Corona Update 30 Dec 2020

Today a short update about a tool to visualize the evolution of  SARS-CoV-2.

 

 

 

 

 

 

One of the tools is GISAID. In this tool one can easily produce phylogenetic trees of SARS-CoV-2 genomes. There are 3848 genomes sampled between Dec 2019 and Dec 2020. Many thousands of variants of SARS-CoV-2 are circulating. To simplify the matter, they are grouped in clades. A clade is a genetically well defined lineage that has reached a frequency of 20% globally and has spread globally (see Tutorials: Clade Naming & Definitions). Clade 19A and 19B are sampled in 2019 and 20A, 20B, 20C are sampled in 2020. Below is a radial phylogenetic tree with 5 clades:

Radial Phylogenetic Tree of SARS-COV-2
click on image for full size

I like the radial display with 5 clades because the clades are visually well separated. The direction of time is from the centre outwards to the circumference. The tree starts at 30th December 2019  with the reference genome (Wuhan, China) and ends at December 2020.

One can easily switch from one display type to another. The most common tree type is the Rectangular tree. The reader is encouraged to try out different display options and data selections (left panel). A map and a time lapse animation are also available.

The clades are not geographically restricted. To show this, select 'Color by Region':

SARS-COV-2 Rectangular tree with 6 regions indicated.
Time runs from left to right. click on image for full size.

Remarkable: geographic locations are distributed all over the tree. No clade is restricted to one geographic region. This is unnatural for a species. This means different SARS-CO-2 clades have been transported all over the globe. Species have been transported all over the world even before the popularity of air travel, and even before travel by ship, but the genetic fingerprints of SARS-COV-2 offer us unprecedented opportunities to trace the movements of people carrying the virus from continent to continent.

To be continued.

GISAID (website)

GISAID (wikipedia)

Official hCoV-19 Reference Sequence  (GISAID)

Corona updates 2020

This blog post gives short corona updates. Developments are going fast. Here I add very short updates (especially on the evolutionary aspects)  instead of writing many long and detailed blog posts. Most recent on top of the page.

28 December

In the previous update I argued that the new British SARS-CoV-2 variant has outcompeted the existing variants because it has higher transmissibility. But does it also make people more sick than the standard virus? In other words: does it have a higher virulence? The general idea is that there is a trade-off between virulence and transmissibility. If a virus makes you so sick that you stay at home, than the chances of transmission to other people diminish strongly. If you die, the virus is unable to spread to other people. That virus will not cause a pandemic.  On the other hand, if a virus does not make many copies of itself and transmits them to other hosts, the virus will disappear. Making many copies is a burden for the host. To be honest: the host is making those copies! That's why it is a burden. That's why a virus is the ultimate parasite. 

I am not saying that the virus has a strategy. The success of a virus depends on its genetic make-up and how people behave. It is a matter of causes and consequences. However, we could describe the behaviour of a virus as an evolutionary strategy. A successful evolutionary strategy produces the most offspring.

The evolutionary strategy of SARS-CoV-2 appears to be a mix of  virulence and transmissibility. Transmissibility means producing and shedding a lot of copies of itself before the persons begin feeling sick. This is called pre-symptomatic transmission. These persons unknowingly and unintentionally transmit virus particles. Research suggests that up to 45% of infected people are symptom-free transmitters. In younger people transmissibility seems to be maximized.

The second part of the mixed strategy is producing a very high number of virus particles in a subgroup of people, for example in older people. The downside is that these people will get very sick and die. Virulence is high. This is a short term strategy. It is a dead end. Maybe it is better to consider this a side effect of the successful high transmission strategy. In the end, the effect is that SARS-CoV-2 kills people and at the same time spreads around the globe. It resulted in a pandemic. At least, that is the situation in this phase of its evolution. Two facts will determine the long-term evolutionary success of SARS-CoV-2: new mutations and our behaviour.

How the coronavirus escapes an evolutionary trade-off that helps keep other pathogens in check.

25 december

Britse epidemiologen hebben een analyse gemaakt van de nieuwe B.1.1.7 virus variant. Resultaten: van de 17 mutaties hebben 3 een potentieel biologische effect: N501Y, P681H en del69-70. De andere 14 zijn of neutraal of nog onbekend. De eerste twee mutaties zijn aminozuur wijzigingen en de derde is een deletie van aminozuren 69 en 70 van het Spike eiwit. Die ontbreken dus. Uit in vitro experimenten is gebleken dat deze deletie de infectiviteit vergroot. Opvallend effect van de deletie is dat sommige standaard commericiële PCR testen een False Negative geven: ze detecteren de Britse variant niet. Dat is natuurlijk problematisch. Die PCR testen moeten zo spoedig mogelijk vervangen worden door testen die de nieuwe variant wel detecteren.
De epidemiologen concluderen dat de sterke toename van de nieuwe variant niet toegeschreven kan worden aan veranderende sociale interacties of mobiliteit. De variant is dus gestegen in frequentie door het selectief voordeel van de mutaties. Positieve selectie dus. Exacter: differentiële reproductie van genetische varianten in de virus populatie gebaseerd op een fenotypisch effect. Tevens is hiermee aangetoond dat een deletie niet altijd schadelijk hoeft te zijn, maar selectief voordeel kan hebben.

Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England

19 december 

Een Engels team van wetenschappers maakte de vondst bekend van een nieuwe Sars-CoV-2 variant B.1.1.7 die zeer waarschijnlijk in Engeland ontstaan is. Het bijzondere is dat hij verschilt van de bestaande varianten door de unieke combinatie van 17 mutaties die kennelijk in 1 keer ontstaan zijn. En dat is uniek in de korte geschiedenis van het virus. De specifieke combinatie van mutaties is niet eerder waar genomen. Tot nu toe zijn er geen evolutionaire voorlopers gevonden. Wat het meest de pers heeft gehaald is het feit dat de mutant een sterke toename vertoont onder de nieuwe gevallen. Op 9 december had de variant in London al een frequentie bereikt van 60%. De variant is sterk geassocieerd met nieuwe gevallen in Engeland. De politiek heeft hier snel op gereageerd. 

Wetenschappers verschillen van mening over de vraag of die sterke toename door toeval (superspreader event) of door selectief voordeel verklaard moet worden. Feit is dat de variant andere varianten verdringt. Een argument voor de hypothese dat deze variant een selectief voordeel heeft is het feit dat het virus onderdeel dat voor aanhechting aan de menselijke cel zorgt (Spike) maar liefst 8 mutaties heeft. En dat blijkt bepaald niet nadelig voor de verspreiding van het virus te zijn. Dat de variant selectief voordeel heeft kan bevestigd worden door deze te kweken op menselijke cellen in het laboratorium met als controle de standaard corona stam.

Dit is de originele publicatie van de groep die de variant ontdekt en beschreven heeft:

Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. 

 

SONY 90mm macro lens and SONY A6400 camera: amazing performance without tripod and with image stabilization

12 Oct 2020 Episyrphus balteatus. marmalade hoverfly.
f/7.1. 1/1250 sec. ISO 10.000 [GK_04342.JPG]

When I bought the SONY 90 mm macro lens, the man in the camera shop looked at me and said: buying a macro lens in October?! The autumn is a good time for mushroom photography! I bought the lens at that moment because it has been out of stock for months.

Well, yes, there are a lot of mushroom in October, but there are also insects flying and crawling. See for example the tiny fly above photographed on 12 October.

Pieris brassicae (detail) 14 Oct.
f/10.0 1/8000 sec. ISO 10.000 [GK_4469]

Two days later I detected this caterpillar of the cabbage butterfly on a cabbage (picture above).

dragonfly detail 700x700 pixels. 3 Nov 2020
f/4.5. 1/1000 sec ISO 800. [GK_04813]
Sympetrum striolatum (?) (Bruinrode heidelibel)

On 3 November there was a dragonfly sitting on a bench in the park! I am not sure what species it is, it could be a Common darter male. This is certainly late in the year to observe a dragonfly. The picture shows the attachment of the 4 wings to the body. Impressive piece of engineering!

3 Nov. Citroenvlinder
Gonepteryx rhamni
Common brimstone
f/2.8. 1/4000 sec. ISO 400.

Also on 3 November a butterfly sunbathing! One of the last butterflies of this year? I could not come close enough for a good macro.

7 Nov 2020 Episyrphus balteatus.
Dutch: snorzweefvlieg,
Englisch: marmalade hoverfly
original: 6000x4000; this detail: 1000x800 pixels.

On 7 November this tiny hoverfly (above) was resting on Hedera helix in our garden just long enough to take a picture. Temperature: 14°C.!

Suillia spec. (7 Nov.) resting on mushroom
f/7.1. 1/400 sec. ISO 8000. 2239x1661 pixels

This is a fly of the species-rich Suillia genus, which contains 130 species. They are very difficult to identify without a microscope, but are beautiful. They are similar to the famous Drosophila species.

9 Nov: Neomyia cornicina (?) (O=99.9%) [GK_04920A]

 

9 Nov: Neomyia cornicina (?)
f/7.1. 1/4000 sec. ISO 4000. [GK_04922A]

The next day I spotted a marmalade hoverfly warming up in the sun. A perfect situation for macro:

10 Nov: Episyrphus balteatus (detail)
D: Snorzweefvlieg. E: marmalade hoverfly.
f/8.0. 1/500 sec. ISO 1000 [GK_04947]

All pictures are freehand with the SONY A6400 and SONY FE 90 mm F2.8 Macro G OSS lens with autofocus and image stabilization enabled. Original size of pictures: 6000x4000 pixels. The light sensitivity settings varied between ISO 800 and 10.000 and shutter speed settings between 1/500 and 1/4000 sec. Click on images to view full size.

It's amazing that freehand photography with this lens delivers such detailed and sharp macro pictures! It seems, this macro lens is designed for freehand photography. I am really happy with the results. 

Still sharper details should be possible with lower ISO values and a tripod and/or artificial light, but I did not yet try this.

So: October and November are certainly not lost months for macro photography: several fly species, a butterfly, a dragonfly and a
caterpillar. Relevant info: I am located in The Netherlands.

If you have any comments or questions, please use the comments field below.

 

PS: I planned to publish this post a month earlier. But I decided to give priority to the new book of Paul Nurse!