The main thread has several hundred posts a day talking about social/political aspects of covid19 , including speculation and arguments, so posts with factual content get swamped in the main thread. People have posted useful information but it gets hard to find in a thread with 400+ new posts each day. So I am starting up this one. Please don’t post any puns about Mexican beers here.
Four days ago, I posted a graphic showing sequence analysis of over 1100 virus isolates, colour coded according to country of origin. In this figure, the closer the dots are to each other, the more alike (and hence more related) are the viruses that infected the people they were isolated from. Similarly, the further apart, the more different they are. Different families are referred to as “clades” and are labelled eg as A2, B1 etc. The closer to the centre, the earlier that particular virus was isolated and sequenced.

Then yesterday, this one with another 300 sequences. Red indicates US samples; purple, China. Note that the large number of isolates from 3 to 6 o’clock in that figure are not descended from the Wuhan isolates.
Also note that in the large US cluster there are a few light blue dots. These are isolates sequenced in Australia by people who brought them back as souvenirs from the USA.

Today, there are ANOTHER 300+ sequences available. This shows not only what a huge effort is going on studying the virus but also the amazing sequencing technology that is available these days. Just twenty years ago, it would have taken a large, very well funded team well over a year to obtain just one sequence.
Most of the new sequences are coming from Iceland, which worldomaps says has one of the highest per capita death rates. Most virus isolates there and in Europe are from a different family (clade) that infected people in Wuhan. Maybe this clade is more virulent, which would explain why the death rate is higher in Europe than it was in China.
Finally @chris_64 posted this yesterday, from a paper that published the first sequences. This shows that the SARS-CoV2 (which we refer to as Covid19) is more closely related to a virus isolated from a bat in Yunnan than it is to other human (or indeed pangolin) coronaviruses.

The position of three of those 4 isolates in our radial map is shown here for reference:
Probably worth shouting out. That those with computers capable of, that can and want to feel like they are assisting. Look into folding@home or Rosetta@home to utilise your computer to aid in the sequencing and imaging above.
My question didn’t get answered in other thread:
Not sure if I’ve seen it posted by anyone yet, but for those people who are positive for the virus but are asymptomatic the whole time and never have problems, after how long is it usually at which they are not infectious anymore? 14 days? 28 days?
Q: Just curious if there has there been any discussion/analysis on where the sequence changes are occurring and if some of the changes explain increased virulence/death rates? i.e. the comment on Iceland
The complication is host-virus interactions. There must be genetic factors that make some people more susceptible. At thi stage we have no idea what these may be (ACER is an obvious candidate).
But some virus variants may affect some people differentially.
So we are looking at a matrix of viral variants vs human variants. Too early for any analysis here - too few subjects per cell.
This is a classic case for systems genetics analysis. Whoever invented that term?
All of the Italian samples since February are in the A2a group but less than 10% of the Australian samples are. So IF this group is more virulent it is lucky that we have less of it.
Q2: (kind of a follow up to my first one) I assume these families/clades are generated based on the nucleotide sequences. What happens if they use the protein sequences, therefore considering nonsynonymous vs synonymous mutations, how do the relationships look? Or isn’t this done?
Employers with a turnover below $A50 million who remain active in a business sense during the next 6 months will receive financial assistance from the Federal Government of at least $20,000 per employer and up to a maximum of $100,000 per employer, in two stages.
Stage1 covers the period from 1 March to 30 June 2020.
Stage 2 cover the period from 1 July to 30 September 2020.
The assistance is provided as a “credit” against the liability of the business with respect to the relevant Activity Statement. If the credit exceeds the amount owed to the ATO on the Activity Statement, it is paid as a refund to the business.
The amount for Stage 1
If the employer lodges quarterly , for the quarter to 31 March 2020, the cash boost the employer receives is equal to the amount of tax withheld from ordinary salary and wages with a minimum of $10,000 and a maximum of $50,000 .
If the employer lodges monthly , for the month of March 2020, the cash boost the employer receives is equal to 3 times the amount of tax withheld from ordinary salary and wages as disclosed in the employer’s relevant BAS,with a minimum of $10,000 and a maximum of $50,000 .
The amount for Stage 2
If the employer lodges quarterly , for the quarters ending 30 June 2020 and 30 September 2020, the cash boost the employer receives is equal to 50% of the cash flow boost in the previous 2 quarters , subject to the minimum of $10,000 and a maximum of $50,000 for this second period.
If the employer lodges monthly , for the months of June, July, August and September 2020, the cash boost the employer receives is equal to 25% of the total cash boost in the 4 months from March to June 2020 , subject to the minimum of $10,000 and a maximum of $50,000 for this second period.
Eligibility
Your business is eligible if it:
held an ABN on 12 March 2020and continues to be active (in practical terms, this means the business must keep lodging Activity Statements)
has an aggregated annual turnover under $50 million, and
made eligible payments (e.g., paid salary or wages) you are required to withhold from (even if the amount you need to withhold is zero).
How to claim the Cash Boost:
You don’t actually apply for the cash boost, as the ATO will work out whether you are eligible and the amount you are eligible for, once you lodge the March activity statement.
Also, you must keep lodging activity statements – at least until September 2020.
The cash flow boost is a tax free payment to employers and is automatically calculated by the ATO. There are no new forms required.
In short, you MUST:
Lodge the Activity Statement for the business for March 2020 – this will trigger the entitlement to the Stage 1 ‘credit’
Lodge Activity statements up to September 2020 – this will keep alive, any entitlement to the Stage 2 ‘credit’
On 29 March 2020, the Government announced a wage guarantee will include people who have already lost their jobs as a result of the coronavirus outbreak, and is designed to keep employees connected to their employers.
Details to come.
More information:
Moratorium on rental evictions
On 29 March 2020, the Government announced a six-month moratorium on rental evictions
The prime minister says following national cabinet that there will be a moratorium on evictions for the next six months on the basis of “financial stress”.
“If they are unable to meet their commitments and so there would be a moratorium on evictions for the next six months under those rental arrangements. Now there is a lot more work to be done here and my message to tenants, particularly commercial tenants, and commercial landlords, is a very straightforward one – we need you to sit down, talk to each other and work this out, about looking at the businesses which have been closed, businesses that may have had a significant reduction in their revenues, and we need landlords and tenants to sit down and come up with arrangements that enable them to get through this crisis ”.
Small to medium enterprises (SME) business loan guarantees
The Government has established what it terms the “coronavirus SME guarantee scheme”, under which it will provide a guarantee of 50% to SME lenders for new unsecured loansto be used for working capital . SMEs with a turnover of up to $50m will be eligible to receive these loans.
The scheme seeks to enhance the willingness and ability of banks to provide credit to SMEs with the Scheme able to support $40bn of lending to SMEs. The Government will provide eligible lenders with a guarantee for loans with the following terms :
maximum total size of loans of $250,000 per borrower;
the loans will be up to 3 years, with an initial 6 month repayment holiday ; and
the loans will be in the form of unsecured finance, meaning that borrowers will not have to provide an asset as security for the loan.
Loans will be subject to lenders’ credit assessment processes with the expectation that lenders will look through the cycle to sensibly take into account the uncertainty of the current economic conditions .
As part of the loan products available, the Government will encourage lenders to provide facilities to SMEs that only have to be drawn if needed by the SME. This will mean that the SME will only incur interest on the amount they draw down. If they do not draw down any funds from the facility, no interest will be charged, but they will retain the flexibility to draw down in the future should they need to.
The Scheme will commence by early April 2020 and be available for new loans made by participating lenders until 30 September 2020.
How to apply?
Speak to your bank
More information:
Coronavirus supplement / Other welfare assistance
Coronavirus supplement
The Government will provide a temporary COVID-19 supplement of $550 a fortnight to new and existing income support recipients from 27 April 2020 for 6 months . For existing welfare recipients, the supplement will be paid in addition to their usual payment.
The COVID-19 supplement will be provided to people who receive any of the following:
Please visit the Minister for Families and Social Services’ webpage for Ministerial announcements on DSS related measures.
Expanded eligibility & qualification for Jobseeker and Youth Allowance payments
The Government has also expanded eligibility and qualification criteria for the Job Seeker Payment and the Youth Allowance (job seeker) Payment for 6 months to assist:
sole traders and self-employed people (so they can continue to operate their businesses) – from what I can see, a person is ‘self-employed’ if they are a contractor (that is, they are not an employee for someone else)
people caring for someone infected or in isolation as a result of COVID-19.
People will not be required to present a medical certificate to claim JSP if they are affected by Coronavirus and in a period of isolation and therefore temporarily unable to work.
If people are sick, have to self-isolate, or caring for someone exposed to Coronavirus they may be able to qualify for JSP on the basis of temporary inability to work. These people will not be subject to mutual obligation requirements if on payment for this reason.
If people lose their jobs or have less hours of work as a result of economic conditions resulting from Coronavirus they may be able to qualify for JSP subject to meeting other eligibility requirements.
Also, I found the following information from Centrelink’s service guide, which explains who is considered to be a jobseeker for purposes of the Jobseeker Payment…
Overview
There are 2 ways in which a person can be regarded as unemployed for JSP purposes:
the person is unemployed as that term applies for the purposes of JSP (see ‘Unemployed - general usage’ below), OR
the person is not unemployed but the delegate has decided to treat them as unemployed under section 595 (see ‘Unemployed - section 595’ below).
Act reference: SSAct section 595 Persons may be treated as unemployed
Unemployed - general usage
For the purposes of JSP, an unemployed person is, in broad terms, someone who does not have paid work but wants to have paid work. An essential requirement is that the person has a present intention and some capacity to be part of the labour market. It is not sufficient that the person is simply without work and wants to work.
Example: Young children are not in paid employment, but their lack of attachment to the labour market (e.g. as job seekers) precludes them being considered unemployed. Similarly, people who have completely retired from the workforce do not have paid work, but are not unemployed as they have no connection to the labour market and are not looking for work.
A person without work who wants to work but is fully committed to an activity that is incompatible with labour market attachment would also not be regarded as unemployed in the general sense. For example, a person with full-time caring commitments may not be able to look for or undertake paid work despite wishing to do so. However, in some cases, people undertaking activities that would prevent them being regarded as unemployed in the general sense can still be treated as unemployed (see ‘Unemployed - section 595’ below).
A person who has had paid work during a period may also not be generally regarded as unemployed throughout that period, regardless of the hours worked or the amount paid. However, in some circumstances such a person may be treated as unemployed (see ‘Unemployed - section 595’ below).
The extent of a person’s compliance with mutual obligation requirements can be useful in determining whether a person is genuinely committed to engagement with the labour market (see ‘Relationship between mutual obligation requirements compliance and unemployed status’ below).
Unemployed - section 595
Section 595 gives the Secretary the discretion to treat a person as unemployed where the person would not be regarded as unemployed in the general sense. Use of the discretion supports the objective of increasing or maintaining a person’s engagement in the labour market.
The most common use of the discretion is to enable a person who undertakes paid work to continue to be regarded as unemployed and therefore qualified for payment. A person on JSP is generally required to look for and undertake suitable work. The JSP income test is intended to support this by ensuring that people benefit financially by taking up paid work. This objective would be undermined if a person in paid employment could not be regarded as unemployed, since the person would not qualify for JSP even if they had an entitlement to part-rate JSP under the income test. The discretion to treat an employed person as unemployed for JSP purposes should therefore be exercised in such a way as to further the objective of increased workforce participation, rather than providing a disincentive for people to increase their hours of work.
Although employment is actively encouraged for JSP recipients, the section 595 discretion is not always exercised to disregard employment. For example, a person who is working less than the number of hours required to satisfy their mutual obligation requirements, and who is not willing to look for or undertake alternative work, may not be considered unemployed. As a general rule, however, where the person has employment and also satisfies mutual obligation requirements, they will be considered unemployed under social security law.
Section 595 is also used to continue to treat as unemployed a person who is undertaking an activity the Secretary considers appropriate.
Example: A person participating in drug and alcohol treatment as an activity in their Job Plan is considered to be unemployed during their participation in treatment.
Act reference: SSAct section 595 Persons may be treated as unemployed
Relationship between mutual obligation requirements compliance & unemployed status
While mutual obligation requirements are not directly related to the issue of whether a person is unemployed, compliance with requirements will be an indicator of whether the person’s intended or actual engagement with the labour market is genuine and sufficient.
When determining if a person is unemployed, the following factors may be considered:
-whether the person is undertaking sufficient work to fully satisfy their mutual obligation requirements, i.e.
undertaking suitable work to their assessed capacity, whether full-time or part-time (person with a partial capacity to work (1.1.P.65), or principal carer (1.1.P.412), and job seekers 55 years of age and older), and
earning sufficient income from that work
-whether the person is prepared to fully satisfy their mutual obligation requirements by actively seeking and being willing to undertake suitable work and/or undertaking other approved activities to improve their chances of getting work
-what activities the person is currently pursuing, and whether these are consistent with the person being able to look for and undertake suitable paid work
-whether the amount of the person’s income, including earnings, precludes payment under the income test.
Leave from employment (including stand downs without pay)
A person who is on unpaid leave can be considered to be unemployed if they are not able to resume their employment (e.g. the employer refuses to re-engage them before the expiry of the leave) and they are willing to look for suitable work or meet other participation requirements during the period of leave.
Example: A teacher granted unpaid leave for 3 terms to travel overseas returns to Australia after 1 term but, as the school principal has signed a contract with a replacement teacher for the 3 terms, the school cannot re-engage the teacher until the period of approved leave expires. The teacher can be granted JSP providing he/she is willing to look for alternative suitable work until such time as he/she resumes employment.
Employees, including apprentices, who are stood down without pay, are regarded as unemployed for the duration of the stand down. As a result, they may be paid JSP, provided the other qualification requirements are met.
Temporary removal of assets test for certain payments
The Government has temporarily waived the assets test, for:
the Job Seeker Payment,
the Youth Allowance (job seeker) Payment and
Parenting payment
Income testing still applies , consistent with current arrangements.
Also from 25 March 2020, access to payments has become easier with a temporary removal of the requirement for an Employment Separation Certificate, proof of rental arrangements and verification of relationship status.
Two economic support payments
The Government is providing two $750 economic support payments to recipients of social security and veterans’ payments, ABSTUDY living allowance, farm household allowance and Family Tax Benefit, as well as holders of a PCC, CSHC or Commonwealth Gold Card (basically, pensioners).
The first economic support payment of $750 will be paid to people residing in Australia and, on a day in the period 12 March 2020 to 13 April 2020 , receiving either:
age pension; disability support pension; carer payment; parenting payment; wife pension; widow B pension; ABSTUDY (living allowance);austudy payment; bereavement allowance;newstart allowance/jobseeker payment; youth allowance; partner allowance; sickness allowance; special benefit; widow allowance; FTB, including DOP; carer allowance; pensioner concession card; Commonwealth seniors health card; veteran service pension; veteran income support supplement; veteran compensation payments, including lump sum payments, war widow/er pension, and veteran payment; DVA PCC holders; DVA Education Scheme recipients; disability pensioners at the temporary special rate; DVA income support pensioners at $0 rate; Veteran Gold Card holders; farm household allowance.
The second economic support payment of $750 will be paid to people residing in Australia and receiving a qualifying payment or concession card on 10 July 2020 . The qualifying payments and concession cards are the same as those for the first economic support payment but will not be paid to people who receive the COVID-19 supplement .
How to get the $750 payment
Services Australia (Centrelink) and DVA will automatically deliver the first economic support payment from 31 March 2020 and the second economic support payment from 13 July 2020.
Early access to super savings
The government will allow people to withdraw $10,000 in 2020 income year, and another $10,000 in 2021 income year, from their super savings.
I suggest people exhaust all other options before resorting to this – keep your super!!!
More information
ATO assistance
Options available to assist businesses impacted by COVID-19 include:
Deferring by up to six months the payment date of amounts due through the business activity statement (including PAYG instalments), income tax assessments, fringe benefits tax assessments and excise
Allow businesses on a quarterly reporting cycle to opt into monthly GST reporting in order to get quicker access to GST refunds they may be entitled to
Allowing businesses to vary Pay As You Go (PAYG) instalment amounts to zero for the March 2020 quarter. Businesses that vary their PAYG instalment to zero can also claim a refund for any instalments made for the September 2019 and December 2019 quarters
Remitting any interest and penalties, incurred on or after 23 January 2020, that have been applied to tax liabilities
Working with affected businesses to help them pay their existing and ongoing tax liabilities by allowing them to enter into low interest payment plans.
Employers will still need to meet their ongoing super guarantee obligations for their employees.
How to apply:
Anyone impacted by COVID-19 is advised to contact the ATO to request assistance on our Emergency Support Infoline 1800 806 218 , when they are ready, to discuss their situation.
For more information, go to:
State Government assistance
Daniel Andrews announced on 28 March 2020, $10,000 grants for small business who do not pay payroll tax.
That is a brilliant summary - I suggest that it gets pinned as it’s own thread (with comments locked). Odds are several people may need exactly this advice, and it can be a pain in the ■■■ filtering through a whole thread to find one post.
