A Coronavirus Perspective

I wanted to make some quick points about Coronavirus, mainly from a medical perspective. Firstly, nature is a great leveller. Self enforced or socially enforced isolation means less flights, less travelling on roads, less consumption and reduced human activity. That leaves its mark on the planet...for the better. There is far less NO2 over Italy being picked up from space. The virus has achieved what years of climate conferences could not. If you push the dice too far, at some point, nature will find a way of redressing the balance.

Worries about economic growth, recessions etc are not misplaced. However, ever increasing growth at the cost of killing the planet is self defeating. As is often said, shrouds don't have pockets. We survived 5 or 10 years ago when we were poorer, and had a lower GDP, didn't we?

Second, a lot of hope is being laid at the door of vaccines. A vaccine won't be ready in time to stem the epidemic. Even if it is lab ready, it takes a long time to be ready for the bench. Abbreviating Phase I trials to speed a vaccine through Phases II & III will not have good consequences, as Gerald Ford found out in 1976 when he fast-tracked a vaccine to the general population after a swine flu scare. People died or fell ill with the jab while the swine-flu outbreak never materialised. Ford lost the election.

Finally, there's been quite a bit of talk about strengthening one's immune system to "prepare" for the virus. This is attractive in theory but may not have legs to stand on. Pharmacologically, there are far more ways of suppressing the immune system than stimulating it. And the latter, when implemented, is targeted towards various cancers rather than infections, for eg IL-2 many years ago for renal cancer, CTLA-4 antibodies such as ipilimumab for melanoma, PD-1 and PD-L1 checkpoint inhibitors for NSCC of lung, etc, and CAR-T for acute B-cell lymphoblastic leukaemias.

Furthermore, the premise that a strong immunity saves you from a virus itself needs to be examined carefully. While COVID-19 is more likely to kill the elderly and infirm, it has spared children, whose immune system is not fully developed before 2 years of age (that's why you use conjugate vaccine in very young children- they can't form antibodies to capsular polysaccharides, unless you tag on a protein). Furthermore, among the deceased were some young people without pre-existing illnesses- like the doctor in Wuhan who raised the alarm. These young men & women died of an hyperactive immune response, manifested as the cytokine storm, typically occurring during the second week of illness, with death occurring around 18 days after falling ill. This is the same sort of response that kills AIDS patients carrying an opportunistic infection after being started on HAART-called IRIS. It's the immune system doing the killing here, not the virus. There are case reports of COVID-19 patients being treated with JAK inhibitors, for example, to turn down the cytokine storm. For relatively young people therefore, it is by no means straightforward.

To find an explanation for this, looking at the way the immune system deals with the virus might be instructive. Acute viral infections are dealt with principally by CD8 positive cytotoxic T cells and Natural Killer cells, which directly lyse virus infected cells with perforin and granzymes, and through Type I and Type III interferons, which are released in large quantities by plasmacytoid dendritic cells. While the interferon pathway is meant to overcome viruses, it can be a double edged sword.

To illustrate, single stranded RNA from viruses stimulates Toll-like receptor 7, which then leads to switching on of an adaptor protein called MyD88. MyD88 can lead to two completely different pathways. One pathway leads through kinases caled IRAK1 & IRAK4 to turn on Interferon regulatory factors-5&7 in the nucleus, leading to production of alpha & beta interferons, which in turn stimulate several interferon inducible genes to fight the virus. The other pathway though leads through IRAK4 & IRAK2 to turn on NF kappa B, and thus produces cytokines like TNF alpha and IL-6 which lead to a lot of damage- ie necrosis of innocent bystander tissues through the cytokine storm.

My suspicion is that, in a subset of patients, COVID-19 is preferentially activating this second pathway.

A Critique of the 2019 EULAR/ACR Classification Criteria for Lupus

New criteria have been published for classifying Lupus, following deliberations by around 200 Lupus experts. Previous criteria lacked either specificity or sensitivity. For example, while the ACR 1997 criteria had a high specificity, this came at the cost of sensitivity, while the 2012 SLICC criteria had higher sensitivity, but low specificity, and as a result, had a positive likelihood ratio of only 6. The 2019 revision combines the sensitivity of 2012 with the specificity of 1997, with an impressive positive likelihood ratio of just under 14.

The 2019 criteria can be found in this paper:

https://onlinelibrary.wiley.com/doi/pdf/10.1002/art.40930

However, it is not without faults.

While, the authors take great care to repeatedly stress that a diagnosis of Lupus should only be considered if other likely causes of the various phenotypes have been ruled out, in practice, faced with an ANA positive patient without a previous diagnosis of Lupus, there is every opportunity for trip-ups. For example, an Afro-caribbean lady with ethnic neutropenia (and thus leucopenia) presenting with fever and seizures due to an undiagnosed CNS infection, perhaps due to Herpes Simplex, would be classified as SLE.

Similarly, a middle aged white woman with SCLE and positive ANA would be classified as Lupus if she had joint pains without objective synovitis- not an uncommon scenario at all.

IMO, the following areas need more attention.

Exclusion of lymphopenia is not justifiable. Yes, lymphopenia can be non-specific, but this is only when it is accompanied by neutrophilia, such as with bacterial infections. Isolated, unexplained and persistent lymphopenia in somebody with a normal neutrophil count should arouse suspicion for SLE.

IMO, including delirium & psychosis without including CSF criteria is an error. The case for diagnosing Lupus would be far higher in a delirious or psychotic patient with a positive ANA, if the CSF showed high protein, with or without lymphocytic pleocytosis (or neutrophilic, if there was Lupus vasculitis) and a high IgG index, including a threshold value of CSF IgG of 6 mg/dl. Excluding the latter from the criteria means that most labs would be under no obligation to offer these tests.

Furthermore, excessive weightage- a full 6 points, has been given to joint involvement. This latter itself would not be a problem, except for the fact that 2 or more tender joints and early morning stiffness, lasting for 30 minutes or more, qualifies as "joint involvement". Most subjects with FMS would therefore score 6 points on these grounds alone, and would only need another 4 points to be classified as Lupus, if they were ANA positive.

The removal of haematuria from the classification criteria is not a welcome development. Proteinuria of >0.5 g/24 hours is not at all uncommon in ill inpatients and has myriad causes amongst outpatients, including diabetes and hypertension. Combining proteinuria with haematuria (but correctly dropping pyuria) would have increased the specificity for Lupus nephropathy.

While the criteria specify a threshold of 40 U/l for anticardiolipin antibodies, the same is not done for antibodies to beta-2 glycoprotein 1. The latter is not at all uncommon across the general population in low titres.

An opportunity has been lost in not weighting the combination of low C3 & C4 more heavily. Low C3 and low C4 in isolation is quite common. Low C3 for example, can be found with activation of the alternative pathway such as with severe bacterial infections. Low C3 is often reported as an one-off by our lab, only to be revised to normal range on repeat.

Again, low C4 is a common inherited condition among Caucasians with the HLAB8/DR3 haplotype, and is not associated with Lupus in these subjects.

However, there are very few conditions outside Lupus that lead to low levels of both C3 & C4. To ascribe only 4 points to this combination, while allowing 3 for isolated low C3 or C4 is puzzling.

Finally, there is now growing appreciation that a positive dsDNA, particularly on ELISA, is very non-specific and crops up quite frequently in subjects who have no signs of CTD. Specifying that dsDNA be positive on Crithidia would have increased its usefulness, but even here, the test is not uncommonly positive in subjects with Type 1 Autoimmune hepatitis. It attracts a very high score-6 points-in the revised criteria.

The panelists have overlooked hyperglobulinemia, one of the most common findings in subjects with SLE from consideration. I can understand the concerns about its non-specificity, but if alopecia or oral ulcers can be ascribed 2 points, there is no reason why hyperglobulinemia can't have a similar weightage.

97% of Third & Fourth Branchial Cysts/Sinuses are Left Sided

Third or 4th branchial remnants are the rarest of branchial pouch anomalies. They are almost always left sided- as many of 97% of cases are on the left.

They may present as lateral neck swelling in a child or adolescent, or recurrent lateral cervical abscesses or recurrent lateral thyroiditis. CT may show a communication with the pyriform fossa, indicated that the lesion is in fact a sinus.

Treatment includes surgical removal or cauterisation with Trichloroacetic acid.

The Punchiest Three-letter Word in English

As a failed literati of sorts (all those unwritten and therefore unpublished books), one never loses one's fascination for the little words that inveigle their way into English usage. They are ubiquitous, crop up in the unlikeliest of places, and read...and then forgotten, never to be looked up. You kind of guess what they mean, but they are just too insignificant, not be glorified through dictionary trawling or by daily usage.

One such word is (sic).

Yes, the word, if one may call a mere slip of three letters that, is only used in brackets, and is often italicised.

I have come across it many times, but never looked it up...until today, when I stumbled upon it while reading a medical paper. The author was quoting an article that used a term incorrectly, and reproduced it verbatim, but postfaced it with a (sic).

Here's an easy to understand example- an excerpt from Bloomberg in 2015, "This proved too much for Robert Barnett, the Washington superlawyer and long time adviser to the Clintons, who fired off an e-mail lighting into her senior staff: "STOP IT!!!! I have help [sic] my tongue for weeks. ..."

It is easy to understand that the user is highlighting an error in the text, but using the suffix to indicate that he has left it unaltered, just so that you don't get the idea that he can't spell...

But what on earth does (sic). mean? I mean, literally?

Here it gets interesting. People have virtually come to blows on its derivation, and it took me a while to make some sense of this little, 3-letter monster.

A popular explanation is that (sic) is part of "Sic transit Gloriam", or "There, but for the grace of God, go I". The implication obviously being, thank goodness, I am not a scatterbrain like the chap I am quoting.

A linguist begs to differ. He thinks Sic is short for Sicut, a Latin word which, for those familiar with Latin choral works, crops up in Sicut erat in principio... or 'As it was in the beginning'.

The Americans like to keep things simple. Notice how they got rid of the "a" in aetiology or the "u" in favourite (thus, unfortunately disembowelling one of the only two words in English that boast all five vowels)? It was therefore not particularly surprising to come across two American gentlemen, respectively from PA & CA, expand (sic) as Spelling InCorrect, and Stated In Context.

Others followed with "Something is changed" and "Standard Idiom Communique"...Whew! Who would have thunk (sic) a little itsy bitsy word would have so many fathers?

The term was apparently used to describe George Bush Junior's bloopers as Stupid Incoming Comments..

But my quest had to end somewhere. It seems (sic) is simply Latin for "thus"
or "such".

Germans might disagree. Apparently, in German sic refers to a whale's vagina.

The Woman with SLE and Life-Threatening Pneumococcal Sepsis

Recently, I was called upon to give my opinion on an Afro Caribbean lady with well controlled SLE who had been admitted to ICU with Pneumococcal septicaemia. She was in her late 30s, had well controlled SLE with normal complements, and was on hydroxychloroquine but not steroids or other immunosuppressives. A blood film showed no evidence of Howell Jolly bodies. She had not received Pneumococcal vaccination.

Fortunately, she recovered, but it was touch and go for several weeks.

So why did the lady who was not hyposplenic, hypocomplementemic, and not on immunosuppressive agents, develop life threatening invasive Pneumococcal infection?

Invasive Pneumococcal infection is uncommon, but not rare in SLE. Around 4.7-7.1% of patients develop this infection at some point. While the other factors mentioned above may contribute, the principal risk factor is polymorphism for the FcgammaRIIa gene.(henceforth, written as FcyRIIa).

There are 3 classes of Fcy receptors- FcyRI (CD64), RFcyRII (CD32), and FCyRIII (CD16). FcvRI is a high affinity receptor that is capable of binding to monomeric Ig. The other classes are low-affinity receptors, which can only bind to multimeric or clustered Ig.

FcyRII is subdivided into FcyRIIa, FcyRIIb and FcyRIIc receptors. The first and third are activating receptors, which act through intracellular ITAM motifs, while FcyRIIb is an inhibitory receptor, that acts through ITIM motif.

FcyRI is mostly an activating receptor, although very occasionally it inhibits.

FcyRIII receptors have 2 subtypes- FcyRIIIa and FcyRIIIb. The first is present on cells of mononuclear-macrophage lineage and NK cells, while the second appears in neutrophils.

Thus, neutrophils have two principal FcyR receptors- FcyRIIa, and FcyRIIIb.

FcyRIIa has 2 alleles, depending on the presence of histidine or arginine at position 131 of the extracellular domain receptor peptide- designated as H131 or R131. They are expressed co-dominantly.

The two alleles have equal prevalence amongst Caucasians and Afro-Caribbeans. The prevalence of R131 is only 10% amongst Asians.

While all FcyR receptors bind IgG1 and IgG3 containing immune complexes well, only subjects who are homozygous for H131 at FcyRIIa bind IgG2 containing immune complexes well. Homozygotes for R131 bind IgG2 poorly, while H/R 131 heterozygotes have intermediate binding to IgG2.

This is important because IgG2 is the only class of immunoglobulins that provides protection against polysaccharide antigens present in the capsule of organisms such as Pneumococcus, Haemophilus influenzae and Meningococcus.

While IgG1 and IgG3 bind complement well, IgG2 does so poorly. Thus immune complexes containing IgG2 are inordinately dependent on Fc receptor mediated clearance, rather than complement-mediated clearance.

Several studies have shown that subjects who are homozygous for the R131 polymorphism for FcyRIIa are more susceptible to invasive Pneumococcal and other encapsulated organisms, irrespective of their complement status. Subjects who also have low complement are at even greater risk.

This is particularly true for Lupus, as the R131 allele is over-represented in Lupus- around 65%.

IgG2 antibodies are also the main subclass found in anti-C1q antibodies, thus conferring a higher risk of Lupus nephritis in R131 homozygotes. However, antibodies to C1q are uncommon, therefore the predisposition to Pneumococcal invasive infection can exist in subjects who do not have Lupus nephritis, as with the lady described above.

Similar polymorphisms exist for FcyRIIIa and FCyRIIIb.

With FcyRIIIa, present in mononuclear and NK cells, the polymorphism is F176 or V176. The former are likely to suffer more infections as they phagocytose IgG1 and IgG3 containing immune complexes poorly. Anti dsDNA and anti-nucleosome antibodies are of IgG1 or IgG3 subclass, and immune complexes containing these subclasses are cleared poorly by macrophages and monocytes, thus increasing the risk of Lupus in these subjects.

With FcvRIIIb, a GPI linked receptor present only in neutrophils, there are two alleles- NA1 and NA2. NA2 homozygotes have poor neutrophil induced phagocytosis of immune complexes compared with NA1 homozygotes and thus are at greater risk of Lupus and certain infections. Those who are homozygous for both R131 and NA2 are at risk of overwhelming meningococcal sepsis.

It is important to immunise all Lupus patients against Pneumococcus.

The Two Sides of CSF1 Receptor- Tenosynovial Giant Cell Tumour and Corticobasal Degeneration

A translocation in 1p13 leads to constitutional activation of Colony Stimulating Factor in a small proportion of synoviocytes in Tenosynovial Giant Cell Tumour (TGCT- previously called PVNS). They attract macrophages, which have the cognate receptor, CSF1R, leading to a proliferative state resembling a benign tumour in the synovium of joints or tendon sheath. The process can be localised, as in digits, or diffuse as in the knee.

So what happens if CSF1 is inactivated? The CSF1 receptor acts through and adaptor called DAP12 or TYROBP. This adaptor is also shared by another signalling entity called TREM2. When there is homozygous inactivation of either TREM2 or TYROBP, a condition called Nasu Hakola Disease results. This condition manifests as very early presenile dementia and bone cysts, often resulting in fractures. Death occurs around age 30.

Similarly, inactivating mutations of CSF1R results in a variant of Corticobasal Degeneration called Hereditary Diffuse Encepahalopathy with Spheroids.

Interestingly, heterozygous mutations in TREM2 leads to late onset Alzheimer's Disease.

Monoclonal Antibodies to CSF1R are in clinical trial for treating TGCT. The most well known is PLX3397 or Pexidartinib. A broader, more nonspecific inhibition is performed by the tyrosine kinase inhibitor Imatinib.

FcRn: Using IV Immunoglobulin to Treat Antibody Mediated Disorders

Intravenous Immunoglobulin (IVIG) is used to treat a variety of disorders. Among these conditions, a number are mediated by antibodies- such as Guillain Barre Syndrome, CIDP, Inflammatory Myositis, Multifocal Motor Neuropathy, Myasthenia Gravis & Rasmussen Syndrome.

But how do infusions of pooled antibodies from thousands of donors (each IVIG aliquot must be derived from at least a thousand donors) mitigate the consequences of pathogenic antibodies already present in the patient?

A number of mechanisms have been proposed, among them the presence of "anti-idiotype" antibodies in the infused IVIG. Thus, among the pooled antibodies, there will be a fraction that will treat the epitopes on pathogenic antibodies as "antigen" and thus neutralise them. Secondly, naive B cells binding to infused IgG through the B cell receptor will activate inhibitory ITIM motifs -"Immune Tyrosine Inhibitory Motif" and thus lead to B cell anergy. These B cells will no longer develop into memory B calls, and thus will not produce pathogenic antibodies.

While the above mechanisms are plausible, it does not explain why IVIg works well only for IgG mediated disorders such as the ones described above, but not for disorders mediated by IgM- such as MAG associated peripheral neuropathies seen in association with IgM paraprotein.

After the infusion of IVIg in subjects with pathogenic IgG antibodies such as Myasthenia Gravis, the putative IgG antibodies decline by up to 40% over a matter of several weeks. There is now sufficient evidence to suggest that this fall is due to increased degradation of these antibodies, rather than reduced production thereof.

But how does infusing IVIg increase the breakdown of intrinsic culprit antibodies?

The answer lies in a group of intracellular receptors called the "Neonatal Fc Receptor" or simply FcRn. While these were so named because they were first isolated in the gut of newborn rats, these receptors are in fact widely present in adults. The greatest concentration is in endothelial cells, but they are also found in antigen presenting cells. FcRn containing cells such as endothelial cells take up IgG by pinocytosis. In the acidic environment of endosomes-pH 6.0- FcRn binds to the Fc portion of IgG. The endosome than travels through the cell until it fuses with the cellular membrane to release the bound IgG back into the circulation. As long as sufficient FcRn receptors are available to take up circulating IgG, the effect is to recycle IgG and thus increase its half life in the circulation. However, FcRn does not bind IgM or IgA. This is the salient reason why IgG is the predominant antibody class in blood ahead of IgM and IgA- not because it's produced more, but because it is recycled repeatedly by FcRn receptors, increasing its half life, while no such thing happens with IgM or igA.


This principle is ingeniously exploited in antibody mediated diseases such as inflammatory myositides. When pooled human IVIg is infused, the "overload" of total IgG- in the infusate (more than 95% of infused IVIg is of IgG class) and intrinsic IgG- saturates the FcRn receptors. Thus, endosomal recycling is no longer possible. Instead the endosomes release pinocytosed IgG to lysosomes, where igG is degraded. Thus, infused igG leads to an overall increase in the breakdown of all IgG- including pathogenic antibodies, leading to a gradual and modest fall in the titre of pathogenic antibodies.

FcRn of course has other roles. Remember, it was first isolated in neonates. In the foetus, FcRn serves to transfer IgG across the placenta from the mother- again explaining why IgG is the only class of immunoglobulin to undergo transplacental transfer.

Recirculation of IgG has other benefits- when the amount of injected IgG is modest, i.e. the FcRn receptors are not saturated, it serves to extend the survival of monoclonal antibodies now in wide use inside the body. Again, it would not have escaped your notice that all monoclonal antibodies are of IgG class.

To summarise, FcRn explains the following observations:
1. Why IgG is the predominant class of antibody in blood
2. Infusion of IVIg reduces the level of pathogenic antibodies in humorally mediated disorders
3. Why IgG is the only class of immunoglobulin to be transferred from mother to foetus in utero
4. Why monoclonal antibodies are entirely of IgG derivation