When immunologists culture the novel coronavirus — SARS-CoV-2 — in the presence of low amounts of human antibodies, it gained three mutations that endowed it with antibody evasion abilities within 90 days. One of the mutations is E484K in the SARS-CoV-2 spike protein, where amino acid at position 484 mutated from glutamic acid (E) to lysine (K).

“The experiment wasn’t necessarily supposed to work,” said Jason S. McLellan, an associate professor specializing in virology and co-author of the study (released as pre-print) that artificially evolved SARS-CoV-2 in the lab. …

The first proven coronavirus reinfection occurred in August 2020, where a 33-year-old man got reinfected with a different SARS-CoV-2 variant or strain with the D614G mutation. The detection of two distinct SARS-CoV-2 strains rules out the possibility of viral reactivation or persistence that may be caused by the same initial virus.

Soon, more reports of reinfections emerged, nearly all of which were due to the D614G mutation. Now, with the advent of N501Y mutation in the U.K. and South Africa, which has spread to over 20 more countries, more reinfection cases can be expected. …

The recent advent of a new coronavirus strain or variant in the U.K. and other countries — called N501Y (or VUI-2020/01 or lineage B.1.1.7) — have raised only concerns. The vaccine efficacy is questioned. The increased transmissibility would mean higher death counts, even though the virus’s lethality remains the same.

“With increased transmissibility and similar disease severity, the variant does, however, raise alarm: without increased control to slow its spread, there will be an increased impact on already stressed and pressurized health facilities,” Hans Henri P. Kluge, MD, Regional Director for Europe at the WHO, said in a statement yesterday.

However, a paper published in the journal Immunological Letters this month, titled “Are the emerging SARS-COV-2 mutations friend or foe?” offers interesting insights into the coronavirus mutations, arguing why such mutations may not be entirely unfavorable for humans. …

Regrettably, for patients with Covid-19, being released from the hospital or testing negative SARS-CoV-2 does not always mean a full recovery. It’s estimated that 10–30% of cases will turn into long-Covid, where symptoms such as dyspnea (shortness of breath), fatigue, cognitive problems, joint pain, myalgia, and gastrointestinal and cardiac issues persist for a month or more. But in my own research review posted as pre-print, the actual prevalence of long-Covid may be higher than the estimated 10–30%.

Strangely, long-Covid can happen to anyone who got infected by SARS-CoV-2, even children, students, and those who only had mild-to-moderate Covid-19. “Most of the patients that I see who are suffering from [long-Covid] syndrome were not hospitalized,” said Jessica Dine, MD, a pulmonary specialist and associate professor at the University of Pennsylvania. …

It has been another month, and I hope everything’s good at your end. As usual, here’s a short account of the articles Microbial Instincts or I covered in December (friend linked). I hope you will find some of these helpful or thought-provoking.

1. Covid-19 May Have Started Before Dec 2019, Increasing Evidence Shows: A study from the U.S. CDC detected SARS-CoV-2-specific antibodies in donated blood samples between 13–16 December 2019. As antibodies take 1–3 weeks to form, the actual infection in this study might be much earlier. Other countries — China, Italy, Brazil, and Spain — have also found evidence that Covid-19 might have appeared before December 2019. If this is true, it may help explain why SARS-CoV-2 genomes were already stable in early 2020. …

Within a year of the pandemic, science has developed many vaccines for Covid-19, with a few already gaining FDA approval for public use. But many are still worried about the potential undiscovered side effects of such vaccines, which this article aims to address.

All candidate vaccines —the mRNA, DNA, viral vectored, recombinant protein, viral-like particles, and peptide-based vaccines—use the coronavirus’s spike protein to induce immunity in some way or another. Even live attenuated and inactivated vaccines using the whole virion (in a weakened form) still rely on the spike protein, at least partly, to induce immunity.

The CDC has stated that the spike protein of SARS-CoV-2 is harmless, which assures that current Covid-19 vaccines would be safe. But recent studies — in animals and cultured cells — have found that this may not be entirely true, although these studies must be interpreted more cautiously. …

A new SARS-CoV-2 strain called N501Y has been spreading widely in London and south-east England. “The spread is being driven by the new variant of the virus,” the U.K. Prime Minister, Boris Johnson, said in a press conference. “It appears to spread more easily and may be up to 70% more transmissable than the earlier strain.” This new strain caused about 60% of SARS-CoV-2 infections in London, reported Chris Whitty, England's chief medical officer. As a result, the country was initiating a lockdown yesterday. Many other countries have also restricted travel from the U.K.

Anyways, let’s see what the scientific literature has to say on this newly emerged SARS-CoV-2 strain. …

A few days ago, a preprint titled “SARS-CoV-2 RNA reverse-transcribed and integrated into the human genome” was released in bioRxiv. Judging from the title, we can tell it would spark some controversy and debate.

“We describe evidence that SARS-CoV-2 RNAs can be reverse transcribed in human cells by reverse transcriptase (RT) from LINE-1 elements or by HIV-1 RT, and that these DNA sequences can be integrated into the cell genome and subsequently be transcribed,” the authors summarized. …