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2.
Natl Sci Rev ; 9(4): nwab223, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1821756

ABSTRACT

In the spread of SARS-CoV-2, there have been multiple waves of replacement between strains, each of which having a distinct set of mutations. The first wave is a group of four mutations (C241T, C3037T, C14408T and A23403G [this being the amino acid change D614G]; all designated 0 to 1 below). This DG (D614G) group, fixed at the start of the pandemic, is the foundation of all subsequent waves of strains. Curiously, the DG group is absent in early Asian samples but present (and likely common) in Europe from the beginning. European data show that the high fitness of DG1111 requires the synergistic effect of all four mutations. However, the European strains would have had no time to evolve the four DG mutations (0 to 1), had they come directly from the early Asian DG0000 strain. Very likely, the European DG1111 strain had acquired the highly adaptive DG mutations in pre-pandemic Europe and had been spreading in parallel with the Asian strains. Two recent reports further support this twin-beginning interpretation. There was a period of two-way spread between Asia and Europe but, by May 2020, the European strains had supplanted the Asian strains globally. This large-scale replacement of one set of mutations for another has since been replayed many times as COVID-19 progresses.

3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-296434

ABSTRACT

Background: The onset of various kidney diseases have been reported after COVID-19 vaccination. However, detailed clinical and pathological examination of kidney injury in patients receiving inactivated vaccines are lacking.<br><br>Methods: We screened and analyzed patients with newly diagnosed kidney diseases after inactivated SARS-CoV-2 vaccination in Peking University First Hospital from January 2021 to August 2021. We obtained samples of blood, urine, and renal biopsy tissues. Clinical and laboratory information, as well as light microscopy, immunostaining and ultrastructural observation were described. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein and Nucleoprotein were stained using immune-fluorescence technique in the kidney biopsy samples. SARS-CoV-2 specific antibodies were tested using magnetic particle chemiluminescence immunoassay.<br><br>Findings: The study group included 17 patients, including immune complex mediated kidney diseases (IgA nephropathy, membranous nephropathy and lupus nephritis), podocytopathy (minimal change disease and focal segmental glomerulosclerosis) and others (antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis, anti-GBM nephritis, acute tubulointerstitial nephritis, and thrombotic microangiopathy). Seven patients (41.18%) developed renal disease after the first dose and 10 (58.82%) after the second dose. We found no definitive evidence of SARS-CoV-2 Spike protein or Nucleoprotein deposition in the kidney biopsy samples. Serological markers implicated abnormal immune responses in predisposed individuals. Treatment and follow-up (median = 86 days) showed that biopsy diagnosis informed treatment and prognosis in all patients.<br><br>Interpretation: We observed various kidney diseases following inactivated SARS-CoV-2 vaccine administration. Our findings provide an evidence against direct vaccine protein deposition as the major pathomechanism, but implicate abnormal immune responses in predisposed individuals. These findings expand our understanding of inactivated SARS-CoV-2 vaccine renal safety.<br><br>Funding: This study was funded by National Natural Science Foundation of China (91742205, 82170711, 81800636, 82070733, 81625004), Clinical Medicine Plus X—Young Scholars Project of Peking University (PKU2021LCXQ017), the Fundamental Research Funds for the Central Universities, CAMS Innovation Fund for Medical Sciences (2019-I2M-5-046), Yunnan Provincial Science and Technology Department (202102AA100051 and 202003AC100010, China), and Beijing Young Scientist Program (BJJWZYJH01201910001006).<br><br>Declaration of Interest: The authors declare no competing interests.<br><br>Ethical Approval: This study was approved by the institutional review board of Peking University First Hospital (2021-352) and the Committee on Human Subject Research and Ethics of Yunnan University (CHSRE2021020). Written Informed Consent Form was obtained from each participant.

4.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-296402

ABSTRACT

The COVID-19 pandemic poses a great threat to human society. SARS-CoV-2 is mainly transmitted through social contact;however, it is highly debated whether cold-chain related transmission has occurred and can be identified in the epidemic areas of COVID-19. Here, we provide a new method and distinguish two transmission routes by detecting a lineage-specific reduction of SARS-CoV-2 mutation rate. After analyzing 1,610,125 SARS-CoV-2 genomic sequences, we find that two outbreaks in Xinfadi-Beijing and Auckland are cold-chain related and respectively caused by two mutation-dormant variants. A Dalian outbreak in July 2020 and a Yingkou outbreak ten months later are epidemiologically connected and derived from a cold-chain related variant. Mutation-dormant variants are detected during the spread of spike D614G variant and the Delta Variant of Concern. Cold-chain contaminations repeatedly caused by epidemiologically connected patients are also found and have resulted in infections. Moreover, the COVID-19 outbreak in Wuhan is likely to be cold-chain related. A systematic identification reveals that the frequency of cold-chain related transmission is in the order of magnitude of 0.1-10%. Our results indicate that that cold-chain related transmission is rare but happens globally.

5.
Zool Res ; 42(6): 834-844, 2021 11 18.
Article in English | MEDLINE | ID: covidwho-1515719

ABSTRACT

Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks. A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses (SC2r-CoVs). Here, we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species, and detected positive signals in muscles of four Manis javanica and, for the first time, one M. pentadactyla. Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia. Using in-solution hybridization capture sequencing, we assembled a partial pangolin SC2r-CoV (pangolin-CoV) genome sequence of 22 895 bp (MP20) from the M. pentadactyla sample. Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M. javanica seized by Guangxi Customs. A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated. Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated. Given the potential infectivity of pangolin-CoVs, the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.


Subject(s)
COVID-19/veterinary , Evolution, Molecular , Pangolins/virology , SARS-CoV-2/genetics , Animals , Genome, Viral , Phylogeny , RNA, Viral/genetics
8.
Sens Actuators B Chem ; 327: 128899, 2021 Jan 15.
Article in English | MEDLINE | ID: covidwho-756853

ABSTRACT

The recent pandemic outbreak of COVID-19 caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a threat to public health globally. Thus, developing a rapid, accurate, and easy-to-implement diagnostic system for SARS-CoV-2 is crucial for controlling infection sources and monitoring illness progression. Here, we reported an ultrasensitive electrochemical detection technology using calixarene functionalized graphene oxide for targeting RNA of SARS-CoV-2. Based on a supersandwich-type recognition strategy, the technology was confirmed to practicably detect the RNA of SARS-CoV-2 without nucleic acid amplification and reverse-transcription by using a portable electrochemical smartphone. The biosensor showed high specificity and selectivity during in silico analysis and actual testing. A total of 88 RNA extracts from 25 SARS-CoV-2-confirmed patients and eight recovery patients were detected using the biosensor. The detectable ratios (85.5 % and 46.2 %) were higher than those obtained using RT-qPCR (56.5 % and 7.7 %). The limit of detection (LOD) of the clinical specimen was 200 copies/mL, which is the lowest LOD among the published RNA measurement of SARS-CoV-2 to date. Additionally, only two copies (10 µL) of SARS-CoV-2 were required for per assay. Therefore, we developed an ultrasensitive, accurate, and convenient assay for SARS-CoV-2 detection, providing a potential method for point-of-care testing.

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