21 Dec 2021 Episode 207 Latest on omicron and other perspectives in Peru

Tue, 12/21/2021 - 17:41

Episode 207: Omicron and “side effects” of COVID and Peru

Dear colleagues,

After the update on omicron, I will leave my “comfort zone” and explore some of the reported “collateral effects” of COVID-19 in Peru (next time Kenya).


Ep 207-1: Evaluation by Imperial College (updated 20 Dec):

  • Doubling time of omicron only 2 days
  • Relatively  more prevalent in 18-29 yrs old, Londoners and Africans
  • Low immunity by previous infection with delta: 5.4 X more chance on reinfection
  • Less than 20 % protection against infection after “basic vaccination’ and still 50-80 % after booster (the latter is higher than some previous models, based on in vitro neutralization tets
  • No clear evidence that omicron is less severe.   

Researchers at Imperial College London compared 11,329 people with confirmed or likely Omicron infections with nearly 200,000 people infected with other variants. So far,  they see "no evidence of Omicron having lower severity than Delta, judged by either the proportion of people testing positive who report symptoms, or by the proportion of cases seeking hospital care after infection." 

Ep 207-2: Overview of CDC on Dec 16 does not contain really new info, but nicely presented

Ep 207-3: Press communication, claiming that 73 % of new cases in US are omicron, even 90 % in New York area !!  I would like to see confirmation by CDC (which I do not find).

Ep 207-4: Megani Molteni writes a didactic paper in STAT on Dec 17 to explain why omicron spreads so fast: it uses the ACE-2 cellular receptor more efficiently, preferentially infects cells of the small airways and multiplicates very fast, creating highly infectious aerosols with resulting “superspreading events” (infection of multiple people by one infected person at once).

Ep 207-5:  Xiaoqi Yu in medRxiv 20 Dec shows that a third dose with the inactivated Sinopharm vaccine BBIBP-CorV induces a 6 x increased level of neutralizing antibodies against Wuhan virus 1 month after 3rd dose, as compared to 1 month after 2nd dose. 

Neutralization against Omicron was only evaluated after the booster and was 20 X lower than against wild-type.

These data are in line with earlier observations with mRNA vaccines. However, it has been shown repeatedly that in vivo protection against Wuhan strain was lower with the inactivated vaccines and that immune responses were waning faster as compared to mRNA vaccines.  Hence, the in vivo level of protection agaibst omicron remains to be shown…

Ep 207-6: Michael Glocker in medRxiv 15 Dec gives a very different, even counter-intuitive  perspective, based on molecular analysis of the receptor binding domain (RBD) and free energy calculations of interaction with the ACE-2 receptor. 

  • Omicron variants a reduced spike protein  binding to ACE2 receptor protein possibly:
    • enhancing viral fitness / transmissibility
    • and resulting in a delayed induction of danger signals as tradeoff.
  • More virus is produced but less per cell accompanied with delayed Covid19 immunogenicity and pathogenicity.  (because each cell receives less danger signals)

→ More virus is assumed to be required to initiate inflammatory immune responses.

  • The omicron spike protein carries the N679K, P681H, N679K, D614G exchanges [19,20] which may assist in enhancing transmissibility


So, in other words: the omicron “fools” the immune system by having less virus per cell (less “danger” signal, less immune reaction), but infecting many cells and producing lots of virus that is more easily transmitted….

Remains to be seen what the implication is on the late inflammatory reaction, which produces most of the severe pathology.  

For those who are interested in the latest rumors on “Overlegcomité / Comié de Consertation” in Belgium  see attachment https://www.gva.be/cnt/DMF20211221_94028087?utm_source=gva&utm_medium=newsletter&utm_campaign=newsletter_corona&utm_content=news&adh_i=c1159037e96544c57c38ad58752354fb&adh_i=c1159037e96544c57c38ad58752354fb&M_BT=643828224237



Medical aspects

Ep 207-7: Pérez-Lazo Coinfection in hospitalized COVID in Lima July-Nov 2020:

  • Over 50 % of adult patients (154/195) presented with co-infections, which were dominated by the bacteria Mycoplasma pneumoniae and/or Chlamydia pneumoniae.  Co-infected viruses (Adeno, RSV) were much less frequent and Influenza was absent.   This is a much higher co-infection risk as compared to data from Europe and US, where Influenza (and aspergillosis) are more represented.
  • The comorbidity profile of co-infected subjects was not different from non-coinfected.
  • Coinfected subjects presented more sepsis (33 % versus 20 %), but mortality was not higher.   

Ep 207-8: Karuna PLoS Medicine Neut Ab after COVID in US and Peru (July-Oct 2020)

  • NAb titers after SARS-CoV-2 infection peaked approximately 1 month post-diagnosis and declined 3X in the next month
  • Remarkably, NAb were HIGHER in men, severe COVID, diabetics and with higher BMI, but lower with hypertension.  No difference according to race and smoking


Ep 207-9: A speculative comment on the effect of COVID and lockdowns on TB control:

  • On one hand, transmission could have decreased by the COVID measures
  • On the other hand control programs have been strongly reduced, with lower detection and follow-up.


Ep 207-10: Agolli in Avicenna Med J reviews papers on fetal complications in over 2500 SARS-CoV-2 pregnant women.  The main outcome are 174 (6.5 %) cases of abortion.  The authors conclude, however, is that, besides COVID itself, the environment of the pandemic itself, affecting

health care quality and access, is responsible, as it was mainly observed in disfavored populations.


Ep 207-11:  Carme, Davilla: newborns from SARS-CoV-2 seropositive mothers in Medwave Dec 2021

  • Neonatal SARS-CoV-2 infection is rare (34 from 1488 SARS-CoV-2 positive mothers = 3.2 %)
  • Most infected infants are asymptomatic.
  • Vaginal delivery, breastfeeding, and joint isolation did not related with complications.
  • Infants under remote and in-person follow-up showed favorable clinical evolution

Ep 207-12: COVID in Peruvian physicians was 20 % in the one of the most affected regions (Loretto), with 0.7 % deaths.

Societal aspects

Ep 207-13: Huancahuire-Vega J  Nutr Metab Nov 2021 on Eating and lifestyle changes during social isolation in July 2020


Important frequency of overweight and sleep changes

Despite slight increase in physical activity and increase in healthy eating habits;


Important note: Online questionnaire: table 1 shows that 99 % had completed secondary school and 50 % university or graduate degree. Hence representative for an “upper class”!!   


Ep 207-14:  Hernández-Vásquez on effect of health insurance on Out-Of-Pocket expenditures during COVID pandemic in Peru   Int J Health Policy Manag  Dec 2021


  • No difference in the mean amount of out-of-pocket (OOP) spending on healthcare between the population with and without insurance, before and after the mandatory lockdown due to the coronavirus disease 2019 (COVID-19) in Peru, suggesting that, on average, having health insurance in Peru does not significantly impact the amount of money spent on health as compared to not being insured.
  • There was no difference in the proportion of people who incurred OOP spending both before and after the implementation of lockdown; thus, on average, individuals with insurance in Peru, still spend money on healthcare at a similar rate to those without insurance.
  • After the implementation of lockdown, the mean amount of OOP spending increased compared to what was observed at baseline, suggesting that in Peru the implementation of this strict nationwide intervention left the population unattended and required them to spend additional resources to meet their healthcare needs.


Implication: Structural limitations in the healthcare system that are shared by many low- and middle-income countries.

These systems must be fortified and contingency plans for times of national health crises should ensure that the healthcare needs of the population are covered so that individuals do not have to resort to spending the limited resources that they have, placing them at risk of incurring catastrophic health expenditure.


Ep 207-15: Study on street vendors in Lima attracts attention to informal workers, who cannot stay at home. 

The International Labor Organization warns that 1.6 billion informal workers are at risk of losing their livelihoods during the pandemic.


Ep 207-16: Perez Brumer on “vaccine gate”:

Nearly 500 experimental doses of an ongoing COVID-19 trial were given not in the trial, but to leading politicians, such as the former President and his wife, and other high-level health officials and academic leaders at the universities overseeing ethical compliance and administration of the trial


However, sensationalisation of the event has distracted from the existing precarious health system in Peru and the ways in which long-existing abuses of power evident prior to the pandemic limit a just response to it.


Ep 207-17: Fear  of COVID; linked to anxiety and depression in Latin America: about a quarter of the participants presented symptoms of generalized anxiety disorder and a major depressive episode.


Best wishes,