Accidental discovery of a second immuno-compromised patient with accelerated viral evolution

 

 

 Corona Update 25 January 2021

I discovered a second immuno-compromised patient with accelerated evolution by accident. I wanted to know whether the spontaneous mutations occurring in the first immuno-compromised patient could also be found in the general human population. 

I searched for a specific 4AA deletion in the Spike protein in the NCBI SARS-CoV-2 database. I selected all sequences of 1269 AA (4 amino acids shorter than the standard 1273 Spike protein). I added the standard Spike protein length of 1273 AA until I hit the maximum number of 500 sequences that are allowed in one search. The result: 27 sequences of length 1269 of which 16 showed the deletion 141-144 (see previous blog). Unexpectedly, two of them showed me the way to a second immuno-compromised patient (Fig. 1).

Fig 1. Two new sequences with the 141-144 deletion:
QNQ32127; QNQ32151

 

Fig 2. The publication that describes the virus sequence (source).

Usually the sequences in the database are a 'Direct Submission'. They are not published. But the source of these new sequences (Fig.1) revealed that they were part of a

'Case Study: Prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised cancer patient' [1]. 

That's how I discovered my second immuno-compromised patient.

Fig. 3. Long-term SARS-CoV-2 shedding [1] with within-patient variation

It is an immuno-compromised individual persistently testing positive for SARS-CoV-2. Remarkably: it is an asymptomatic individual! The virus mutated and created genetic diversity. This cannot be explained by contamination or secondary infection because the viral genomes of this patient cluster as a mono-phyletic clade*).

 

This strongly suggests evolution

The authors state: "Throughout the course of infection, there was marked within-host genomic evolution of SARS-CoV-2. Deep sequencing revealed a continuously changing virus population structure with turnover in the relative frequency of the observed genotypes over the course of infection. (...) Potential factors contributing to the observed within-host evolution is prolonged infection and the compromised immune status of the host, possibly resulting in a different set of selective pressures compared with an immune-competent host. These differential selective pressures may have allowed a larger genetic diversity with continuous turnover of dominant viral species throughout the course of infection." [1],[2].

The convalescent plasma therapy was not successful. But it is expected to be a selective pressure on the virus.

Apart from demonstrating evolution, there is an important public health lesson: "an estimated 3 million people in the United States have some form of immuno-compromising condition, including individuals with HIV infection".

 

The mutations

Fig. 4. Two deletions. red arrow: 21 nt. yellow: 12 nt. (click to enlarge)
first row (black) shows nt, second row shows AA (colored)

Table 2 Consensus Sequence Variants in Clinical Samples from the Individual and SARS-CoV-2 Isolates Compared with Reference USA/WA1/2020 (MN985325.1) [1].

 

Two in-frame*) deletions were observed in the Spike glycoprotein coding region:

1) A 21 nt in-frame deletion (residues 21,975–21,995) was found in the N-terminal domain (NTD) of S1, leading to a 7-amino-acid deletion (amino acids [AA] 139–145) 

2) A 12 nt deletion (residues 21,982–21,993) was detected in the day 70 isolate, leading to a 4-AA deletion (AA 141–144) in the NTD.

As can be seen from Fig. 4 the two deletion strains of the virus disappear on day 85 and 105.

*) Abbr

Abbr = abbreviations.

nt = nucleotides or bases. Three bases code for 1 AA.

AA = amino acids. 

mono-phyletic clade = an evolutionary group of organisms with one common ancestor.

in-frame deletions = deletions in DNA/RNA that leave the codons (triplets) intact: for example a 3 or 6 base deletion which removes only intact  codons. A 1 or 2 base deletion is out-of-frame and causes troubles.

viral shedding =  the release of virus particles (in the air) (wikipedia)

The authors did not state explicitly, but these results could -just as the patient in my previous blog- be compared with anti-biotic resistance after an unsuccessful anti-biotic treatment.

Update 26 January. 

Small text update: "I searched for a specific 4AA deletion in the Spike protein in the NCBI SARS-CoV-2 database."

Update 27 January: 

added Table 2 with overview of all mutations.

 

Notes

1. Case Study: Prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised cancer patient. 23 Dec 2020
2. There was no selection effect detected in in vitro experiments of mutated virus strains.