 ± 0.51, 20 ± 0.49, 21.7 ± 0.38, and 23.1 ± 0.43, respectively. F test value shows ≥ 1, which was statistically significant. All assays showed an efficiency of < 120% and R squares were < 0.99, which is well above the required threshold value. Thus, when taking the CDC-modified assay as a gold standard, the other four assays demonstrated a p value of 0.0000, concordance at 100%, and a Kappa at 1.000. A maximum-likelihood (ML) tree was constructed and compared based on full-length SARS-CoV-2 with Wuhan isolate. These isolates are closely related to the B.1.617 lineage and reference sequences. Therefore, we conclude that all RT-PCR kits assessed in this study shall be used for routine diagnostics of COVID-19 in patients. Supplementary information: The online version contains supplementary material available at 10.1007/s00580-022-03356-y.

13.
Int J Environ Res Public Health ; 19(14)2022 Jul 19.
Article in English | MEDLINE | ID: covidwho-1938822

ABSTRACT

Over 60 countries have integrated wastewater-based epidemiology (WBE) in their COVID-19 surveillance programs, focusing on wastewater treatment plants (WWTP). In this paper, we piloted the assessment of SARS-CoV-2 WBE as a complementary public health surveillance method in susceptible communities in a highly urbanized city without WWTP in the Philippines by exploring the extraction and detection methods, evaluating the contribution of physico-chemical-anthropogenic factors, and attempting whole-genome sequencing (WGS). Weekly wastewater samples were collected from sewer pipes or creeks in six communities with moderate-to-high risk of COVID-19 transmission, as categorized by the City Government of Davao from November to December 2020. Physico-chemical properties of the wastewater and anthropogenic conditions of the sites were noted. Samples were concentrated using a PEG-NaCl precipitation method and analyzed by RT-PCR to detect the SARS-CoV-2 N, RdRP, and E genes. A subset of nine samples were subjected to WGS using the Minion sequencing platform. SARS-CoV-2 RNA was detected in twenty-two samples (91.7%) regardless of the presence of new cases. Cycle threshold values correlated with RNA concentration and attack rate. The lack of a sewershed map in the sampled areas highlights the need to integrate this in the WBE planning. A combined analysis of wastewater physico-chemical parameters such as flow rate, surface water temperature, salinity, dissolved oxygen, and total dissolved solids provided insights on the ideal sampling location, time, and method for WBE, and their impact on RNA recovery. The contribution of fecal matter in the wastewater may also be assessed through the coliform count and in the context of anthropogenic conditions in the area. Finally, our attempt on WGS detected single-nucleotide polymorphisms (SNPs) in wastewater which included clinically reported and newly identified mutations in the Philippines. This exploratory report provides a contextualized framework for applying WBE surveillance in low-sanitation areas.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Humans , Philippines/epidemiology , Pilot Projects , RNA, Viral , SARS-CoV-2/genetics , Waste Water , Wastewater-Based Epidemiological Monitoring
14.
Pathogens ; 11(7)2022 Jul 08.
Article in English | MEDLINE | ID: covidwho-1928620

ABSTRACT

In Poland, the first case of SARS-CoV-2 infection was confirmed in March 2020. Since then, many circulating virus lineages fueled rapid pandemic waves which inflicted a severe burden on the Polish healthcare system. Some of these lineages were associated with increased transmissibility and immune escape. Mutations in the viral spike protein, which is responsible for host cell recognition and serves as the primary target for neutralizing antibodies, are of particular importance. We investigated the molecular epidemiology of the SARS-CoV-2 clades circulating in Southern Poland from February 2021 to August 2021. The 921 whole-genome sequences were used for variant identification, spike mutation, and phylogenetic analyses. The Pango B.1.1.7 was the dominant variant (n = 730, 89.68%) from March 2021 to July 2021. In July 2021, the B.1.1.7 was displaced by the B.1.617.2 lineage with 66.66% in July 2021 and 92.3% in August 2021 frequencies, respectively. Moreover, our results were compared with the sequencing available on the GISAID platform for other regions of Poland, the Czech Republic, and Slovakia. The analysis showed that the dominant variant in the analyzed period was B.1.1.7 in all countries and Southern Poland (Silesia). Interestingly, B.1.1.7 was replaced by B.1.617.2 earlier in Southern Poland than in the rest of the country. Moreover, in the Czech Republic and Slovakia, AY lineages were predominant at that time, contrary to the Silesia region.

15.
Neurology ; 98(18 SUPPL), 2022.
Article in English | EMBASE | ID: covidwho-1925446

ABSTRACT

Objective: To report the first case of COVID-19 associated acute necrotizing encephalopathy (ANE) without pulmonary disease in a patient with an extremely high interleukin-6 (IL-6) level and Ran Binding Protein 2 (RANBP2) mutation. Background: NA Design/Methods: A 29-year-old Burmese woman recently immunized with BBIBP32-CorV (Sinopharm) presented with alteration of consciousness. Her body temperature was 37 degrees Celsius, blood pressure 42/31 mmHg, heart rate 130 bpm, respiratory rate 20 per minute, and oxygen saturation 98%. Respiratory examination was unremarkable. Neurological examination revealed stupor but preserved brainstem reflexes. Results: Non-contrast computerized tomography of the brain showed symmetrical hypodense lesions involving bilateral thalami and cerebellar hemispheres characteristic of ANE. No pulmonary infiltration was found on chest radiograph. SARS-CoV-2 was detected by PCR;whole genome sequencing later confirmed the Delta variant. RANBP2 gene analysis revealed heterozygous Thr585Met mutation. Serum IL-6 was 7,390 pg/mL. Urinalysis showed pyelonephritis. Her clinical course was complicated by seizure, septic shock, acute kidney injury, and acute hepatic failure. She later developed coma and passed away in 6 days. Conclusions: ANE is caused by cytokine storm leading to necrosis and hemorrhage of the brain. RANBP2 missense mutation strongly predisposes this condition by affecting mitochondrial function, viral entry, cytokine signaling, immune response, and blood-brain barrier maintenance. Also, inactivated vaccine has been reported to precipitate massive production of cytokines by antibody dependent enhancement. The true incidence of COVID-19 associated ANE is not known as were the predictors of its development. We propose two factors that could participate in the pathogenesis of ANE in COVID-19. Further study is needed to confirm this hypothesis specifically in the post-vaccination period. Role of RANBP2 mutation and its application in COVID-19 and ANE should be further elaborated.

16.
Virus Evol ; 8(2): veac052, 2022.
Article in English | MEDLINE | ID: covidwho-1922335

ABSTRACT

The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. Here, we use deep sequencing to investigate the transmission of viral genetic variation among individuals during a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak that infected the vast majority of crew members on a fishing boat. We deep-sequenced nasal swabs to characterize the within-host viral population of infected crew members, using experimental duplicates and strict computational filters to ensure accurate variant calling. We find that within-host viral diversity is low in infected crew members. The mutations that did fix in some crew members during the outbreak are not observed at detectable frequencies in any of the sampled crew members in which they are not fixed, suggesting that viral evolution involves occasional fixation of low-frequency mutations during transmission rather than persistent maintenance of within-host viral diversity. Overall, our results show that strong transmission bottlenecks dominate viral evolution even during a superspreading event with a very high attack rate.

18.
Clin Microbiol Infect ; 2022 Jul 02.
Article in English | MEDLINE | ID: covidwho-1914264

ABSTRACT

OBJECTIVES: To describe Delta/Omicron SARS-CoV-2 variants co-infection detection and confirmation during the fifth wave of COVID-19 pandemics in France in 7 immunocompetent and epidemiologically unrelated patients. METHODS: Since December 2021, the surveillance of Delta/Omicron SARS-CoV-2 variants of concern (VOC) circulation was performed through prospective screening of positive-samples using single nucleotide polymorphism (SNP) PCR assays targeting SARS-CoV-2 S-gene mutations K417N (Omicron specific) and L452R (Delta specific). Samples showing unexpected mutational profiles were further submitted to whole genome sequencing (WGS) using three different primer sets. RESULTS: Between weeks 49-2021 and 02-2022, SARS-CoV-2 genome was detected in 3,831 respiratory samples, of which 3,237 (84.5%) were screened for VOC specific SNPs. Unexpected mutation profiles suggesting a dual Delta/Omicron population were observed in 7 nasopharyngeal samples (0.2%). These co-infections were confirmed by WGS. For 2 patients, the sequence analyses of longitudinal samples collected 7 to 11 days apart showed that Delta or Omicron can outcompete the other variant during dual infection. Additionally, for one of these samples, a recombination event between Delta and Omicron was detected. CONCLUSIONS: This work demonstrates that SARS-CoV-2 Delta/Omicron co-infections are not rare in high virus co-circulation periods. Moreover, co-infections can further lead to genetic recombination which may generate new chimeric variants with unpredictable epidemic or pathogenic properties that could represent a serious health threat.

19.
Journal of Public Health in Africa ; 12(SUPPL 1):36-37, 2022.
Article in English | EMBASE | ID: covidwho-1913137

ABSTRACT

Background: Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging coronavirus that is endemic in dromedary camels. Kenya's >3 million camels have high seroprevalence of antibodies against MERS-CoV, with scant evidence of human infection, possibly due to a lower zoonotic potential of Clade C viruses, predominantly found in African camels. Methods: Between April 2018-March 2020, we followed camels aged 0-24 months from 33 camel-keeping homesteads within 50Km of Marsabit town through collecting deep nasal swabs and documenting signs of illness in camels every two weeks. Swabs were screened for MERS-CoV by reverse transcriptase (RT)-polymerase chain reaction (PCR) testing and virus isolation performed on PCR positive samples with cycle threshold (CT) <20. Both the isolates and swab samples (CT <30) were subjected to whole genome sequencing. Human camel handlers were also swabbed and screened for symptoms monthly and samples tested for MERS-CoV by RT-PCR. Results: Among 243 calves, 68 illnesses were recorded in 58 camels (53.9%);50/68 (73.5%) of illnesses were recorded in 2019, and 39 (57.3%) were respiratory symptoms (nasal discharge, hyperlacrimation and coughing). A total of 124/4,702 camel swabs (2.6%) from 83 (34.2%) calves in 15 (45.5%) enrolled compounds were positive for MERS-CoV RNA. Cases were detected between May-September 2019 with three infection peaks, a similar period when three (1.1%) human PCR-positive but asymptomatic cases were detected among 262 persons handling these herds. Sequencing of camel specimens revealed a Clade C2 virus with identical 12 nucleotide deletion at the 3' end of OFR3 region and one nucleotide insertion at the 5' region but lacked the signature ORF4b deletions of other Clade C viruses. Interpretation: We found high levels of transmission of distinct Clade C MERS-CoV among camels in Northern Kenya, with likely spillover infection to humans. These findings update our understanding of MERS-CoV epidemiology in this region.

20.
Virologie ; 26(2):140, 2022.
Article in English | EMBASE | ID: covidwho-1912877

ABSTRACT

For many years, our laboratory has been developing cellular models for the study of human pathogenic viruses with RNA genomes, in order to study the replication of these pathogens, to propose new therapeutic pathways, to screen and test inhibitors. In response to the COVID-19 outbreak, we have set up the tools for the study of SARS-CoV-2 replication. First, clinical and reference SARS-CoV-2 strains have been successfully isolated and amplified using Vero E6 cells in the BSL3 facility of Bordeaux University (UB'L3, www.mfp.cnrs.fr/wp/larecherche/ andevir/ubl3/). We set up the monitoring of SARS-CoV-2 replication using conventional RT-qPCR quantification as well as evaluation of the cytopathic effect by microscopic observation or content analysis. Using VERO cells, we are now able to precisely titer viral supernatant (determination of the TCID50) and screen for potential antiviral molecule (determination of EC50 and CC50). We have developed a full-length Spike sequencing based on a Sanger approach1 as well as whole genome sequencing by nanopore technology, allowing the tracking of emerging variants. In parallel, we developed various other models to study SARS-CoV-2 replication including Calu-3 cells, modified human cells expressing Ace2 (e.g. 293T, U2OS) or even more complex cellular models (reconstituted human airway epithelium, vessels) according to the biological question to resolve. As an example, bronchial epithelia reconstituted from biopsies of adult or child donors were used to evaluate the inflammatory response upon SARS-CoV-2 infection in an age-dependent manner [2] (see poster G. Beucher). Similarly reconstituted blood vessels were used to study the impact of SARS-CoV- 2 infection on the vascular system and determine whether clinical observations (blood brain barrier damages, myocarditis) are due to direct infection of cells or indirect effects. Finally, we evaluate the efficacy of different chemical or physical processes for viral inactivation in air or on surfaces.

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