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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has many variants; some are or have been believed to be of particular importance. By January 2021 as many as 300,000 variants have been identified.[1] This article deals with notable variants.
The sequence WIV04/2019, belonging to the GISAID S clade / Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN) A clade, is thought likely to be the original sequence infecting humans, known as 'sequence zero'.[2]
Nomenclature
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| Rambaut et al. lineages | Notes to Rambaut et al.[4] | Nextstrain clades, 2021[5] | GISAID clades | Notable variants or mutations |
|---|---|---|---|---|
| A.1–A.6 | 19B | S | contains “sequence zero”[2] | |
| B.3–B.7, B.9, B.10, B.13–B.16 | 19A | L | ||
| O[a] | ||||
| B.2 | V | |||
| B.1 | B.1.5–B.1.72 | 20A | G | Lineage B.1 in the Rambaut et al. system |
| B.1.9, B.1.13, B.1.22, B.1.26, B.1.37 | GH | |||
| B.1.3–B.1.66 | 20C | Includes CAL.20C[6] | ||
| 20G | Predominant in US generally, Jan '21[6] | |||
| 20H | Includes 501.V2 aka (20C/501Y.V2 or) 20H/501Y.V2 or B.1.351 lineage | |||
| B.1.1 | 20B | GR | Includes B.1.1.207 | |
| 20D | Includes P.1, aka B.1.1.248 | |||
| 20F | ||||
| 20I | Includes VOC-202012/01 aka (20B/501Y.V1 or) 20I/501Y.V1 or lineage B.1.1.7 | |||
| B.1.177 | 20E (EU1)[5] | GV[a] | Derived from 20A[5] |
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No nomenclature for evolutionary lineages of SARS-CoV-2 is universally accepted,[8] but as of January 2021[update], the World Health Organization is working on 'standard nomenclature for SARS-CoV-2 variants that does not reference a geographical location'.[9]
While there are many thousands of variants of SARS-CoV-2,[10] subtypes of the virus can be put into much larger groupings such as lineages or clades. Several different nomenclatures for these subtypes have been proposed.
- As of January 2021[update], GISAID—referring to SARS-CoV-2 as hCoV-19[11]—had identified eight global clades (S, O, L, V, G, GH, GR, and GV).[12]
- In 2017, Hadfield et al. announced Nextstrain, intended 'for real-time tracking of pathogen evolution'.[13] Nextstrain has later been used for tracking SARS-CoV-2, identifying 11 major clades[b] (19A, 19B, and 20A–20I) as of January 2021[update].[14]
- Rambaut et al. of the Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN) software team proposed that lineages be used for subtypes of SARS-CoV-2 in 2020;[15] as of December 2020[update], five major lineages (A, B, B.1, B.1.1, and B.1.177) had been identified.[16]
Notable variants
Lineage B.1.1.207
First sequenced in August 2020 in Nigeria,[17] the implications for transmission and virulence are unclear but it has been listed as an emerging variant by the US Centers for Disease Control.[18] Sequenced by the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria, this variant has a P681H mutation, shared in common with UK's VOC-202012/01. It shares no other mutations with VOC-202012/01 and as of late December 2020 this variant accounts for around 1% of viral genomes sequenced in Nigeria, though this may rise.[17]
Lineage B.1.1.7 / Variant of Concern 202012/01
First detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the previous month,[19]Variant of Concern 202012/01 (VOC-202012/01),[20] was previously known as the first Variant Under Investigation in December 2020 (VUI – 202012/01)[21] and also as lineage B.1.1.7 or 20I/501Y.V1 (formerly 20B/501Y.V1).[4][22][23] Since then, its prevalence odds have doubled every 6.5 days, the presumed generational interval.[24][25] It is correlated with a significant increase in the rate of COVID-19 infection in United Kingdom, associated partly with the N501Y mutation. There is some evidence that this variant has 30–70% increased transmissibility,[26] and early analyses suggest an increase in lethality.[26]
Cluster 5
In early November 2020, Cluster 5, also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI),[27] was discovered in Northern Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening. A lockdown and travel restrictions were introduced in seven municipalities of Northern Jutland to prevent the mutation from spreading, which could compromise national or international responses to the COVID-19 pandemic. By 5 November 2020, some 214 mink-related human cases had been detected.[28]
The World Health Organization (WHO) has stated that cluster 5 has a 'moderately decreased sensitivity to neutralizing antibodies'.[29] SSI warned that the mutation could reduce the effect of COVID-19 vaccines under development, although it was unlikely to render them useless. Following the lockdown and mass-testing, SSI announced on 19 November 2020 that cluster 5 in all probability had become extinct.[30]
501.V2 variant
On 18 December 2020, the 501.V2 variant, also known as 501.V2, 20H/501Y.V2 (formerly 20C/501Y.V2), or lineage B.1.351,[23] was first detected in South Africa and reported by the country's health department.[31] Researchers and officials reported that the prevalence of the variant was higher among young people with no underlying health conditions, and by comparison with other variants it is more frequently resulting in serious illness in those cases.[32][33] The South African health department also indicated that the variant may be driving the second wave of the COVID-19 epidemic in the country due to the variant spreading at a more rapid pace than other earlier variants of the virus.[31][32]
Scientists noted that the variant contains several mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y,[31][34] K417N, and E484K.[35][36] The N501Y mutation has also been detected in the United Kingdom.[31][37]
Lineage P.1
Lineage P.1 was detected in Tokyo on 6 January 2021 by the National Institute of Infectious Diseases (NIID). The new lineage was first identified in four people who arrived in Tokyo having travelled from the Amazonas state on 2 January 2021.[38] On 12 January 2021, the Brazil-UK CADDE Centre confirmed 13 local cases of the P.1 new lineage in the Amazon rain forest.[39] This variant of SARS-CoV-2 has been named P.1 lineage (although it is a descendant of B.1.1.28, the name B.1.1.28.1 is not permitted and thus the resultant name is P.1) and has 17 unique amino acid changes, 10 of which in its spike protein, including N501Y and E484K.[39] The new lineage was absent in samples from March to November from Manaus, Amazonas state, but it was identified in 42% of the samples from December 2020 collected in the same city, suggesting a recent increase in frequency.[39]
A separate preprint by Voloch et al. identified another sub-lineage of the B.1.1.28 lineage circulating in the state of Rio de Janeiro, Brazil, now named P.2 lineage,[40] that harbours the E484K mutation. The P.2 lineage is not directly related with the P.1 lineage identified in Manaus.[39][41] Although both lineages harbour the E484K mutation, the mutation was acquired independently through convergent evolution.[39][better source needed]
Lineage B.1.429 / CAL.20C
CAL.20C[42] was first observed by researchers at Cedars-Sinai Medical Center in July 2020 in one of 1,230 virus samples collected in Los Angeles County. The variant, designated lineage B.1.429, contains mutation L452R and was not detected again in Southern California until October 2020. In November 2020, the CAL.20C variant accounted for 36 percent of samples collected at Cedars-Sinai Medical Center, and by January 2021, the CAL.20C variant accounted for 50 percent of samples.[43] In a joint press release by University of California, San Francisco, California Department of Public Health, and Santa Clara County Public Health Department[44], the variant was also detected in multiple counties in Northern California. From November to December 2020, the frequency of the variant in sequenced cases from Northern California rose from 3% to 25%.[45]. In a preprint, CAL.20C is described as belonging to clade 20C and contributing approximately 36% of samples, while an emerging variant from the 20G clade accounts for some 24% of the samples in a study focused on Southern California. Note however that in the US as a whole, the 20G clade predominates, as of January 2021.[6]
Germany
On 19 January 2021, a new variant, as yet unsequenced, was found in 35 patients in a hospital in Garmisch-Partenkirchen, Germany. Further tests are being carried out on virus samples from the patients in order to identify the prevalence and mortality rate of the variant.[46][47]
Notable mutations
D614G
D614G is a mutation that affects the spike protein of SARS-CoV-2. The frequency of this mutation in the viral population has increased during the pandemic. G (glycine) has replaced D (aspartic acid) in many countries, especially in Europe though more slowly in China and the rest of East Asia, supporting the hypothesis that G increases the transmission rate, which is consistent with higher viral titers and infectivity in vitro.[2] In July 2020, it was reported that the more infectious D614G SARS-CoV-2 variant had become the dominant form in the pandemic.[48][49][50][51] PHE confirmed that the D614G mutation had a 'moderate effect on transmissibility' and was being tracked internationally.[52]
The global prevalence of D614G correlates with the prevalence of loss of smell (anosmia) as a symptom of COVID-19, possibly mediated by higher binding of the RBD to the ACE2 receptor or higher protein stability and hence higher infectivity of the olfactory epithelium.[53]
Variants containing the D614G mutation are considered to be part of the G clade by GISAID[2] and the B.1 clade by the PANGOLIN tool.[54]
E484K
E484K has been reported to be an 'escape mutation' from at least one form of monoclonal antibody against SARS-CoV-2, indicating there may be a 'possible change in antigenicity'.[55] The P.1. lineage described in Japan and Manaus[56], the P.2 lineage (also known as B.1.1.248 lineage, Brazil)[57] and 501.V2 (South Africa) both exhibit this mutation.[55] The name of the mutation, E484K, refers to an exchange whereby the glutamic acid (E) is replaced by lysine (K) at position 484.[58] Monoclonal and serum-derived antibodies are reported to be from 10 to 60 times less effective in neutralizing virus bearing the E484K mutation.[59][60]
N501Y
N501Y denotes a change from asparagine (N) to tyrosine (Y) in amino-acid position 501.[52] This change is believed by Public Health England to increase binding affinity because of its position inside the spike glycoprotein's receptor-binding domain, which binds ACE2 in human cells;[61] data also support the hypothesis of increased binding affinity from this change.[61] Variants with N501Y include P.1 (Brazil/Japan),[55][62] Variant of Concern 202012/01 (UK), 501.V2 (South Africa), and COH.20G/501Y (Columbus, Ohio). This last became the dominant form of the virus in Columbus in late December 2020 and January and appears to have evolved independently of other variants.[63][64]
New Variant Assessment Platform
On 26 January 2021, the British government said it would share its genomic sequencing capabilities with other countries in order to increase the genomic sequencing rate and trace new variants.[65] As of January 2021, more than half of all genomic sequencing of COVID-19 was carried out in the UK.[66]
mRNA vaccine effectiveness
A preliminary study by Pfizer, Inc. has indicated that there is, at most, only minor reduction of the company's mRNA vaccine effectiveness against different SARS-CoV-2 variants.[67]
Summary
| First detection | Rambaut et al. classification | Other names | Notable mutations | Clinical changes | Spread | |||
|---|---|---|---|---|---|---|---|---|
| Location | Date | Transmissibility | Virulence | Antigenicity | ||||
| Nigeria | August 2020 | B.1.1.207 | P681H[18] | No evidence of change | No evidence of change | No evidence of change | ||
| United Kingdom | September 2020 | B.1.1.7 | VOC-202012/01, 20B/501Y.V1 | N501Y, 69–70del, P681H[68] | Evidence of 30–70% increased transmissibility[26] | Potentially 30% more lethal[26] | No evidence of change | Global |
| Denmark | October 2020 | N/A | Cluster 5, ΔFVI-spike (SSI)[27] | Y453F, 69–70deltaHV[27] | No evidence of change | No evidence of change | 'Moderately decreased sensitivity to neutralising antibodies'[29] | Likely extinct[30] |
| South Africa | December 2020 | B.1.351 | 501.V2, 20C/501Y.V2 | N501Y, K417N, E484K[36] | Evidence of increased transmissibility (SADoH) | No evidence of change | Undergoing investigation (E484K mutant) | Global |
| Japan Brazil | January 2021 | P.1 | B.1.1.248 | N501Y, E484K[69][70][71] | Undergoing investigation (N501Y mutant) | No evidence of change | Undergoing investigation (E484K mutant) | Global |
wikigb.comVariants of SARS-CoV-2
Quick Access
Windows
Mac
Chrome OS
Linux
Android
Update driver in Windows
Windows
Since Jiusion microscopes use a standard webcam chipset, they will automatically install default webcam (UVC) drivers when plugged into a host device. They can be used with any webcam apps. User can select one or more to install.
| Win10 built-in camera app | xploview | Amcap | Coolingtech | |
| Easy to install | √ | √ | × | × |
| User Friendly | √ | √ | × | × |
| Snap button works | × | √ | √ | × |
| Zoom button works | × | × | √ | × |
| Measure function | × | × | × | √ |
| Support | Win10 Only | Win7/8/10 | Win7/8/10 | Win7/8/10 |
Windows 10 user please make sure the 'Camera' in privacy settings is on.
1) Win10 built-in camera app
If you are Win10 user, you can plug the microscope to the Win10 computer and open this app to use the microscope directly. You can click 'Windows' logo on the left and find the 'Camera' app. The downside is that you can't use the snap and zoom buttons in this app.
2) xploview
2.1 Download the xploview
xploview.exe(3.87MB) Windows XP, Vista, 7, 8, 10 | 32 or 64 bit
2.2 Install the xploview
Double click the “xploview” to start installation. Select your first language and click “Next”.
Click “Browse” if you want to install to other fodders. Click “Next”.
Click “Install”.
Wait for the installation to complete. Click 'Finish' to complete the installation.
2.3 Remove the microscpe lens cover and connect it to the computer
2.4 Open the xploview
Click ①'Settings' –② 'Device' to select 'USB2.0 UVC PC Camera' on the dropdown. Click 'Apply'. Note the zoom button doesn’t work on this software.
3) Amcap
3.1 Download the Amcap
Amcap is a custom Windows (XP and above) software package designed specifically to work with the microscope.
Amcap.zip(3.38MB) Windows XP, Vista, 7, 8 | 32 or 64 bit
Amcap.exe(9.46MB) Windows 10 | 32 or 64 bit
Please tap this link to send an email to us if you can't download it jiusion@outlook.com
3.2 Extract the Amcap.zip
Step 1: Right Click the Amcap.zip and select 'Extract All'. Step 2: Click 'Browser' to select a location to save the Amcap and click 'Extract'. Step 3: Double click the extracted folder 'Amcap' to open it.
3.3 Install the Amcap
Double click the “setup.exe” to install the Amcap. Select ①Next - ②Next - ③Install - ④Yes - ⑤Finish - ⑥No, I will restart my computer later and Finish.
3.3 Remove the microscpe lens cover, plug the microscope and open the Amcap
Connect the microscope to the computer. Right click the Amcap and select 'Run as administrator' to open the Amcap software. Click 'Devices' to select the 'GL USB2.0 UVC Camera Device'.If you can't find the 'GL USB2.0 UVC Camera Device', please tapUpdate driver in Windowsto set up.
3.4 Setup the location to save pictures and videos
Pictures
: Select “Capture” – Snapshot Location – Find or new a folder and click “Open”. You can double click the Snap button to take a picture.Videos: Click “File” – “Set Capture File”. Find and select an avi format video file. Click “Open”.
4) CoolingTech
Coolingtech measurement software is compatible with Windows 7 8 10.4.1 Download the CoolingTech
What we provided in this link is a installation-free green version. You can delete directly if you want to uninstall it. Click link as below to download the Coolingtech.zip.
Coolingtech.zip(2.55MB) Windows XP, Vista, 7, 8, 10 | 32 or 64 bit
4.2 Extract the Coolingtech.zip
Once the download is finished, right click the 'Coolingtech.zip' to select 'Extract All...' to extract files out.
4.3 Open the CoolingTech software
Please ritght click the CoolingTech.exe to select 'Run as administrator' to open the CoolingTech.exe. As it is a installation-free version, you can open the Coolingtech folder and run the “CoolingTech.exe” as admin to use the Coolingtech measurement software. Close other webcam software like camera app, xploview and Amcap if you can't see anything in this software. Please note the snap and zoom buttons don’t work in this software. If the software occur errors or want to get a diffence measurement software, please contact us via our customer service email jiusion@outlook.com.
Mac
Digital Viewer App is compatible with general purpose Mac microscope software from Plugable Technologies company. Install the app as below and open it. Plug the microscope to the Mac. Click “Settings” – “Device” to select “USB2.0 UVC PC Camera” on the dropdown to make the microscope work. MacOS10.14 and above users and need to allow the 'Digital Viewer' app to access camera in 'System Preferences' - 'Security & Privacy'. Note the zoom button doesn’t work on this software. Please tap this email to contact us if you can't use the microscope on Mac jiusion@outlook.com
Digital_Viewer_3.3.30.pkg(8.66MB) macOS (10.13.4 and later) | 64 bit
Digital_Viewer_3.1.06.dmg(2.67MB) Older macOS / OS X versions (10.5 and later) | 32 bit
Remove the microscpe lens cover
Chrome OS
We don’t have drivers for Chrome OS as Jiusion microscopes can be used with the default Camera app that comes with Chrome. Go to Settings > Advanced Settings > Privacy > Content Settings > Camera, and change the device in the dropdown to “USB Microscope”. Access your camera and your magnified object should appear on the screen.
Remove the microscpe lens cover
Linux
Search for the application Cheese and click install. Once the installation is completed, open the application cheese. If the program displays your other camera, click on the word cheese in the top bar to access you preferences. In the webcam tab click on the dropdown menu and select USB Microscope.
Remove the microscpe lens cover
Android
Please note that Android support is on a case-by-case basis. Device manufacturers must have support for USB Video Class devices built in or this will not work.
Step 1: Install app
You can install the 3rd party camera app like “OTG View”, “inskam” “AN98” as below or install from Google Play. Note it may report unsafe as you didn't install from Google Play. You can choose to continue with the installation or install it from the Google Play. We recommend that Android 10 users install the AN98 app and Android 11 users install the inskam app.
Download the installation package directly:
OTG View.apk(17.52MB) Android 4.4 and above
inskam.apk(85.88MB) Android 4.4 and above
AN98.apk(14.01.MB) Android 4.0 and above
Download from Google Play:
OTG View, inskam, AN98
Step 2: Turn on the OTG function
Some phones may need to turn on the OTG manually by flicking downwards on the top side of the screen(Oneplus brand) or tapping Setting - Additional Settings – OTG(Oppo or Vivo brand). Please skip to step 3 if you can't find these options.
Step 3: Connect the microscope to the Android phone
Micro USB phone user please flip a piece on the USB plug from the microscope and plug the micro usb to the phone. Type C phone user please use the type c adapter to connect the microscope to the type c phone. Open the app (USB Camera/inskam/AN98) to use the microscope.
1)If the microscope LED doesn't light up, before contacting us, please check the led dial on the cable and make sure it is on. Please tap this email link jiusion@outlook.com to send us email. It is micro usb or type c connection problem. We will exchange the adapter to you.
2)If the microscope LED lights up but no images on app, please install another 2 apps or tap this email jiusion@outlook.com and email to us. It might be app version or microscope problem. We will send the app suitable for your phone. If it is a microscope problem, we will replace it for you free of charge.
Remove the microscpe lens cover
Update driver in Windows
Method 1: Uninstall the 'GL USB2.0 UVC Camera Device' driver in Control Panel
Open the 'Control Panel' - 'Uninstall a grogram' - 'GL USB2.0 UVC Camera Device'. Right click and select 'uninstall'. That’s all.
Step 1 You can find the Control panel by searching 'Control Panel' on Cortana. Or right click 'This PC' and select 'Properties' - 'Control Panel Home
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'. Click 'Uninstall a program'.Step 2 Select the “GL USB2.0 UVC Camera Device” and right click to select “Uninstall/Change”. If it reports error, please follow the method 2.
Step 3 The microscope driver will switch to 'USB2.0 UVC PC Camera'. Open the Amcap or other microscope software to use the microscope.
What Is A Usb Devices
Method 2: Uninstall the 'GL USB2.0 UVC Camera Device' driver in Device Manager
Step 1 Open the Device Manager (search 'Device Manager' in Cortana or click 'Control Panel > System and Security > System). Click 'Imaging devices' and right-click the 'GL USB2.0 UVC Camera Device'. Select 'Uninstall device'.
Step 2
Rainbow China Usb Devices Driver Download Windows 7
Select 'Delete the driver software for this device' and click 'Uninstall'.Rainbow China Usb Devices Driver Download Win 7